/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
Warning: $CNS_SOLVE not defined. Some tests skipped.
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.exec python -V
Python 2.5b1
libtbx.env_run LIBTBX_BUILD bin/python -V
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/env_run.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
Python 2.5b1
libtbx.show_host_and_user
libtbx.show_host_and_user: Command not found.
libtbx.show_build_path
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/py25b1/build
libtbx.show_bin_path
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_bin_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/py25b1/build/bin
libtbx.show_lib_path
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_lib_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/py25b1/build/lib
libtbx.show_dist_paths libtbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/libtbx
libtbx.show_repository_paths
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_repository_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist
libtbx.show_build_options
grep Build.mode
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_options.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
Build mode: release
libtbx.show_commands
grep refresh
head -1
libtbx.assert_stdin libtbx.refresh
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_commands.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.show_all_on_path
/net/rosie/scratch1/rwgk/py25b1/build/bin
phenix.show_build_path
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/py25b1/build
phenix.show_dist_paths phenix
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/phenix
phenix.python -V
Python 2.5b1
libtbx.show_dist_paths libtbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/run_tests.py
libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/introspection.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/introspection.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.str_utils import size_as_string_with_commas
Virtual memory size: 10,649,600
Resident set size:    3,284,992
Stack size:              90,112
Memory total:  16,744,742,912
Memory free:    1,979,035,648
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/tst_utils.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/tst_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import utils
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/str_utils.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/str_utils.py:85: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import show_diff
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility # for sum
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:99: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/table_utils.py:99: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst_tokenizer.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst_tokenizer.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.phil import tokenizer
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst.py
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import phil
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.show_dist_paths boost_adaptbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
boost.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/run_tests.py
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational.py
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational_truediv.py
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_rational_truediv.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/boost_adaptbx/tst_optional.py
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.show_dist_paths scitbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/run_tests.py
/net/rosie/scratch1/rwgk/dist/scitbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_1
Total OK: 435

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_2
Total OK: 268

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_3
Total OK: 164

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_4
Total OK: 1420

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_af_5
Total OK: 22

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_vec3
Total OK: 59

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_mat3
Total OK: 82

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_sym_mat3
Total OK: 71

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_mat_ref
Total OK: 60

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/array_family/tst_accessors
Total OK: 1721

/net/rosie/scratch1/rwgk/py25b1/build/scitbx/serialization/tst_base_256
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_map.py
/net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.stl import map
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_set.py
/net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_set.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.stl import set
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/stl/set.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_vector.py
/net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/stl/tst_vector.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.stl import vector
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/regression_test.py
/net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/regression_test.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_flex.py
/net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_shared.py
/net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_shared.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import shared
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/boost_python/slice.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py
/net/rosie/scratch1/rwgk/dist/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
data_size = 1000 n_repeats = 30000
  use_pointers = False
    use_iterators = 0 time = 0.09 s overhead = 0.00 s (d[p[i]] -6.82118e-09)
    use_iterators = 1 time = 0.09 s overhead = 0.00 s (d[*p++] -6.82118e-09)
  use_pointers = True
    use_iterators = 0 time = 0.09 s overhead = 0.00 s (*dp[i]  -6.82118e-09)
    use_iterators = 1 time = 0.09 s overhead = 0.00 s (**dpi++ -6.82118e-09)
    use_iterators = 2 time = 0.09 s overhead = 0.00 s (**dpp++ -6.82118e-09)
data_size = 10000 n_repeats = 3000
  use_pointers = False
    use_iterators = 0 time = 0.17 s overhead = 0.00 s (d[p[i]] -6.54835e-08)
    use_iterators = 1 time = 0.17 s overhead = 0.00 s (d[*p++] -6.54835e-08)
  use_pointers = True
    use_iterators = 0 time = 0.17 s overhead = 0.00 s (*dp[i]  -6.54835e-08)
    use_iterators = 1 time = 0.17 s overhead = 0.00 s (**dpi++ -6.54835e-08)
    use_iterators = 2 time = 0.17 s overhead = 0.00 s (**dpp++ -6.54835e-08)
data_size = 100000 n_repeats = 300
  use_pointers = False
    use_iterators = 0 time = 0.50 s overhead = 0.00 s (d[p[i]] 1.39698e-07)
    use_iterators = 1 time = 0.45 s overhead = 0.00 s (d[*p++] 1.39698e-07)
  use_pointers = True
    use_iterators = 0 time = 0.52 s overhead = 0.00 s (*dp[i]  1.39698e-07)
    use_iterators = 1 time = 0.46 s overhead = 0.00 s (**dpi++ 1.39698e-07)
    use_iterators = 2 time = 0.46 s overhead = 0.00 s (**dpp++ 1.39698e-07)
data_size = 1000000 n_repeats = 30
  use_pointers = False
    use_iterators = 0 time = 1.23 s overhead = 0.01 s (d[p[i]] 1.67619e-07)
    use_iterators = 1 time = 1.16 s overhead = 0.01 s (d[*p++] 1.67619e-07)
  use_pointers = True
    use_iterators = 0 time = 1.23 s overhead = 0.01 s (*dp[i]  1.67619e-07)
    use_iterators = 1 time = 1.16 s overhead = 0.01 s (**dpi++ 1.67619e-07)
    use_iterators = 2 time = 1.16 s overhead = 0.01 s (**dpp++ 1.67619e-07)
data_size = 10000000 n_repeats = 3
  use_pointers = False
    use_iterators = 0 time = 1.48 s overhead = 0.14 s (d[p[i]] -2.44615e-06)
    use_iterators = 1 time = 1.40 s overhead = 0.14 s (d[*p++] -2.44615e-06)
  use_pointers = True
    use_iterators = 0 time = 1.49 s overhead = 0.14 s (*dp[i]  -2.44615e-06)
    use_iterators = 1 time = 1.40 s overhead = 0.14 s (**dpi++ -2.44615e-06)
    use_iterators = 2 time = 1.40 s overhead = 0.14 s (**dpp++ -2.44615e-06)
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py
/net/rosie/scratch1/rwgk/dist/libtbx/stdlib.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  class rec(object):
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/matrix.py:282: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/misc.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/misc.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import adopt_init_args # XXX backward compatibility 2005_07_29
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/math_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py
/net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil
/net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_random_transform.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_graph.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/python_utils/tst_graph.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.python_utils import graph_tools as gt
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_math.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_math.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
time_eigensystem_real_symmetric: 2.052 micro seconds
Testing compatibility of cmath_lgamma and slatec_dlngam... OK
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_r3_rotation.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_r3_rotation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
u+s,u,s: 2.18 2.14 0.04

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_resample.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_resample.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_line_search.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_line_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_gaussian.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_gaussian.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.examples import immoptibox_ports
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
u+s,u,s: 17.97 17.90 0.07

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_quadrature.py
/net/rosie/scratch1/rwgk/dist/scitbx/math/boost_python/tst_quadrature.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/tst_superpose.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/tst_superpose.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.math.superpose import kabsch_rotation, least_squares_fit
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/sieve_of_eratosthenes.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/minpack/tst.py
/net/rosie/scratch1/rwgk/dist/scitbx/include/scitbx/minpack/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import minpack
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py
/net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/scitbx/lbfgs/boost_python/tst_lbfgs.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/lbfgsb/boost_python/tst_lbfgsb.py
/net/rosie/scratch1/rwgk/dist/scitbx/lbfgsb/boost_python/tst_lbfgsb.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import lbfgsb
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/fftpack/boost_python/tst_fftpack.py
/net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil
/net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/random.py:43: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil
/net/rosie/scratch1/rwgk/dist/scitbx/fftpack/boost_python/tst_fftpack.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
u+s,u,s: 1.53 1.50 0.03

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/flex_array_loops.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/flex_array_loops.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
10.0
11.0
12.0

10.0
11.0
12.0

0 10.0
1 11.0
2 12.0

100.0
110.0
120.0

200.0
210.0
220.0

OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_recipe.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_recipe.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.lbfgs
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
refinery
compute_functional_and_gradients
callback_after_step
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.lbfgs
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/lbfgs_linear_least_squares_fit.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
fit.slope: -3.1494292235
fit.y_intercept: 1.83564357154
 x_obs  y_obs y_calc  diff
  1.00  -1.31  -1.31   0.00
  2.00  -4.46  -4.46   0.00
  3.00  -7.61  -7.61   0.00
  4.00 -10.77 -10.76  -0.01
  5.00 -13.94 -13.91  -0.03
  6.00 -17.03 -17.06   0.03
  7.00 -20.23 -20.21  -0.02
  8.00 -23.31 -23.36   0.05
  9.00 -26.51 -26.51  -0.00
 10.00 -29.68 -29.66  -0.02

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/chebyshev_lsq_example.py:56: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import data_plots
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/data_plots.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
Trying to determine the best number of terms 
 via cross validation techniques

Fitting with 14 terms

Least Squares residual: 1.596703
  R2-value            : 0.004557

Maximum deviation between fitted and error free data:
    0.235
Mean deviation between fitted and error free data:
    0.038

Maximum deviation between fitted and observed data:
    0.254
Mean deviation between fitted and observed data:
    0.109

Showing 10 points
   x    y_obs y_ideal y_fit
 0.010  1.165  1.195  1.189
 0.099  1.870  2.061  2.064
 0.188  0.791  0.814  0.837
 0.277  0.655  0.448  0.458
 0.366  1.948  2.025  1.918
 0.455  2.212  2.322  2.327
 0.545  1.050  0.980  0.990
 0.634  1.106  1.301  1.286
 0.723  2.703  2.931  2.957
 0.812  2.425  2.646  2.663
Preparing output for loggraph in a file called
   chebyshev.loggraph

libtbx.python /net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/immoptibox_ports.py
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/examples/immoptibox_ports.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
Skipping: exercise_lbfgsb() with meyer_function
u+s,u,s: 7.78 7.72 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/regression/scitbx/tst_math_erf.py
/net/rosie/scratch1/rwgk/dist/regression/scitbx/tst_math_erf.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.math import erf_verification, erf, erfc, erfcx
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK
libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py --Quick
/net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/math/boost_python/tst_math.py
/net/rosie/scratch1/rwgk/dist/cctbx/math/boost_python/tst_math.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import math_module
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/math_module.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py
/net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/cctbx/array_family/boost_python/tst_flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  from math import pi, cos, asin, sqrt
/net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  from math import pi, cos, asin, sqrt
/net/rosie/scratch1/rwgk/dist/cctbx/uctbx/boost_python/tst_uctbx.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_sgtbx.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py
/net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/sgtbx/boost_python/tst_N_fold_rot.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/crystal/tst_ext.py
/net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/crystal/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/adptbx/boost_python/tst_adptbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/adptbx/boost_python/tst_adptbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py
/net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/miller/boost_python/tst_miller.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_xray_scattering.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import xray_scattering
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math.gaussian # base class for gaussian
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_henke.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_henke.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import henke
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/fp_fdp.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_icsd_radii.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_icsd_radii.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import icsd_radii
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/icsd_radii.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_neutron.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_neutron.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import neutron
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/neutron.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_sasaki.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_sasaki.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import sasaki
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/fp_fdp.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_tiny_pse.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_tiny_pse.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import tiny_pse
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/tiny_pse.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_wavelengths.py
/net/rosie/scratch1/rwgk/dist/cctbx/eltbx/boost_python/tst_wavelengths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.eltbx import wavelengths
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/wavelengths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/xray/boost_python/tst_xray.py
/net/rosie/scratch1/rwgk/dist/cctbx/xray/boost_python/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/maptbx/boost_python/tst_maptbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/maptbx/boost_python/tst_maptbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import maptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/dmtbx/boost_python/tst_dmtbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/dmtbx/boost_python/tst_dmtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import dmtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/translation_search/boost_python/tst_translation_search.py
/net/rosie/scratch1/rwgk/dist/cctbx/translation_search/boost_python/tst_translation_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import translation_search
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/geometry_restraints/tst_ext.py
/net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/geometry_restraints/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py
/net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/cctbx/include/cctbx/adp_restraints/tst_ext.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.shelx import from_ins
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/from_ins.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py --Quick
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.uctbx import reduction_base
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.23 0.18 0.05
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_subgroups.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_subgroups.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.sgtbx import subgroups
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_lattice_symmetry.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_lattice_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
bravais type: P 1
bravais type: P 1 2 1
bravais type: C 1 2 1
bravais type: P 2 2 2
bravais type: C 2 2 2
bravais type: F 2 2 2
bravais type: I 2 2 2
bravais type: P 4 2 2
bravais type: I 4 2 2
bravais type: P 6 2 2
bravais type: R 3 2 :H
bravais type: P 4 3 2
bravais type: I 4 3 2
bravais type: F 4 3 2
u+s,u,s: 8.69 8.66 0.03

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py P3
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 3
u+s,u,s: 0.39 0.33 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_site_constraints.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_site_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reflection_statistics.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.development import debug_utils
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_harker.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_harker.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.sgtbx import harker
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/symbol_confidence.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/symbol_confidence.py:56: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/bravais_types.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/bravais_types.py:36: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_lookup_utils.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_lookup_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py I41/acd
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
u+s,u,s: 0.33 0.27 0.06
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py I41/acd
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
u+s,u,s: 2.78 2.70 0.08

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pair_asu_table.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pair_asu_table.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
u+s,u,s: 3.56 3.46 0.10

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_asu_clusters.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_asu_clusters.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_coordination_sequences.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_coordination_sequences.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py R-3mr
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal import close_packing
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
time groel_sampling: 0.55 seconds
R -3 m :R
u+s,u,s: 1.39 1.32 0.07
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py I41/acd
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.development import random_structure
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
u+s,u,s: 5.66 5.57 0.09
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 1.19 1.12 0.07
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py P312
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 3 1 2
u+s,u,s: 0.40 0.36 0.04

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py P41
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import dmtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 41
u+s,u,s: 0.43 0.37 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import euclidean_model_matching as emma
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 1.12 1.05 0.07

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import find_centre_of_inversion
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.46 0.37 0.09

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.42 0.36 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.xray import minimization
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
u+s,u,s: 0.48 0.39 0.09

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import statistics
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math.gaussian # base class for gaussian
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
P 31
u+s,u,s: 0.55 0.49 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
u+s,u,s: 2.32 2.26 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 1.98 1.87 0.11
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
u+s,u,s: 7.96 7.88 0.08

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/maptbx/tst_real_space_refinement.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/maptbx/tst_real_space_refinement.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
u+s,u,s: 2.18 2.12 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import maptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.49 0.40 0.09

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.45 0.38 0.07
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.81 0.75 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
u+s,u,s: 1.58 1.50 0.08

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py F222
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import translation_search
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
F 2 2 2
u+s,u,s: 0.60 0.49 0.11

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.pymol import pml_stick, pml_write
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_lbfgs.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_lbfgs.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.geometry_restraints.distance_least_squares \
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_geometry_restraints_2.py:348: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  try: from mmtbx.monomer_library import pdb_interpretation
u+s,u,s: 1.40 1.30 0.10

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.eltbx.xray_scattering
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math.gaussian # base class for gaussian
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
P 31
u+s,u,s: 0.44 0.35 0.09

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.cns import reflection_reader
CNS not available.

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.cns import reflection_reader
CNS not available.

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import adptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.shelx.write_ins import LATT_SYMM
sh: shelxl: command not found
SHELX not available.

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pointgroup_tools.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_pointgroup_tools.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/sub_lattice_tools.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/sub_lattice_tools.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
u+s,u,s: 0.47 0.41 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_best_cell.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_best_cell.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal.find_best_cell import alternative_find_best_cell as fbc
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

grep max_penalty
tail -1
libtbx.show_dist_paths cctbx
libtbx.assert_stdin 44: aP      triclinic, matrix    (1, 0, 0, 0, 1, 0, 0, 0, 1) max_penalty=0.00%
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py:16: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/crystal/burzlaff_zimmermann_dewolff.py:19: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.command_line.lattice_symmetry import metric_subgroups
if ( `libtbx.show_dist_paths PyCifRW` == None ) then
libtbx.show_dist_paths PyCifRW
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.show_dist_paths PyCifRW
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.python /net/rosie/scratch1/rwgk/dist/PyCifRW/example_quartz.py
/net/rosie/scratch1/rwgk/dist/PyCifRW/example_quartz.py:28: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx, sgtbx, crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Quartz
Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Number of scatterers: 2
At special positions: 2
Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Si   Si     3 ( 0.5000  0.0000  0.0000) 1.00 0.0000
O    O      6 ( 0.4152  0.2076  0.1667) 1.00 0.0000
Miller array info: None
Observation type: None
Type of data: double, size=7
Type of sigmas: None
Number of Miller indices: 7
Anomalous flag: False
Unit cell: (4.9965, 4.9965, 5.457, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
(1, 0, 0) 15.6039104868
(1, 0, 1) 36.377014613
(1, 0, 2) 7.92275811058
(1, 1, 0) 15.0429918303
(1, 1, 1) 0.822934329217
(2, 0, 0) 15.6804655415
(2, 0, 1) 13.3231807159
OK
endif
libtbx.show_dist_paths phenix
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
phenix.python /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py --Quick
/net/rosie/scratch1/rwgk/dist/phenix/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
libtbx.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py C2
/net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
C 1 2 1
u+s,u,s: 0.98 0.90 0.08

libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_examples.py --Quick
/net/rosie/scratch1/rwgk/dist/cctbx/run_examples.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
/net/rosie/scratch1/rwgk/py25b1/build/exe_dev/cctbx.getting_started
unit cell: (11,12,13,90,100,90)
space group: C 1 2 1
symmetry operations: 
  x,y,z
  -x,y,-z
  x+1/2,y+1/2,z
  -x+1/2,y+1/2,-z

/net/rosie/scratch1/rwgk/py25b1/build/exe_dev/cctbx.sym_equiv_sites
unit cell: (11,12,13,90,100,90)
space group: C 1 2 1

symmetry operations: 
  x,y,z
  -x,y,-z
  x+1/2,y+1/2,z
  -x+1/2,y+1/2,-z

original_site:(0,0.13,0.51)
special_op: 0,y,1/2
is_special_position: 1
coordinates[0] = (0,0.13,0.5)
coordinates[1] = (0.5,0.63,0.5)

original_site:(0,0.13,0.53)
special_op: x,y,z
is_special_position: 0
coordinates[0] = (0,0.13,0.53)
coordinates[1] = (0,0.13,-0.53)
coordinates[2] = (0.5,0.63,0.53)
coordinates[3] = (0.5,0.63,-0.53)

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/getting_started.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/getting_started.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Unit cell: (11, 12, 13, 90, 100, 90)
Space group: C 1 2 1 (No. 5)
x,y,z
-x,y,-z
x+1/2,y+1/2,z
-x+1/2,y+1/2,-z

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/analyze_adp.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/analyze_adp.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Input Ucif: (0.17000000000000001, 0.17000000000000001, 0.19, 0.089999999999999997, 0, 0)
Warning: ADP tensor is incompatible with site symmetry.
Averaged Ucif: (0.16666666666666666, 0.16666666666666666, 0.19, 0.083333333333333329, 0.0, 0.0)
Eigenvectors and values:
  v=(0.00000 0.00000 1.00000)  lambda=0.1900
  v=(0.90954 -0.41561 0.00000)  lambda=0.1667
  v=(0.41561 0.90954 -0.00000)  lambda=0.1667

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/g_exp_i_partial_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/g_exp_i_partial_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.examples.exp_i_alpha_derivatives \
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_exp_i_alpha_derivatives.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.examples.g_exp_i_alpha_derivatives \
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_g_exp_i_alpha_derivatives.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.examples.structure_factor_derivatives \
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_2.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_2.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_3.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_3.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
u+s,u,s: 7.36 7.26 0.10

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py --tag=internal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_structure_factor_derivatives_4.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
P 1
strudat tag: EDI
u+s,u,s: 5.34 5.23 0.11

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/site_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/site_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/u_star_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/u_star_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.examples.exp_i_alpha_derivatives import least_squares
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/exp_i_alpha_derivatives.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx import matrix
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/all_axes.py P31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/all_axes.py:13: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Space group: P 31 (No. 144)

Rotation type, Axis direction, Intrinsic part, Origin shift
('1', '-', '-', '-')
('3', '[0,0,1]', '(0,0,1/3)', '(0,0,0)')
('3', '[0,0,1]', '(0,0,1/3)', '(1/3,2/3,0)')
('3', '[0,0,1]', '(0,0,1/3)', '(2/3,1/3,0)')
('3', '[0,0,1]', '(0,0,2/3)', '(0,0,0)')
('3', '[0,0,1]', '(0,0,2/3)', '(1/3,2/3,0)')
('3', '[0,0,1]', '(0,0,2/3)', '(2/3,1/3,0)')

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_phase_o_phrenia.py P2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/tst_phase_o_phrenia.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.examples import phase_o_phrenia
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 1 2 1
Number of scatterers: 1
At special positions: 0
Unit cell: (7.82191, 10.1685, 13.2972, 90, 109, 90)
Space group: P 1 2 1 (No. 3)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Hg1  Hg     2 ( 0.8444  0.7580  0.4206) 1.00 0.0000
1.01997  0.00000  0.51804  0.00000
0.0579313  0.50000  0.51989  0.00000
0.0458863  0.00000  0.01467  0.00000
0.0423267  0.43849  0.73176  0.30706
0.0417496  0.43522  0.29739  0.31214
0.0285953  0.50000  0.01661  0.50000
0.0275397  0.00000  0.38158  0.50000
0.0236526 -0.00462  0.01598  0.30704
0.0109534  0.50000  0.03812  1.00000
u+s,u,s: 0.44 0.38 0.06

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/map_skewness.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/map_skewness.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Number of scatterers: 20
At special positions: 0
Unit cell: (13.5341, 17.5943, 23.0079, 83, 109, 129)
Space group: P 1 (No. 1)

Miller array info: None
Observation type: None
Type of data: complex_double, size=312
Type of sigmas: None
Number of Miller indices: 312
Anomalous flag: False
Unit cell: (13.5341, 17.5943, 23.0079, 83, 109, 129)
Space group: P 1 (No. 1)

fudge factor, phase difference, map skewness: 0.00,  0.00, 2.427
fudge factor, phase difference, map skewness: 0.10,  9.11, 2.319
fudge factor, phase difference, map skewness: 0.20, 18.38, 1.923
fudge factor, phase difference, map skewness: 0.30, 26.84, 1.6
fudge factor, phase difference, map skewness: 0.40, 37.42, 0.9556
fudge factor, phase difference, map skewness: 0.50, 41.88, 0.7947
fudge factor, phase difference, map skewness: 0.60, 54.57, 0.2354
fudge factor, phase difference, map skewness: 0.70, 61.09, 0.2007
fudge factor, phase difference, map skewness: 0.80, 78.31, -0.01075
fudge factor, phase difference, map skewness: 0.90, 82.85, 0.007508
fudge factor, phase difference, map skewness: 1.00, 88.95, -0.06533

Number of scatterers: 20
At special positions: 0
Unit cell: (19.71, 25.623, 33.5069, 90, 109, 90)
Space group: C 1 2 1 (No. 5)

Miller array info: None
Observation type: None
Type of data: complex_double, size=338
Type of sigmas: None
Number of Miller indices: 338
Anomalous flag: False
Unit cell: (19.71, 25.623, 33.5069, 90, 109, 90)
Space group: C 1 2 1 (No. 5)

fudge factor, phase difference, map skewness: 0.00,  0.00, 2.586
fudge factor, phase difference, map skewness: 0.10,  8.16, 2.447
fudge factor, phase difference, map skewness: 0.20, 18.14, 2.074
fudge factor, phase difference, map skewness: 0.30, 26.13, 1.483
fudge factor, phase difference, map skewness: 0.40, 40.42, 0.8995
fudge factor, phase difference, map skewness: 0.50, 44.18, 0.666
fudge factor, phase difference, map skewness: 0.60, 54.97, 0.2334
fudge factor, phase difference, map skewness: 0.70, 63.68, 0.08674
fudge factor, phase difference, map skewness: 0.80, 73.35, 0.0479
fudge factor, phase difference, map skewness: 0.90, 79.38, -0.1527
fudge factor, phase difference, map skewness: 1.00, 88.45, 0.09656

Number of scatterers: 20
At special positions: 0
Unit cell: (19.3453, 25.1489, 32.887, 90, 90, 90)
Space group: P 21 21 21 (No. 19)

Miller array info: None
Observation type: None
Type of data: complex_double, size=390
Type of sigmas: None
Number of Miller indices: 390
Anomalous flag: False
Unit cell: (19.3453, 25.1489, 32.887, 90, 90, 90)
Space group: P 21 21 21 (No. 19)

fudge factor, phase difference, map skewness: 0.00,  0.00, 2.67
fudge factor, phase difference, map skewness: 0.10,  8.48, 2.435
fudge factor, phase difference, map skewness: 0.20, 19.81, 1.894
fudge factor, phase difference, map skewness: 0.30, 30.42, 1.315
fudge factor, phase difference, map skewness: 0.40, 36.22, 0.8785
fudge factor, phase difference, map skewness: 0.50, 48.27, 0.349
fudge factor, phase difference, map skewness: 0.60, 55.81, 0.3359
fudge factor, phase difference, map skewness: 0.70, 61.67, 0.1178
fudge factor, phase difference, map skewness: 0.80, 75.70, -0.05378
fudge factor, phase difference, map skewness: 0.90, 84.76, 0.06294
fudge factor, phase difference, map skewness: 1.00, 83.79, -0.06893

Number of scatterers: 20
At special positions: 0
Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120)
Space group: R 3 2 :H (No. 155)

Miller array info: None
Observation type: None
Type of data: complex_double, size=371
Type of sigmas: None
Number of Miller indices: 371
Anomalous flag: False
Unit cell: (36.5694, 36.5694, 62.168, 90, 90, 120)
Space group: R 3 2 :H (No. 155)

fudge factor, phase difference, map skewness: 0.00,  0.00, 2.682
fudge factor, phase difference, map skewness: 0.10,  9.31, 2.094
fudge factor, phase difference, map skewness: 0.20, 20.39, 1.909
fudge factor, phase difference, map skewness: 0.30, 23.40, 1.752
fudge factor, phase difference, map skewness: 0.40, 35.97, 1.037
fudge factor, phase difference, map skewness: 0.50, 44.23, 0.6243
fudge factor, phase difference, map skewness: 0.60, 55.96, 0.1541
fudge factor, phase difference, map skewness: 0.70, 62.99, 0.1125
fudge factor, phase difference, map skewness: 0.80, 76.50, 0.0861
fudge factor, phase difference, map skewness: 0.90, 83.30, 0.1264
fudge factor, phase difference, map skewness: 1.00, 96.67, -0.08465

Number of scatterers: 20
At special positions: 0
Unit cell: (72.6848, 72.6848, 72.6848, 90, 90, 90)
Space group: F 4 3 2 (No. 209)

Miller array info: None
Observation type: None
Type of data: complex_double, size=434
Type of sigmas: None
Number of Miller indices: 434
Anomalous flag: False
Unit cell: (72.6848, 72.6848, 72.6848, 90, 90, 90)
Space group: F 4 3 2 (No. 209)

fudge factor, phase difference, map skewness: 0.00,  0.00, 3.156
fudge factor, phase difference, map skewness: 0.10,  7.14, 2.937
fudge factor, phase difference, map skewness: 0.20, 14.46, 2.499
fudge factor, phase difference, map skewness: 0.30, 27.93, 1.453
fudge factor, phase difference, map skewness: 0.40, 34.75, 0.9865
fudge factor, phase difference, map skewness: 0.50, 49.06, 0.2723
fudge factor, phase difference, map skewness: 0.60, 54.71, 0.2318
fudge factor, phase difference, map skewness: 0.70, 64.03, 0.07332
fudge factor, phase difference, map skewness: 0.80, 71.43, 0.02207
fudge factor, phase difference, map skewness: 0.90, 83.93, 0.178
fudge factor, phase difference, map skewness: 1.00, 89.03, -0.06762

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_table.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_table.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
0,0,0
1/2,1/2,1/2
x,y,z
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_constraints.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/site_symmetry_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Unit cell: (12, 12, 15, 90, 90, 120)
Space group: P 6 (No. 168)
special position operator: 1/3,2/3,z
exact location of special position: (0.33333333333333331, 0.66666666666666663, 0.0)
n_indep: 1
site_shifted: (0.33333333333333331, 0.66666666666666663, 0.10000000000000001)
independent_gradients: (0.02,)
independent_curvatures: (6.0,)
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/adp_symmetry_constraints.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/adp_symmetry_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/unit_cell_refinement.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/unit_cell_refinement.py:44: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
( 0,  1,  1)   8.81 -  12.52 =  -3.71
( 0,  0,  2)  12.23 -  17.74 =  -5.51
( 0,  2,  0)  12.71 -  17.74 =  -5.03
( 1,  1,  0)  12.97 -  12.52 =   0.45
( 0,  1,  2)  13.79 -  19.85 =  -6.06
( 0,  2,  1)  14.11 -  19.85 =  -5.74
( 1,  1,  1)  14.35 -  15.35 =  -1.00
( 1,  0,  2)  16.68 -  19.85 =  -3.17
( 1,  2,  0)  17.03 -  19.85 =  -2.82
( 0,  2,  2)  17.67 -  25.19 =  -7.52
( 1,  1,  2)  17.86 -  21.77 =  -3.91
( 0,  1,  3)  19.47 -  28.22 =  -8.75
( 1,  2,  2)  21.03 -  26.74 =  -5.71
( 1,  3,  0)  22.26 -  28.22 =  -5.96
( 0,  2,  3)  22.41 -  32.28 =  -9.87
( 1,  1,  3)  22.56 -  29.63 =  -7.07
( 2,  0,  0)  22.72 -  17.74 =   4.98
( 1,  3,  1)  23.10 -  29.63 =  -6.53
( 2,  1,  1)  24.40 -  21.77 =   2.63
( 0,  0,  4)  24.60 -  35.92 = -11.32
( 1,  2,  3)  25.17 -  33.53 =  -8.36
( 0,  1,  4)  25.43 -  37.07 = -11.64
( 2,  0,  2)  25.87 -  25.19 =   0.68
( 2,  2,  0)  26.11 -  25.19 =   0.92
( 0,  4,  1)  26.32 -  37.07 = -10.75
( 2,  1,  2)  26.66 -  26.74 =  -0.08
( 2,  2,  1)  26.84 -  26.74 =   0.10
( 1,  0,  4)  27.15 -  37.07 =  -9.92
( 0,  2,  4)  27.78 -  40.33 = -12.55
( 1,  1,  4)  27.90 -  38.18 = -10.28
( 0,  4,  2)  28.44 -  40.33 = -11.89
( 1,  4,  1)  28.72 -  38.18 =  -9.46
( 2,  2,  2)  28.92 -  30.98 =  -2.06
( 1,  3,  3)  29.02 -  39.27 = -10.25
( 2,  1,  3)  30.08 -  33.53 =  -3.45
( 2,  3,  1)  30.49 -  33.53 =  -3.04
( 1,  4,  2)  30.69 -  41.38 = -10.69
( 0,  3,  4)  31.34 -  45.34 = -14.00
( 0,  1,  5)  31.56 -  46.29 = -14.73
( 2,  2,  3)  32.12 -  37.07 =  -4.95

functional:      2321.58 gradient norm:      1207.44
functional:      1351.63 gradient norm:      763.055
LBFGS step
functional:      460.578 gradient norm:      305.314
LBFGS step
functional:      193.168 gradient norm:      143.672
LBFGS step
functional:      47.9382 gradient norm:      71.6896
LBFGS step
functional:      19.9431 gradient norm:      89.0333
functional:      5.22162 gradient norm:      23.2996
LBFGS step
functional:     0.773471 gradient norm:      15.0906
LBFGS step
functional:    0.0424125 gradient norm:     0.859899
LBFGS step
functional:    0.0347316 gradient norm:     0.305121
LBFGS step
functional:    0.0335577 gradient norm:     0.152589
LBFGS step
functional:    0.0328786 gradient norm:     0.127443
LBFGS step
functional:    0.0318193 gradient norm:     0.219987
LBFGS step
functional:    0.0289939 gradient norm:     0.427834
LBFGS step
functional:    0.0231493 gradient norm:     0.637841
LBFGS step
functional:    0.0265728 gradient norm:      2.44424
functional:    0.0197091 gradient norm:      1.24135
LBFGS step
functional:    0.0103005 gradient norm:     0.846735
LBFGS step
functional:   0.00286258 gradient norm:      0.33518
LBFGS step
functional:   0.00135783 gradient norm:    0.0748069
LBFGS step
functional:   0.00126888 gradient norm:    0.0240333
LBFGS step
functional:   0.00125005 gradient norm:    0.0241467
LBFGS step
functional:   0.00115246 gradient norm:    0.0586707
LBFGS step
functional:  0.000998979 gradient norm:     0.066586
LBFGS step
functional:   0.00289854 gradient norm:     0.873259
functional:  0.000926904 gradient norm:     0.164675
LBFGS step
functional:  0.000721104 gradient norm:      0.10673
LBFGS step
functional:  0.000496383 gradient norm:    0.0156637
LBFGS step
functional:  0.000436098 gradient norm:    0.0187089
LBFGS step
functional:  0.000405012 gradient norm:    0.0141628
LBFGS step
functional:  0.000437224 gradient norm:    0.0606772
functional:   0.00040312 gradient norm:    0.0132963
LBFGS step
functional:  0.000400413 gradient norm:   0.00486466
LBFGS step
functional:  0.000400027 gradient norm:   0.00909801
LBFGS step
functional:  0.000399624 gradient norm:   0.00699387
LBFGS step
functional:  0.000398287 gradient norm:   0.00462518
LBFGS step
functional:  0.000395683 gradient norm:   0.00493142
LBFGS step
functional:  0.000391549 gradient norm:   0.00839497
LBFGS step
functional:  0.000397074 gradient norm:    0.0313135
functional:  0.000389325 gradient norm:   0.00955157
LBFGS step
functional:  0.000387577 gradient norm:     0.029918
LBFGS step
functional:  0.000384514 gradient norm:   0.00250443
LBFGS step
functional:  0.000384214 gradient norm:   0.00179238
LBFGS step
functional:  0.000384067 gradient norm:   0.00168088
LBFGS step
functional:  0.000383912 gradient norm:   0.00139472
LBFGS step

( 0,  1,  1)   8.81 -   8.81 =   0.00
( 0,  0,  2)  12.23 -  12.23 =   0.00
( 0,  2,  0)  12.71 -  12.71 =   0.00
( 1,  1,  0)  12.97 -  12.97 =   0.00
( 0,  1,  2)  13.79 -  13.79 =   0.00
( 0,  2,  1)  14.11 -  14.11 =  -0.00
( 1,  1,  1)  14.35 -  14.34 =   0.01
( 1,  0,  2)  16.68 -  16.68 =   0.00
( 1,  2,  0)  17.03 -  17.04 =  -0.01
( 0,  2,  2)  17.67 -  17.67 =  -0.00
( 1,  1,  2)  17.86 -  17.86 =   0.00
( 0,  1,  3)  19.47 -  19.47 =   0.00
( 1,  2,  2)  21.03 -  21.02 =   0.01
( 1,  3,  0)  22.26 -  22.26 =   0.00
( 0,  2,  3)  22.41 -  22.41 =  -0.00
( 1,  1,  3)  22.56 -  22.56 =  -0.00
( 2,  0,  0)  22.72 -  22.71 =   0.01
( 1,  3,  1)  23.10 -  23.10 =   0.00
( 2,  1,  1)  24.40 -  24.40 =  -0.00
( 0,  0,  4)  24.60 -  24.60 =  -0.00
( 1,  2,  3)  25.17 -  25.17 =   0.00
( 0,  1,  4)  25.43 -  25.43 =   0.00
( 2,  0,  2)  25.87 -  25.87 =  -0.00
( 2,  2,  0)  26.11 -  26.11 =   0.00
( 0,  4,  1)  26.32 -  26.32 =  -0.00
( 2,  1,  2)  26.66 -  26.66 =  -0.00
( 2,  2,  1)  26.84 -  26.84 =   0.00
( 1,  0,  4)  27.15 -  27.14 =   0.01
( 0,  2,  4)  27.78 -  27.78 =  -0.00
( 1,  1,  4)  27.90 -  27.90 =  -0.00
( 0,  4,  2)  28.44 -  28.44 =  -0.00
( 1,  4,  1)  28.72 -  28.72 =  -0.00
( 2,  2,  2)  28.92 -  28.92 =  -0.00
( 1,  3,  3)  29.02 -  29.02 =   0.00
( 2,  1,  3)  30.08 -  30.08 =  -0.00
( 2,  3,  1)  30.49 -  30.49 =  -0.00
( 1,  4,  2)  30.69 -  30.69 =   0.00
( 0,  3,  4)  31.34 -  31.34 =   0.00
( 0,  1,  5)  31.56 -  31.56 =  -0.00
( 2,  2,  3)  32.12 -  32.12 =   0.00

(7.82934, 13.9295, 14.4747, 89.9925, 89.9881, 89.9857)

u+s,u,s: 0.15 0.11 0.04

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/miller_common_sets.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/miller_common_sets.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
asu a: (0, 1, 2)
asu a: (1, 2, 3)
asu a: (2, 3, 4)
asu a: (3, 4, 5)
asu a: (4, 5, 6)

asu b: (5, 6, 7)
asu b: (0, 1, 2)
asu b: (3, 4, 5)
asu b: (1, 2, 3)
asu b: (4, 5, 6)

common a: (0, 1, 2)
common a: (3, 4, 5)
common a: (1, 2, 3)
common a: (4, 5, 6)

common b: (0, 1, 2)
common b: (3, 4, 5)
common b: (1, 2, 3)
common b: (4, 5, 6)

lone a: (2, 3, 4)

lone b: (5, 6, 7)

asu a: (0, 1, 2) 0.0307678046942
asu a: (1, 2, 3) 0.33752477667
asu a: (2, 3, 4) 0.940635716831
asu a: (3, 4, 5) 0.0700093884992
asu a: (4, 5, 6) 0.278603566608

asu b: (5, 6, 7) 0.851550812603
asu b: (0, 1, 2) 0.928183997514
asu b: (3, 4, 5) 0.0733799609814
asu b: (1, 2, 3) 0.0801495396935
asu b: (4, 5, 6) 0.803735972149

common a: (0, 1, 2) 0.0307678046942
common a: (3, 4, 5) 0.0700093884992
common a: (1, 2, 3) 0.33752477667
common a: (4, 5, 6) 0.278603566608

common b: (0, 1, 2) 0.928183997514
common b: (3, 4, 5) 0.0733799609814
common b: (1, 2, 3) 0.0801495396935
common b: (4, 5, 6) 0.803735972149

lone a: (2, 3, 4) 0.940635716831

lone b: (5, 6, 7) 0.851550812603

OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/steve_collins.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/steve_collins.py:47: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
x,y,z
{{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{0, 0, 0}}
-y+1/4,x+3/4,z+1/4
{{0, -1, 0}, {1, 0, 0}, {0, 0, 1}} {{1/4, 3/4, 1/4}}
y+1/4,-x+1/4,z+3/4
{{0, 1, 0}, {-1, 0, 0}, {0, 0, 1}} {{1/4, 1/4, 3/4}}
x,-y,-z
{{1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{0, 0, 0}}
-x,y+1/2,-z
{{-1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{0, 1/2, 0}}
-x,-y+1/2,z
{{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{0, 1/2, 0}}
y+1/4,x+3/4,-z+1/4
{{0, 1, 0}, {1, 0, 0}, {0, 0, -1}} {{1/4, 3/4, 1/4}}
-y+1/4,-x+1/4,-z+3/4
{{0, -1, 0}, {-1, 0, 0}, {0, 0, -1}} {{1/4, 1/4, 3/4}}
-x,-y,-z
{{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{0, 0, 0}}
y-1/4,-x-3/4,-z-1/4
{{0, 1, 0}, {-1, 0, 0}, {0, 0, -1}} {{-1/4, -3/4, -1/4}}
-y-1/4,x-1/4,-z-3/4
{{0, -1, 0}, {1, 0, 0}, {0, 0, -1}} {{-1/4, -1/4, -3/4}}
-x,y,z
{{-1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{0, 0, 0}}
x,-y-1/2,z
{{1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{0, -1/2, 0}}
x,y-1/2,-z
{{1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{0, -1/2, 0}}
-y-1/4,-x-3/4,z-1/4
{{0, -1, 0}, {-1, 0, 0}, {0, 0, 1}} {{-1/4, -3/4, -1/4}}
y-1/4,x-1/4,z-3/4
{{0, 1, 0}, {1, 0, 0}, {0, 0, 1}} {{-1/4, -1/4, -3/4}}
x+1/2,y+1/2,z+1/2
{{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{1/2, 1/2, 1/2}}
-y+3/4,x+5/4,z+3/4
{{0, -1, 0}, {1, 0, 0}, {0, 0, 1}} {{3/4, 5/4, 3/4}}
y+3/4,-x+3/4,z+5/4
{{0, 1, 0}, {-1, 0, 0}, {0, 0, 1}} {{3/4, 3/4, 5/4}}
x+1/2,-y+1/2,-z+1/2
{{1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{1/2, 1/2, 1/2}}
-x+1/2,y+1,-z+1/2
{{-1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{1/2, 1, 1/2}}
-x+1/2,-y+1,z+1/2
{{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{1/2, 1, 1/2}}
y+3/4,x+5/4,-z+3/4
{{0, 1, 0}, {1, 0, 0}, {0, 0, -1}} {{3/4, 5/4, 3/4}}
-y+3/4,-x+3/4,-z+5/4
{{0, -1, 0}, {-1, 0, 0}, {0, 0, -1}} {{3/4, 3/4, 5/4}}
-x+1/2,-y+1/2,-z+1/2
{{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} {{1/2, 1/2, 1/2}}
y+1/4,-x-1/4,-z+1/4
{{0, 1, 0}, {-1, 0, 0}, {0, 0, -1}} {{1/4, -1/4, 1/4}}
-y+1/4,x+1/4,-z-1/4
{{0, -1, 0}, {1, 0, 0}, {0, 0, -1}} {{1/4, 1/4, -1/4}}
-x+1/2,y+1/2,z+1/2
{{-1, 0, 0}, {0, 1, 0}, {0, 0, 1}} {{1/2, 1/2, 1/2}}
x+1/2,-y,z+1/2
{{1, 0, 0}, {0, -1, 0}, {0, 0, 1}} {{1/2, 0, 1/2}}
x+1/2,y,-z+1/2
{{1, 0, 0}, {0, 1, 0}, {0, 0, -1}} {{1/2, 0, 1/2}}
-y+1/4,-x-1/4,z+1/4
{{0, -1, 0}, {-1, 0, 0}, {0, 0, 1}} {{1/4, -1/4, 1/4}}
y+1/4,x+1/4,z-1/4
{{0, 1, 0}, {1, 0, 0}, {0, 0, 1}} {{1/4, 1/4, -1/4}}

Space group: P 4/m m m (No. 123)

(0, 0, 1) True
(0, 0, 2) True
(0, 0, 3) True
(1, 0, 0) True
(1, 0, 1) False
(1, 0, 2) True
(1, 1, 0) True
(1, 1, 1) True
(1, 1, 2) False
(2, 0, 0) False
(2, 0, 1) True
(2, 1, 0) True
(2, 1, 1) False

Space group: P 4/m m m (No. 123)
x,y,z
-y,x,z
y,-x,z
x,-y,-z
-x,y,-z
-x,-y,z
y,x,-z
-y,-x,-z
-x,-y,-z
y,-x,-z
-y,x,-z
-x,y,z
x,-y,z
x,y,-z
-y,-x,z
y,x,z

special position operator: 0,1/2,0
distance to original site: 0.2
point group of the special position:
x,y,z
x,-y+1,-z
-x,-y+1,-z
-x,y,z

0 13.9976000786
0.01 13.9735949492
0.02 13.902379971
0.5 6.24008847468

0.5 0.0307999998331 0.034200001508
0.8 0.0900999978185 0.0899000018835
0.9 0.111299999058 0.114200003445

0.5 0.0416212081909 0.0341104492545
0.8 0.100048065186 0.0897070690989
0.9 0.12097454071 0.113592810929

OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_primitive_cell.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_primitive_cell.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
Number of scatterers: 2
At special positions: 2
Unit cell: (4.96195, 4.96195, 13.5974, 90, 90, 120)
Space group: R -3 c :H (No. 167)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr    12 ( 0.0000  0.0000  0.3476) 1.00 0.0000
O1   O     18 ( 0.3058  0.0000  0.2500) 1.00 0.0000

Cr1  pair count:   6       <<  0.0000,  0.0000,  0.3476>>
  O1:    1.9654             (  0.0275, -0.3333,  0.4167)
  O1:    1.9654 sym. equiv. (  0.3333,  0.3608,  0.4167)
  O1:    1.9654 sym. equiv. ( -0.3608, -0.0275,  0.4167)
  O1:    2.0157             (  0.3058,  0.0000,  0.2500)
  O1:    2.0157 sym. equiv. (  0.0000,  0.3058,  0.2500)
  O1:    2.0157 sym. equiv. ( -0.3058, -0.3058,  0.2500)
O1   pair count:   4       <<  0.3058,  0.0000,  0.2500>>
  Cr1:   1.9654             (  0.3333, -0.3333,  0.3191)
  Cr1:   1.9654 sym. equiv. (  0.6667,  0.3333,  0.1809)
  Cr1:   2.0157             (  0.0000,  0.0000,  0.3476)
  Cr1:   2.0157 sym. equiv. (  0.0000,  0.0000,  0.1524)

Number of scatterers: 2
At special positions: 2
Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232)
Space group: R -3 c :R (No. 167)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr     4 ( 0.3476  0.3476  0.3476) 1.00 0.0000
O1   O      6 ( 0.5558 -0.0558  0.2500) 1.00 0.0000

Number of scatterers: 10
At special positions: 0
Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232)
Space group: P 1 (No. 1)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr     1 ( 0.3476  0.3476  0.3476) 1.00 0.0000
Cr1  Cr     1 ( 0.1524  0.1524  0.1524) 1.00 0.0000
Cr1  Cr     1 (-0.3476 -0.3476 -0.3476) 1.00 0.0000
Cr1  Cr     1 (-0.1524 -0.1524 -0.1524) 1.00 0.0000
O1   O      1 ( 0.5558 -0.0558  0.2500) 1.00 0.0000
O1   O      1 ( 0.2500  0.5558 -0.0558) 1.00 0.0000
O1   O      1 (-0.0558  0.2500  0.5558) 1.00 0.0000
O1   O      1 (-0.5558  0.0558 -0.2500) 1.00 0.0000
O1   O      1 (-0.2500 -0.5558  0.0558) 1.00 0.0000
O1   O      1 ( 0.0558 -0.2500 -0.5558) 1.00 0.0000

OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_consistency_checks.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/cr2o3_consistency_checks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
Number of scatterers: 2
At special positions: 2
Unit cell: (4.96195, 4.96195, 13.5974, 90, 90, 120)
Space group: R -3 c :H (No. 167)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr    12 ( 0.0000  0.0000  0.3476) 1.00 0.0000
O1   O     18 ( 0.3058  0.0000  0.2500) 1.00 0.0000

Cr1  pair count:   6       <<  0.0000,  0.0000,  0.3476>>
  O1:    1.9654             (  0.0275, -0.3333,  0.4167)
  O1:    1.9654 sym. equiv. (  0.3333,  0.3608,  0.4167)
  O1:    1.9654 sym. equiv. ( -0.3608, -0.0275,  0.4167)
  O1:    2.0157             (  0.3058,  0.0000,  0.2500)
  O1:    2.0157 sym. equiv. (  0.0000,  0.3058,  0.2500)
  O1:    2.0157 sym. equiv. ( -0.3058, -0.3058,  0.2500)
O1   pair count:   4       <<  0.3058,  0.0000,  0.2500>>
  Cr1:   1.9654             (  0.3333, -0.3333,  0.3191)
  Cr1:   1.9654 sym. equiv. (  0.6667,  0.3333,  0.1809)
  Cr1:   2.0157             (  0.0000,  0.0000,  0.3476)
  Cr1:   2.0157 sym. equiv. (  0.0000,  0.0000,  0.1524)

Number of scatterers: 2
At special positions: 2
Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232)
Space group: R -3 c :R (No. 167)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr     4 ( 0.3476  0.3476  0.3476) 1.00 0.0000
O1   O      6 ( 0.5558 -0.0558  0.2500) 1.00 0.0000

Number of scatterers: 10
At special positions: 0
Unit cell: (5.36192, 5.36192, 5.36192, 55.1232, 55.1232, 55.1232)
Space group: P 1 (No. 1)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
Cr1  Cr     1 ( 0.3476  0.3476  0.3476) 1.00 0.0000
Cr1  Cr     1 ( 0.1524  0.1524  0.1524) 1.00 0.0000
Cr1  Cr     1 (-0.3476 -0.3476 -0.3476) 1.00 0.0000
Cr1  Cr     1 (-0.1524 -0.1524 -0.1524) 1.00 0.0000
O1   O      1 ( 0.5558 -0.0558  0.2500) 1.00 0.0000
O1   O      1 ( 0.2500  0.5558 -0.0558) 1.00 0.0000
O1   O      1 (-0.0558  0.2500  0.5558) 1.00 0.0000
O1   O      1 (-0.5558  0.0558 -0.2500) 1.00 0.0000
O1   O      1 (-0.2500 -0.5558  0.0558) 1.00 0.0000
O1   O      1 ( 0.0558 -0.2500 -0.5558) 1.00 0.0000

Cr1  pair count:   6       <<  0.3476,  0.3476,  0.3476>>
  O1:    1.9654             (  0.4442,  0.0558,  0.7500)
  O1:    1.9654             (  0.7500,  0.4442,  0.0558)
  O1:    1.9654             (  0.0558,  0.7500,  0.4442)
  O1:    2.0157             (  0.2500,  0.5558, -0.0558)
  O1:    2.0157             ( -0.0558,  0.2500,  0.5558)
  O1:    2.0157             (  0.5558, -0.0558,  0.2500)
Cr1  pair count:   6       <<  0.1524,  0.1524,  0.1524>>
  O1:    1.9654             (  0.0558, -0.2500,  0.4442)
  O1:    1.9654             (  0.4442,  0.0558, -0.2500)
  O1:    1.9654             ( -0.2500,  0.4442,  0.0558)
  O1:    2.0157             (  0.2500,  0.5558, -0.0558)
  O1:    2.0157             ( -0.0558,  0.2500,  0.5558)
  O1:    2.0157             (  0.5558, -0.0558,  0.2500)
Cr1  pair count:   6       << -0.3476, -0.3476, -0.3476>>
  O1:    1.9654             ( -0.4442, -0.0558, -0.7500)
  O1:    1.9654             ( -0.7500, -0.4442, -0.0558)
  O1:    1.9654             ( -0.0558, -0.7500, -0.4442)
  O1:    2.0157             ( -0.2500, -0.5558,  0.0558)
  O1:    2.0157             (  0.0558, -0.2500, -0.5558)
  O1:    2.0157             ( -0.5558,  0.0558, -0.2500)
Cr1  pair count:   6       << -0.1524, -0.1524, -0.1524>>
  O1:    1.9654             ( -0.0558,  0.2500, -0.4442)
  O1:    1.9654             ( -0.4442, -0.0558,  0.2500)
  O1:    1.9654             (  0.2500, -0.4442, -0.0558)
  O1:    2.0157             ( -0.2500, -0.5558,  0.0558)
  O1:    2.0157             (  0.0558, -0.2500, -0.5558)
  O1:    2.0157             ( -0.5558,  0.0558, -0.2500)
O1   pair count:   4       <<  0.5558, -0.0558,  0.2500>>
  Cr1:   1.9654             (  0.6524, -0.3476,  0.6524)
  Cr1:   1.9654             (  0.8476, -0.1524, -0.1524)
  Cr1:   2.0157             (  0.3476,  0.3476,  0.3476)
  Cr1:   2.0157             (  0.1524,  0.1524,  0.1524)
O1   pair count:   4       <<  0.2500,  0.5558, -0.0558>>
  Cr1:   1.9654             (  0.6524,  0.6524, -0.3476)
  Cr1:   1.9654             ( -0.1524,  0.8476, -0.1524)
  Cr1:   2.0157             (  0.3476,  0.3476,  0.3476)
  Cr1:   2.0157             (  0.1524,  0.1524,  0.1524)
O1   pair count:   4       << -0.0558,  0.2500,  0.5558>>
  Cr1:   1.9654             ( -0.1524, -0.1524,  0.8476)
  Cr1:   1.9654             ( -0.3476,  0.6524,  0.6524)
  Cr1:   2.0157             (  0.3476,  0.3476,  0.3476)
  Cr1:   2.0157             (  0.1524,  0.1524,  0.1524)
O1   pair count:   4       << -0.5558,  0.0558, -0.2500>>
  Cr1:   1.9654             ( -0.6524,  0.3476, -0.6524)
  Cr1:   1.9654             ( -0.8476,  0.1524,  0.1524)
  Cr1:   2.0157             ( -0.3476, -0.3476, -0.3476)
  Cr1:   2.0157             ( -0.1524, -0.1524, -0.1524)
O1   pair count:   4       << -0.2500, -0.5558,  0.0558>>
  Cr1:   1.9654             ( -0.6524, -0.6524,  0.3476)
  Cr1:   1.9654             (  0.1524, -0.8476,  0.1524)
  Cr1:   2.0157             ( -0.3476, -0.3476, -0.3476)
  Cr1:   2.0157             ( -0.1524, -0.1524, -0.1524)
O1   pair count:   4       <<  0.0558, -0.2500, -0.5558>>
  Cr1:   1.9654             (  0.1524,  0.1524, -0.8476)
  Cr1:   1.9654             (  0.3476, -0.6524, -0.6524)
  Cr1:   2.0157             ( -0.3476, -0.3476, -0.3476)
  Cr1:   2.0157             ( -0.1524, -0.1524, -0.1524)

Coordination sequences for ICSD structure
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
TD10: 1345.00

Coordination sequences for P1 structure
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
Cr1 [1, 6, 13, 39, 46, 105, 101, 204, 178, 336, 277]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
O1 [1, 4, 16, 26, 66, 70, 150, 136, 264, 224, 414]
TD10: 1345.00

(2, 2, 2) 86.0508424883 86.0508424883
(4, 4, 4) 113.047557719 113.047557719
(3, 2, 3) 40.4154044721 40.4154044721
(3, 3, 2) 40.4154044721 40.4154044721
(2, 3, 3) 40.4154044721 40.4154044721
(1, 0, 1) 95.4889181855 95.4889181855
(1, 1, 0) 95.4889181855 95.4889181855
(0, 1, 1) 95.4889181855 95.4889181855
(2, 1, 1) 162.211900743 162.211900743
(1, 1, 2) 162.211900743 162.211900743
(1, 2, 1) 162.211900743 162.211900743
(4, 3, 3) 155.00906081 155.00906081
(3, 3, 4) 155.00906081 155.00906081
(3, 4, 3) 155.00906081 155.00906081
(0, -1, 1) 169.838481281 169.838481281
(-1, 0, 1) 169.838481281 169.838481281
(1, -1, 0) 169.838481281 169.838481281
(2, 1, 0) 77.6623864446 77.6623864446
(1, 0, 2) 77.6623864446 77.6623864446
(0, 2, 1) 77.6623864446 77.6623864446
(1, 2, 0) 77.6623864446 77.6623864446
(0, 1, 2) 77.6623864446 77.6623864446
(2, 0, 1) 77.6623864446 77.6623864446
(3, 2, 1) 190.423823139 190.423823139
(2, 1, 3) 190.423823139 190.423823139
(1, 3, 2) 190.423823139 190.423823139
(2, 3, 1) 190.423823139 190.423823139
(1, 2, 3) 190.423823139 190.423823139
(3, 1, 2) 190.423823139 190.423823139
(4, 3, 2) 47.1902503064 47.1902503064
(3, 2, 4) 47.1902503064 47.1902503064
(2, 4, 3) 47.1902503064 47.1902503064
(3, 4, 2) 47.1902503064 47.1902503064
(2, 3, 4) 47.1902503064 47.1902503064
(4, 2, 3) 47.1902503064 47.1902503064
(5, 4, 3) 38.7011643914 38.7011643914
(4, 3, 5) 38.7011643914 38.7011643914
(3, 5, 4) 38.7011643914 38.7011643914
(4, 5, 3) 38.7011643914 38.7011643914
(3, 4, 5) 38.7011643914 38.7011643914
(5, 3, 4) 38.7011643914 38.7011643914
(4, 2, 4) 126.854496289 126.854496289
(4, 4, 2) 126.854496289 126.854496289
(2, 4, 4) 126.854496289 126.854496289
(2, 0, 2) 159.758114444 159.758114444
(2, 2, 0) 159.758114444 159.758114444
(0, 2, 2) 159.758114444 159.758114444
(2, 0, 0) 52.4585599646 52.4585599646
(0, 0, 2) 52.4585599646 52.4585599646
(0, 2, 0) 52.4585599646 52.4585599646
(4, 2, 2) 19.175305094 19.175305094
(2, 2, 4) 19.175305094 19.175305094
(2, 4, 2) 19.175305094 19.175305094
(3, 1, 4) 22.6189348657 22.6189348657
(4, 3, 1) 22.6189348657 22.6189348657
(1, 4, 3) 22.6189348657 22.6189348657
(1, 3, 4) 22.6189348657 22.6189348657
(3, 4, 1) 22.6189348657 22.6189348657
(4, 1, 3) 22.6189348657 22.6189348657
(2, 0, 3) 16.0896242359 16.0896242359
(3, 2, 0) 16.0896242359 16.0896242359
(0, 3, 2) 16.0896242359 16.0896242359
(0, 2, 3) 16.0896242359 16.0896242359
(2, 3, 0) 16.0896242359 16.0896242359
(3, 0, 2) 16.0896242359 16.0896242359
(-1, -2, 1) 53.0970522234 53.0970522234
(1, -1, 2) 53.0970522234 53.0970522234
(-1, 2, 1) 53.0970522234 53.0970522234
(-1, 1, 2) 53.0970522234 53.0970522234
(2, -1, 1) 53.0970522234 53.0970522234
(-2, -1, 1) 53.0970522234 53.0970522234
(0, -1, 2) 18.7461313511 18.7461313511
(0, -2, 1) 18.7461313511 18.7461313511
(-2, 0, 1) 18.7461313511 18.7461313511
(1, -2, 0) 18.7461313511 18.7461313511
(-1, 0, 2) 18.7461313511 18.7461313511
(2, -1, 0) 18.7461313511 18.7461313511
(3, 1, 0) 132.488142531 132.488142531
(1, 0, 3) 132.488142531 132.488142531
(0, 3, 1) 132.488142531 132.488142531
(1, 3, 0) 132.488142531 132.488142531
(0, 1, 3) 132.488142531 132.488142531
(3, 0, 1) 132.488142531 132.488142531
(4, 2, 1) 14.1831500279 14.1831500279
(2, 1, 4) 14.1831500279 14.1831500279
(1, 4, 2) 14.1831500279 14.1831500279
(2, 4, 1) 14.1831500279 14.1831500279
(1, 2, 4) 14.1831500279 14.1831500279
(4, 1, 2) 14.1831500279 14.1831500279
(5, 3, 2) 121.452908825 121.452908825
(3, 2, 5) 121.452908825 121.452908825
(2, 5, 3) 121.452908825 121.452908825
(3, 5, 2) 121.452908825 121.452908825
(2, 3, 5) 121.452908825 121.452908825
(5, 2, 3) 121.452908825 121.452908825
(0, -2, 2) 121.476041154 121.476041154
(-2, 0, 2) 121.476041154 121.476041154
(2, -2, 0) 121.476041154 121.476041154
(1, -1, 3) 39.0693132248 39.0693132248
(-1, 3, 1) 39.0693132248 39.0693132248
(-1, -3, 1) 39.0693132248 39.0693132248
(-3, -1, 1) 39.0693132248 39.0693132248
(-1, 1, 3) 39.0693132248 39.0693132248
(3, -1, 1) 39.0693132248 39.0693132248
(4, 2, 0) 133.588352208 133.588352208
(2, 0, 4) 133.588352208 133.588352208
(0, 4, 2) 133.588352208 133.588352208
(2, 4, 0) 133.588352208 133.588352208
(0, 2, 4) 133.588352208 133.588352208
(4, 0, 2) 133.588352208 133.588352208
(3, 0, 3) 75.3123159831 75.3123159831
(3, 3, 0) 75.3123159831 75.3123159831
(0, 3, 3) 75.3123159831 75.3123159831
(-1, -1, 2) 219.874202958 219.874202958
(1, -2, 1) 219.874202958 219.874202958
(-2, 1, 1) 219.874202958 219.874202958
(4, 1, 1) 75.3123159831 75.3123159831
(1, 1, 4) 75.3123159831 75.3123159831
(1, 4, 1) 75.3123159831 75.3123159831
(3, 0, 4) 7.74006832091 7.74006832091
(4, 3, 0) 7.74006832091 7.74006832091
(0, 4, 3) 7.74006832091 7.74006832091
(0, 3, 4) 7.74006832091 7.74006832091
(3, 4, 0) 7.74006832091 7.74006832091
(4, 0, 3) 7.74006832091 7.74006832091
(-2, -3, 1) 92.880272839 92.880272839
(2, -1, 3) 92.880272839 92.880272839
(-1, 3, 2) 92.880272839 92.880272839
(-1, 2, 3) 92.880272839 92.880272839
(3, -1, 2) 92.880272839 92.880272839
(-3, -2, 1) 92.880272839 92.880272839
(-1, -2, 2) 9.22539071273 9.22539071273
(1, -2, 2) 9.22539071273 9.22539071273
(-2, 2, 1) 9.22539071273 9.22539071273
(-2, 1, 2) 9.22539071273 9.22539071273
(2, -2, 1) 9.22539071273 9.22539071273
(-2, -1, 2) 9.22539071273 9.22539071273
(0, -1, 3) 58.7597521751 58.7597521751
(0, -3, 1) 58.7597521751 58.7597521751
(-3, 0, 1) 58.7597521751 58.7597521751
(1, -3, 0) 58.7597521751 58.7597521751
(-1, 0, 3) 58.7597521751 58.7597521751
(3, -1, 0) 58.7597521751 58.7597521751
(4, 1, 0) 8.38469863314 8.38469863314
(1, 0, 4) 8.38469863314 8.38469863314
(0, 4, 1) 8.38469863314 8.38469863314
(1, 4, 0) 8.38469863314 8.38469863314
(0, 1, 4) 8.38469863314 8.38469863314
(4, 0, 1) 8.38469863314 8.38469863314
(-2, -2, 2) 63.3334064079 63.3334064079
(2, -2, 2) 63.3334064079 63.3334064079
(-2, 2, 2) 63.3334064079 63.3334064079
(4, 0, 0) 76.9075882126 76.9075882126
(0, 0, 4) 76.9075882126 76.9075882126
(0, 4, 0) 76.9075882126 76.9075882126
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/reduced_cell_two_folds.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/reduced_cell_two_folds.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
(-1, -1, -1, 0, 0, 1, 0, 1, 0) (-1, 1, 1) (0, 1, 1)
(-1, -1, 0, 0, 1, 0, 0, -1, -1) (1, -2, 1) (0, 1, 0)
(-1, -1, 0, 0, 1, 0, 0, 0, -1) (-1, 2, 0) (0, 1, 0)
(-1, -1, 0, 0, 1, 0, 0, 1, -1) (-1, 2, 1) (0, 1, 0)
(-1, -1, 1, 0, 0, -1, 0, -1, 0) (1, -1, 1) (0, -1, 1)
(-1, 0, -1, 0, -1, -1, 0, 0, 1) (-1, -1, 2) (0, 0, 1)
(-1, 0, -1, 0, -1, 0, 0, 0, 1) (-1, 0, 2) (0, 0, 1)
(-1, 0, -1, 0, -1, 1, 0, 0, 1) (-1, 1, 2) (0, 0, 1)
(-1, 0, 0, -1, 0, -1, 1, -1, 0) (0, -1, 1) (1, -1, 1)
(-1, 0, 0, -1, 0, 1, -1, 1, 0) (0, 1, 1) (-1, 1, 1)
(-1, 0, 0, -1, 1, -1, 0, 0, -1) (0, 1, 0) (1, -2, 1)
(-1, 0, 0, -1, 1, 0, 0, 0, -1) (0, 1, 0) (-1, 2, 0)
(-1, 0, 0, -1, 1, 1, 0, 0, -1) (0, 1, 0) (-1, 2, 1)
(-1, 0, 0, 0, -1, -1, 0, 0, 1) (0, -1, 2) (0, 0, 1)
(-1, 0, 0, 0, -1, 0, -1, -1, 1) (0, 0, 1) (-1, -1, 2)
(-1, 0, 0, 0, -1, 0, -1, 0, 1) (0, 0, 1) (-1, 0, 2)
(-1, 0, 0, 0, -1, 0, -1, 1, 1) (0, 0, 1) (-1, 1, 2)
(-1, 0, 0, 0, -1, 0, 0, -1, 1) (0, 0, 1) (0, -1, 2)
(-1, 0, 0, 0, -1, 0, 0, 0, 1) (0, 0, 1) (0, 0, 1)
(-1, 0, 0, 0, -1, 0, 0, 1, 1) (0, 0, 1) (0, 1, 2)
(-1, 0, 0, 0, -1, 0, 1, -1, 1) (0, 0, 1) (1, -1, 2)
(-1, 0, 0, 0, -1, 0, 1, 0, 1) (0, 0, 1) (1, 0, 2)
(-1, 0, 0, 0, -1, 0, 1, 1, 1) (0, 0, 1) (1, 1, 2)
(-1, 0, 0, 0, -1, 1, 0, 0, 1) (0, 1, 2) (0, 0, 1)
(-1, 0, 0, 0, 0, -1, 0, -1, 0) (0, -1, 1) (0, -1, 1)
(-1, 0, 0, 0, 0, 1, 0, 1, 0) (0, 1, 1) (0, 1, 1)
(-1, 0, 0, 0, 1, -1, 0, 0, -1) (0, 1, 0) (0, -2, 1)
(-1, 0, 0, 0, 1, 0, 0, -1, -1) (0, -2, 1) (0, 1, 0)
(-1, 0, 0, 0, 1, 0, 0, 0, -1) (0, 1, 0) (0, 1, 0)
(-1, 0, 0, 0, 1, 0, 0, 1, -1) (0, 2, 1) (0, 1, 0)
(-1, 0, 0, 0, 1, 1, 0, 0, -1) (0, 1, 0) (0, 2, 1)
(-1, 0, 0, 1, 0, -1, -1, -1, 0) (0, -1, 1) (-1, -1, 1)
(-1, 0, 0, 1, 0, 1, 1, 1, 0) (0, 1, 1) (1, 1, 1)
(-1, 0, 0, 1, 1, -1, 0, 0, -1) (0, 1, 0) (-1, -2, 1)
(-1, 0, 0, 1, 1, 0, 0, 0, -1) (0, 1, 0) (1, 2, 0)
(-1, 0, 0, 1, 1, 1, 0, 0, -1) (0, 1, 0) (1, 2, 1)
(-1, 0, 1, 0, -1, -1, 0, 0, 1) (1, -1, 2) (0, 0, 1)
(-1, 0, 1, 0, -1, 0, 0, 0, 1) (1, 0, 2) (0, 0, 1)
(-1, 0, 1, 0, -1, 1, 0, 0, 1) (1, 1, 2) (0, 0, 1)
(-1, 1, -1, 0, 0, -1, 0, -1, 0) (-1, -1, 1) (0, -1, 1)
(-1, 1, 0, 0, 1, 0, 0, -1, -1) (-1, -2, 1) (0, 1, 0)
(-1, 1, 0, 0, 1, 0, 0, 0, -1) (1, 2, 0) (0, 1, 0)
(-1, 1, 0, 0, 1, 0, 0, 1, -1) (1, 2, 1) (0, 1, 0)
(-1, 1, 1, 0, 0, 1, 0, 1, 0) (1, 1, 1) (0, 1, 1)
(0, -1, -1, -1, 0, 1, 0, 0, -1) (-1, 1, 0) (-1, 1, 1)
(0, -1, -1, 0, -1, 0, -1, 1, 0) (-1, 0, 1) (-1, 1, 1)
(0, -1, 0, -1, 0, 0, -1, 1, -1) (-1, 1, 1) (-1, 1, 0)
(0, -1, 0, -1, 0, 0, 0, 0, -1) (-1, 1, 0) (-1, 1, 0)
(0, -1, 0, -1, 0, 0, 1, -1, -1) (1, -1, 1) (-1, 1, 0)
(0, -1, 1, -1, 0, -1, 0, 0, -1) (-1, 1, 0) (1, -1, 1)
(0, -1, 1, 0, -1, 0, 1, -1, 0) (1, 0, 1) (1, -1, 1)
(0, 0, -1, -1, -1, 1, -1, 0, 0) (-1, 1, 1) (-1, 0, 1)
(0, 0, -1, 0, -1, 0, -1, 0, 0) (-1, 0, 1) (-1, 0, 1)
(0, 0, -1, 1, -1, -1, -1, 0, 0) (-1, -1, 1) (-1, 0, 1)
(0, 0, 1, -1, -1, -1, 1, 0, 0) (1, -1, 1) (1, 0, 1)
(0, 0, 1, 0, -1, 0, 1, 0, 0) (1, 0, 1) (1, 0, 1)
(0, 0, 1, 1, -1, 1, 1, 0, 0) (1, 1, 1) (1, 0, 1)
(0, 1, -1, 0, -1, 0, -1, -1, 0) (-1, 0, 1) (-1, -1, 1)
(0, 1, -1, 1, 0, -1, 0, 0, -1) (1, 1, 0) (-1, -1, 1)
(0, 1, 0, 1, 0, 0, -1, -1, -1) (-1, -1, 1) (1, 1, 0)
(0, 1, 0, 1, 0, 0, 0, 0, -1) (1, 1, 0) (1, 1, 0)
(0, 1, 0, 1, 0, 0, 1, 1, -1) (1, 1, 1) (1, 1, 0)
(0, 1, 1, 0, -1, 0, 1, 1, 0) (1, 0, 1) (1, 1, 1)
(0, 1, 1, 1, 0, 1, 0, 0, -1) (1, 1, 0) (1, 1, 1)
(1, -1, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 1, 1)
(1, -1, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 1, 0)
(1, -1, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, -1, 1)
(1, 0, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, 0, 1)
(1, 0, 0, -1, -1, 0, -1, 0, -1) (-2, 1, 1) (1, 0, 0)
(1, 0, 0, -1, -1, 0, 0, 0, -1) (-2, 1, 0) (1, 0, 0)
(1, 0, 0, -1, -1, 0, 1, 0, -1) (2, -1, 1) (1, 0, 0)
(1, 0, 0, 0, -1, 0, -1, 0, -1) (-2, 0, 1) (1, 0, 0)
(1, 0, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (1, 0, 0)
(1, 0, 0, 0, -1, 0, 1, 0, -1) (2, 0, 1) (1, 0, 0)
(1, 0, 0, 1, -1, 0, -1, 0, -1) (-2, -1, 1) (1, 0, 0)
(1, 0, 0, 1, -1, 0, 0, 0, -1) (2, 1, 0) (1, 0, 0)
(1, 0, 0, 1, -1, 0, 1, 0, -1) (2, 1, 1) (1, 0, 0)
(1, 0, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 0, 1)
(1, 1, -1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (-2, -1, 1)
(1, 1, 0, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 1, 0)
(1, 1, 1, 0, -1, 0, 0, 0, -1) (1, 0, 0) (2, 1, 1)
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/lebedev_2005_perturbation.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/lebedev_2005_perturbation.py:14: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
s={{6732.6948, -1414.631, -2529.5033},
   {-1414.631, 4437.1585, -884.7347},
   {-2529.5033, -884.7347, 7208.6892}}
m={{0, 0, -1},
   {0, -1, 0},
   {-1, 0, 0}}
rotation type: 2
axis direction: (-1, 0, 1)
score given:      0.06996537
score reproduced: 0.0699653749294
Le Page delta:    0.0848717968347

s={{6176.9399, 260.7664, 128.5781},
   {260.7664, 1340.4385, -14.6349},
   {128.5781, -14.6349, 524.5932}}
m={{-1, 0, 0},
   {0, -1, 0},
   {1, 0, 1}}
rotation type: 2
axis direction: (0, 0, 1)
score given:      0.06177181
score reproduced: 0.0617717889751
Le Page delta:    0.0750886664342

s={{7578.2248, -1951.4527, -1447.0019},
   {-1951.4527, 7501.6385, -256.6406},
   {-1447.0019, -256.6406, 7208.6892}}
m={{-1, 0, 0},
   {0, 0, -1},
   {0, -1, 0}}
rotation type: 2
axis direction: (0, -1, 1)
score given:      0.03867617
score reproduced: 0.0386761646506
Le Page delta:    0.0472278316943

s={{7930.4368, -2942.6005, -1480.2461},
   {-2942.6005, 9333.8785, -429.2985},
   {-1480.2461, -429.2985, 7208.6892}}
m={{0, -1, 0},
   {-1, 0, 0},
   {0, 0, -1}}
rotation type: 2
axis direction: (-1, 1, 0)
score given:      0.11207609
score reproduced: 0.112076089497
Le Page delta:    0.134026806814

s={{8473.7548, -1587.0355, -175.9529},
   {-1587.0355, 4437.1585, -394.5165},
   {-175.9529, -394.5165, 7208.6892}}
m={{-1, 0, 0},
   {0, -1, 0},
   {0, 0, 1}}
rotation type: 2
axis direction: (0, 0, 1)
score given:      0.06714734
score reproduced: 0.0671473468463
Le Page delta:    0.0815139175486

s={{10414.8148, -414.5907, 2452.0864},
   {-414.5907, 2172.6785, -304.2978},
   {2452.0864, -304.2978, 5610.6092}}
m={{1, 0, 0},
   {0, -1, 0},
   {-1, 0, -1}}
rotation type: 2
axis direction: (-2, 0, 1)
score given:      0.06543032
score reproduced: 0.0654303257975
Le Page delta:    0.0794643933624

s={{9817.4017, -451.9168, 1807.5581},
   {-451.9168, 4437.1585, -451.9168},
   {1807.5581, -451.9168, 4212.5292}}
m={{1, 0, 0},
   {0, -1, 0},
   {-1, 0, -1}}
rotation type: 2
axis direction: (-2, 0, 1)
score given:      0.05202084
score reproduced: 0.0520208375975
Le Page delta:    0.063372263802

s={{2814.6208, 446.7217, -65.5759},
   {446.7217, 9333.8785, -646.4419},
   {-65.5759, -646.4419, 3014.4492}}
m={{0, 0, 1},
   {0, -1, 0},
   {1, 0, 0}}
rotation type: 2
axis direction: (1, 0, 1)
score given:      0.03361885
score reproduced: 0.0336188434566
Le Page delta:    0.0410819848677

s={{9103.413, 420.0088, 352.4837},
   {420.0088, 1340.4385, -228.8041},
   {352.4837, -228.8041, 2016.3692}}
m={{1, 0, 0},
   {-1, -1, 0},
   {0, 0, -1}}
rotation type: 2
axis direction: (-2, 1, 0)
score given:      0.10323493
score reproduced: 0.103234924615
Le Page delta:    0.12388279713

s={{9046.4187, 1355.7037, -75.0535},
   {1355.7037, 4437.1585, -403.7364},
   {-75.0535, -403.7364, 1218.2892}}
m={{-1, 0, 0},
   {0, -1, 0},
   {0, -1, 1}}
rotation type: 2
axis direction: (0, 0, 1)
score given:      0.0819319
score reproduced: 0.0819319050724
Le Page delta:    0.0990441384163

OK

libtbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/le_page_1982_vs_lebedev_2005.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/le_page_1982_vs_lebedev_2005.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

set ccp4_symop_lib=`libtbx.show_dist_paths ccp4io`/lib/data/symop.lib
libtbx.show_dist_paths ccp4io
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/convert_ccp4_symop_lib.py
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/examples/convert_ccp4_symop_lib.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
grep Fd-3m convert_ccp4_symop_py_out
libtbx.assert_stdin 227 192 48 Fd-3m PGm3barm CUBIC 'F 41/d -3 2/m' 'F d -3 m'
cctbx.convert_ccp4_symop_lib
diff convert_ccp4_symop_py_out convert_ccp4_symop_cpp_out
libtbx.assert_stdin 
if ( 0 ) then
cctbx.structure_factor_timings /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent 4
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
Number of scatterers: 684
At special positions: 0
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)

Number of Miller indices: 320
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
d_min: 4.0
direct simple: 0.14 seconds
wing_cutoff for following fft calculations: 1.0e-03
S:1*6 O:1*69 N:1*58 C:1*222 H:1*329
  direct cos+sin function: 0.08 seconds, r-factor: 0.000020
  direct cos+sin table:    0.03 seconds, r-factor: 0.000055
  fft exp function:        0.01 seconds, r-factor: 0.000122
  fft exp table:           0.01 seconds, r-factor: 0.000124
S:5+c*6 O:5+c*69 N:5+c*58 C:5+c*222 H:5+c*329
  direct cos+sin function: 0.08 seconds, r-factor: 0.000000
  direct cos+sin table:    0.03 seconds, r-factor: 0.000044
  fft exp function:        0.02 seconds, r-factor: 0.000097
  fft exp table:           0.01 seconds, r-factor: 0.000097
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  direct cos+sin function: 0.08 seconds, r-factor: 0.000000
  direct cos+sin table:    0.03 seconds, r-factor: 0.000044
  fft exp function:        0.02 seconds, r-factor: 0.000095
  fft exp table:           0.01 seconds, r-factor: 0.000095
S:2*6 O:2*69 N:2*58 C:2*222 H:2*329
  direct cos+sin function: 0.08 seconds, r-factor: 0.000003
  direct cos+sin table:    0.03 seconds, r-factor: 0.000040
  fft exp function:        0.01 seconds, r-factor: 0.000116
  fft exp table:           0.01 seconds, r-factor: 0.000116
S:1*6 O:1*69 N:1*58 C:1*222 H:2*329
  direct cos+sin function: 0.08 seconds, r-factor: 0.013726
  direct cos+sin table:    0.03 seconds, r-factor: 0.013798
  fft exp function:        0.01 seconds, r-factor: 0.014112
  fft exp table:           0.00 seconds, r-factor: 0.014131

cctbx.structure_factor_timings /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent --fft_only 3
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
Number of scatterers: 684
At special positions: 0
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)

Number of Miller indices: 728
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
d_min: 3.0
fft exp function wing_cutoff=1.0e-06: 0.11 seconds
wing_cutoff for following fft calculations: 1.0e-03
S:2*6 O:1*69 N:1*58 C:2*222 H:1*329
  fft exp function:        0.01 seconds, r-factor: 0.000086
  fft exp table:           0.01 seconds, r-factor: 0.000087
S:5+c*6 O:5+c*69 N:5+c*58 C:5+c*222 H:5+c*329
  fft exp function:        0.02 seconds, r-factor: 0.000041
  fft exp table:           0.02 seconds, r-factor: 0.000041
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  fft exp function:        0.02 seconds, r-factor: 0.000042
  fft exp table:           0.01 seconds, r-factor: 0.000042
S:2*6 O:2*69 N:2*58 C:2*222 H:2*329
  fft exp function:        0.01 seconds, r-factor: 0.000050
  fft exp table:           0.01 seconds, r-factor: 0.000051
S:1*6 O:1*69 N:1*58 C:1*222 H:2*329
  fft exp function:        0.01 seconds, r-factor: 0.040792
  fft exp table:           0.00 seconds, r-factor: 0.040847

libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/electron_density_sampling.py /net/rosie/scratch1/rwgk/dist/regression/cctbx/1ab1.ent
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/electron_density_sampling.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/structure_factor_timings.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
Number of scatterers: 684
At special positions: 0
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)

wing_cutoff for following fft calculations: 1.0e-03
exp function:
Number of Miller indices: 320
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:1*6 O:1*69 N:1*58 C:1*222 H:1*329
  0.00 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.01 seconds,
d_min=4: 0.00 s / 0.01 s = 0.00
Number of Miller indices: 728
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:1*69 N:1*58 C:2*222 H:1*329
  0.01 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.02 seconds,
d_min=3: 0.01 s / 0.02 s = 0.50
Number of Miller indices: 2370
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:2*69 N:2*58 C:2*222 H:2*329
  0.01 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.03 seconds,
d_min=2: 0.01 s / 0.03 s = 0.33
Number of Miller indices: 18204
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:2*69 N:2*58 C:2*222 H:3*329
  0.07 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.12 seconds,
d_min=1: 0.07 s / 0.12 s = 0.58
exp table:
Number of Miller indices: 320
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:1*6 O:1*69 N:1*58 C:1*222 H:1*329
  0.01 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.01 seconds,
d_min=4: 0.01 s / 0.01 s = 1.00
Number of Miller indices: 728
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:1*69 N:1*58 C:2*222 H:1*329
  0.00 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.01 seconds,
d_min=3: 0.00 s / 0.01 s = 0.00
Number of Miller indices: 2370
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:2*69 N:2*58 C:2*222 H:2*329
  0.00 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.01 seconds,
d_min=2: 0.00 s / 0.01 s = 0.00
Number of Miller indices: 18204
Anomalous flag: False
Unit cell: (40.759, 18.404, 22.273, 90, 90.7, 90)
Space group: P 1 21 1 (No. 4)
S:2*6 O:2*69 N:2*58 C:2*222 H:3*329
  0.03 seconds,
S:4+c*6 O:4+c*69 N:4+c*58 C:4+c*222 H:4+c*329
  0.06 seconds,
d_min=1: 0.03 s / 0.06 s = 0.50

libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/asu_gallery/jv_asu.py 213
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/asu_gallery/jv_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.web.asu_gallery import jvx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Space group number: 213
libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/direct_space_asu/check_redundancies.py 12 181
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/sgtbx/direct_space_asu/check_redundancies.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.sgtbx.direct_space_asu import reference_table
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Writing asu_gallery files
Space group: P 64 2 2 (No. 181)
Gridding: (12, 12, 12)
number of redundancies: 0+0, Space group: P 64 2 2 (No. 181)
grep -i error
libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/replay.py /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/all_axes_2002_11_22_16_57_14 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/browse_settings_2002_11_22_16_35_50 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/browse_settings_2002_11_22_16_35_58 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_hand_2002_11_22_16_55_27 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_hand_2002_11_22_16_56_35 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_setting_2002_11_22_16_53_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/change_setting_2002_11_22_16_54_28 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2002_11_22_16_45_58 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2002_11_22_17_03_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_02_10 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_03_53 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/emma_2004_05_25_10_05_21 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/explore_symmetry_2002_11_22_16_34_28 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/explore_symmetry_2002_11_22_16_35_25 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/frac_cart_2002_11_22_16_50_33 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/frac_cart_2002_11_22_16_52_04 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/lattice_symmetry_2003_08_28_06_17_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/libtbx_help_2005_08_14_02_41_20 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_05_12_26 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_07_09_15 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_07_16_53 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_52_08 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_53_42 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_55_55 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/phase_o_phrenia_2002_12_31_08_57_00 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/shelx_2002_11_22_16_46_31 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/shelx_2002_11_22_16_46_38 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_32_10 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_33_32 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_21_34_02 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_2005_11_10_22_27_47 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_25_48 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_26_06 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/structure_factors_pdb_2004_12_17_15_26_25 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/wyckoff_2002_11_22_16_47_49 /net/rosie/scratch1/rwgk/dist/regression/cctbx/web/wyckoff_2002_11_22_16_48_33
/net/rosie/scratch1/rwgk/py25b1/build/python/lib/python2.5/pickle.py:1124: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  __import__(module)
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/web/io_utils.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
  cctbx Error: Brick is not available for the given space group representation.
libtbx.show_dist_paths mmtbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/run_tests.py
/net/rosie/scratch1/rwgk/dist/mmtbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/refinement/tst_rigid_body.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.f_model
|-----------------------------------------------------------------------------|
|                                                                             |
| all data [41.9-2.00] high resolution [6.0-2.00] low resolution [41.9-6.00]  |
| r_work = 0.0000      r_work = 0.0000            r_work = 0.0152             |
| r_free = 0.0000      r_free = 0.0000            r_free = 0.0131             |
|                                                                             |
| scale (work) = 1.0000  scale (free) = 1.0000  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ls_wunit_k1:  work = 0.000000E+00  free = 0.000000E+00               |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 41.9535 -  2.8845 1.00   2301  254 0.0000 0.0000  0.0000E+00  0.0000E+00|
|  2:  2.8845 -  2.2896 1.00   2197  237 0.0000 0.0000  0.0000E+00  0.0000E+00|
|  3:  2.2896 -  2.0001 1.00   2153  247 0.0000 0.0000  0.0000E+00  0.0000E+00|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 41.9535 -  2.8845  2301   254 1.000   0.000   0.000   1.000       0.000 |
|  2:  2.8845 -  2.2896  2197   237 1.000   0.000   0.000   1.000       0.000 |
|  3:  2.2896 -  2.0001  2153   247 1.000   0.000   0.000   1.000       0.000 |
|alpha:            min =       1.0000 max =       1.0000 mean =       1.0000  |
|beta:             min =       0.0000 max =       0.0000 mean =       0.0000  |
|figures of merit: min =       1.0000 max =       1.0000 mean =       1.0000  |
|phase err.(work): min =       0.0000 max =       0.0000 mean =       0.0000  |
|phase err.(test): min =       0.0000 max =       0.0000 mean =       0.0000  |
|-----------------------------------------------------------------------------|
test 1: 
High resolution cutoffs for mz-protocol:  ['3.854', '2.000']

            ----------Refinement at resolution: 41.9 - 3.9----------           

|-rigid body refinement: Euler angles xyz (macro cycle = 1; iterations = 17)--|
| resolution range: 41.944 - 3.855 (1010 reflections) convergence test = on   |
| r_work = 0.010563 r_free = 0.009630 target = 0.000112                       |
|                         rotation (deg.)                translation (A)      |
| group    1:    0.0000   0.0000   0.0000      -2.4990  -2.5001  -2.5004      |
|-----------------------------------------------------------------------------|

|-rigid body refinement: Euler angles xyz (macro cycle = 2; iterations = 7)---|
| resolution range: 41.944 - 3.855 (1010 reflections) convergence test = on   |
| r_work = 0.010556 r_free = 0.009638 target = 0.000112                       |
|                         rotation (deg.)                translation (A)      |
| group    1:    0.0000   0.0000   0.0000      -2.4990  -2.5001  -2.5004      |
|-----------------------------------------------------------------------------|

            ----------Refinement at resolution: 41.9 - 2.0----------           

|-rigid body refinement: Euler angles xyz (macro cycle = 1; iterations = 5)---|
| resolution range: 41.944 - 2.000 (6651 reflections) convergence test = on   |
| r_work = 0.000238 r_free = 0.000243 target = 0.000000                       |
|                         rotation (deg.)                translation (A)      |
| group    1:    0.0000   0.0000   0.0000      -2.5000  -2.5000  -2.5000      |
|-----------------------------------------------------------------------------|

|-rigid body refinement: Euler angles xyz (macro cycle = 2; iterations = 4)---|
| resolution range: 41.944 - 2.000 (6651 reflections) convergence test = on   |
| r_work = 0.000217 r_free = 0.000222 target = 0.000000                       |
|                         rotation (deg.)                translation (A)      |
| group    1:    0.0000   0.0000   0.0000      -2.5000  -2.5000  -2.5000      |
|-----------------------------------------------------------------------------|
finite_differences_test: 
|-----------------------------------------------------------------------------|
|                                                                             |
| all data [11.1-1.00] high resolution [6.0-1.00] low resolution [11.1-6.00]  |
| r_work = 0.1137      r_work = 0.1192            r_work = 0.0451             |
| r_free = 0.1137      r_free = 0.1192            r_free = 0.0451             |
|                                                                             |
| scale (work) = 0.9924  scale (free) = 0.9924  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ls_wunit_k1:  work = 7.568666E-03  free = 7.568666E-03               |
|-----------------------------------------------------------------------------|
u+s,u,s: 11.33 11.03 0.30

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math, time, sys, os
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math, time, sys, os
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_model.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.model
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/model.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.001   0.002  0.000|       0.039||            ||  mean   max    min  |
|angl|  0.113   0.948  0.004|       0.269||            ||                     |
|chir|  0.001   0.003  0.001|       0.000||       3.295||      undefined      |
|plan|  0.001   0.001  0.000|       0.031||            ||                     |
|dihe|  4.206  23.983  0.067|       1.925||            ||                     |
|repu|  4.229   4.899  2.642|       1.032||            ||                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.001   0.002  0.000|       0.039||            ||  mean   max    min  |
|angl|  0.113   0.948  0.004|       0.269||            ||                     |
|chir|  0.001   0.003  0.001|       0.000||       3.295||  0.000  0.000  0.000|
|plan|  0.001   0.001  0.000|       0.031||            ||                     |
|dihe|  4.206  23.983  0.067|       1.925||            ||                     |
|repu|  4.229   4.899  2.642|       1.032||            ||                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.012   0.412  0.000|     429.074||            ||  mean   max    min  |
|angl|  1.321  35.828  0.004|     195.506||            ||                     |
|chir|  0.001   0.003  0.001|       0.000||    1770.938||  0.000  0.000  0.000|
|plan|  0.020   0.138  0.000|     190.298||            ||                     |
|dihe| 10.168  69.790  0.067|       7.337||            ||                     |
|repu|  4.052   4.899  0.478|     948.724||            ||                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.001   0.002  0.000|       0.039||            ||  mean   max    min  |
|angl|  0.113   0.948  0.004|       0.269||            ||                     |
|chir|  0.001   0.003  0.001|       0.000||       3.295||      undefined      |
|plan|  0.001   0.001  0.000|       0.031||            ||                     |
|dihe|  4.206  23.983  0.067|       1.925||            ||                     |
|repu|  4.229   4.899  2.642|       1.032||            ||                     |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|                             Wilson B = None                                 |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   0.760    2.240     1.221          |   0.850    1.880     1.187            |
| number of B <   1.0: 12             |  number of B <   1.0: 10              |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 33 total                 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|                             Wilson B = None                                 |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   0.850    1.880     1.187          |   0.850    1.880     1.187            |
| number of B <   1.0: 10             |  number of B <   1.0: 10              |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 33 total                 |
|-----------------------------------------------------------------------------|

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.f_model
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math, time
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math, time
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
P 1
P 4
C 1 2/c 1
u+s,u,s: 24.88 24.59 0.29

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tst_fmodel_fd.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.f_model
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math, time
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/f_model.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math, time
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
P 1
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P -1
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 1 2 1
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
C 1 2/c 1
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 2 2 2
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
I m m a
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 4
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 41
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
I 41/a c d :2
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 3
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 31
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 3 1 m
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
R -3 c :H
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 6
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 63/m m c
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
P 2 3
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
I a -3 d
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4)
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_kunit
   ls_wunit_k1_fixed
   ls_wunit_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_k2
   ls_wexp_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wff_kunit
   ls_wff_k1_fixed
   ls_wff_k1ask3_fixed
   lsm_k1
   lsm_k2
   lsm_kunit
   lsm_k1_fixed
   lsm_k1ask3_fixed
   ml
u+s,u,s: 270.94 268.38 2.56

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/ncs/tst_restraints.py
/net/rosie/scratch1/rwgk/dist/mmtbx/ncs/tst_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import ncs
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import adptbx
u+s,u,s: 0.50 0.46 0.04

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/tst_restraints.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/tst_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import ncs
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/ncs/restraints.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import adptbx
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
u+s,u,s: 2.02 1.91 0.11

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/regression/tst_adp_restraints.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/regression/tst_adp_restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
u+s,u,s: 1.00 0.90 0.10

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/tst_scaling.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import scaling
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/twin_analyses.py:22: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import data_plots
very_quick_erf*15000000 optimized=False: 4.34 s
very_quick_erf*15000000 optimized=True: 0.24 s
quick_ei0*5000000 optimized=False: 1.28 s
quick_ei0*5000000 optimized=True: 0.35 s
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_cif_types.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import cif_types
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_motif.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_motif.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import server
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_selection.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_selection.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 12
      Number of chains: 1
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
  Time building chain proxies: 0.00, per 1000 atoms: 0.00

  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 12
      Number of chains: 1
        Number of residues, atoms: 2, 12
          Unusual residues: {'BNZ%bnz_to_tyr_sidechain': 1}
          Unexpected atoms: {'GLY,CB': 1}
          Classifications: {'undetermined': 1, 'peptide': 1}
          Modifications used: {'bnz_to_tyr_sidechain': 1}
          Link IDs: {'gly_bnz_to_tyr': 1}
  Number of atoms with unknown nonbonded energy type symbols: 1
    " CB  GLY     1 "
  Time building chain proxies: 0.01, per 1000 atoms: 0.83

geo_tyr
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        1.23 -     1.29: 1
        1.29 -     1.35: 0
        1.35 -     1.41: 7
        1.41 -     1.47: 1
        1.47 -     1.53: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CD1 TYR     1 " - " CE1 TYR     1 " 1.382  1.394 -0.012 1.11e+03 1.67e-01
  " CD2 TYR     1 " - " CE2 TYR     1 " 1.382  1.393 -0.011 1.11e+03 1.31e-01
  " CE2 TYR     1 " - " CZ  TYR     1 " 1.378  1.386 -0.008 1.74e+03 1.09e-01
  " N   TYR     1 " - " CA  TYR     1 " 1.458  1.453  0.005 2.77e+03 6.34e-02
  " CG  TYR     1 " - " CD1 TYR     1 " 1.389  1.394 -0.005 2.27e+03 4.84e-02
  ... (remaining 7 not shown)
  Histogram of nonbonded interaction distances:
        2.77 -     3.15: 4
        3.15 -     3.53: 6
        3.53 -     3.90: 8
        3.90 -     4.28: 2
        4.28 -     4.66: 9
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " CD2 TYR     1 " - " CE1 TYR     1 "  2.772 2.533
  " CD1 TYR     1 " - " CE2 TYR     1 "  2.773 2.533
  " CG  TYR     1 " - " CZ  TYR     1 "  2.797 2.267
  " C   TYR     1 " - " CG  TYR     1 "  2.865 2.267
  " O   TYR     1 " - " CG  TYR     1 "  3.226 3.220
  ... (remaining 24 not shown)
  Histogram of dihedral angle deviations from ideal:
        9.88 -    10.28: 1
       10.28 -    10.68: 0
       10.68 -    11.09: 0
       11.09 -    11.49: 0
       11.49 -    11.89: 1
  Dihedral angle restraints sorted by residual:
  " N   TYR     1 "
  " CA  TYR     1 "
  " CB  TYR     1 "
  " CG  TYR     1 "
      ideal   model   delta periodicty    weight residual
     180.00  170.12    9.88     3       4.44e-03 4.34e-01
  " CA  TYR     1 "
  " CB  TYR     1 "
  " CG  TYR     1 "
  " CD1 TYR     1 "
      ideal   model   delta periodicty    weight residual
      90.00   78.11   11.89     2       2.50e-03 3.53e-01
  target: 4.15715
    bond_residual_sum (n=12): 0.630997
    nonbonded_residual_sum (n=29): 0.587045
    angle_residual_sum (n=15): 0.662897
    dihedral_residual_sum (n=2): 0.787227
    chirality_residual_sum (n=1): 0.00143684
    planarity_residual_sum (n=1): 1.48755
  Time first energy calculation (mainly nonbonded setup): 0.00

geo_gly_bnz
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        1.23 -     1.29: 1
        1.29 -     1.35: 0
        1.35 -     1.41: 7
        1.41 -     1.47: 1
        1.47 -     1.53: 2
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  GLY     1 " - " C   GLY     1 " 1.516  1.527 -0.011 3.09e+03 3.98e-01
  " CD1 BNZ     2 " - " CE1 BNZ     2 " 1.382  1.394 -0.012 1.11e+03 1.67e-01
  " CD2 BNZ     2 " - " CE2 BNZ     2 " 1.382  1.393 -0.011 1.11e+03 1.31e-01
  " CE2 BNZ     2 " - " CZ  BNZ     2 " 1.378  1.386 -0.008 1.74e+03 1.09e-01
  " CG  BNZ     2 " - " CD1 BNZ     2 " 1.389  1.394 -0.005 2.27e+03 4.84e-02
  ... (remaining 6 not shown)
  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 1
        2.15 -     2.78: 5
        2.78 -     3.41: 6
        3.41 -     4.03: 10
        4.03 -     4.66: 11
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " CA  GLY     1 " - " CB  GLY     1 "  1.529 1.000
  " N   GLY     1 " - " CB  GLY     1 "  2.455 1.000
  " C   GLY     1 " - " CB  GLY     1 "  2.498 1.000
  " CA  GLY     1 " - " CG  BNZ     2 "  2.534 3.400
  " CD2 BNZ     2 " - " CE1 BNZ     2 "  2.772 2.533
  ... (remaining 28 not shown)
  Histogram of dihedral angle deviations from ideal:
        9.88 -    10.28: 1
       10.28 -    10.68: 0
       10.68 -    11.09: 0
       11.09 -    11.49: 0
       11.49 -    11.89: 1
  Dihedral angle restraints sorted by residual:
  " N   GLY     1 "
  " CA  GLY     1 "
  " CB  GLY     1 "
  " CG  BNZ     2 "
      ideal   model   delta periodicty    weight residual
     180.00  170.12    9.88     3       4.44e-03 4.34e-01
  " CA  GLY     1 "
  " CB  GLY     1 "
  " CG  BNZ     2 "
  " CD1 BNZ     2 "
      ideal   model   delta periodicty    weight residual
      90.00   78.11   11.89     2       2.50e-03 3.53e-01
  target: 15.6457
    bond_residual_sum (n=11): 0.970446
    nonbonded_residual_sum (n=33): 12.4201
    angle_residual_sum (n=13): 0.797076
    dihedral_residual_sum (n=2): 0.787227
    chirality_residual_sum (n=0): 0
    planarity_residual_sum (n=1): 0.670882
  Time first energy calculation (mainly nonbonded setup): 0.00

TODO: compare geometry restraints
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/hydrogens/build_hydrogens.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/hydrogens/build_hydrogens.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/arg.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 12
      Number of chains: 1
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 2.50

Residue name:  ARG%COO ARG
Missing hydrogen atoms:  ['HE', 'HD2', 'HD1', 'H', 'HG2', 'HG1', 'HH22', 'HH21', 'HH12', 'HH11', 'HA', 'HB1', 'HB2']

missing   HE: bond:   NE   HE bond distance = 0.970
          HE: angle:   HE   NE   CZ = 117.900
          HE: angle:   CD   NE   HE = 117.900
Building: HE  ...
missing  HD2: bond:   CD  HD2 bond distance = 0.970
         HD2: angle:  HD1   CD  HD2 = 110.000
         HD2: angle:  HD2   CD   NE = 108.000
         HD2: angle:   CG   CD  HD2 = 109.000
Building:  HD2  and  HD1
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HG2: bond:   CG  HG2 bond distance = 0.970
         HG2: angle:  HG1   CG  HG2 = 110.000
         HG2: angle:  HG2   CG   CD = 108.000
         HG2: angle:   CB   CG  HG2 = 109.000
Building:  HG2  and  HG1
missing HH22: bond:  NH2 HH22 bond distance = 0.860
        HH22: angle: HH21  NH2 HH22 = 120.000
        HH22: angle:   CZ  NH2 HH22 = 120.000
Building: HH22  ...
missing HH12: bond:  NH1 HH12 bond distance = 0.860
        HH12: angle: HH11  NH1 HH12 = 120.000
        HH12: angle:   CZ  NH1 HH12 = 120.000
Building: HH12  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2

Still missing:  ARG ['H']
Build  12  from  13  % =  92.3076923077

('ARG', ['H'])
arg.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 24
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 24
      Number of chains: 1
        Number of residues, atoms: 1, 24
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.42
  Number of scatterers: 24
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       4      7.00
     C       6      6.00
     H      12      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.86 -     1.00: 10
        1.00 -     1.14: 2
        1.14 -     1.28: 2
        1.28 -     1.42: 3
        1.42 -     1.56: 6
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  ARG     1 " - "HA   ARG     1 " 0.980  1.062 -0.082 2.50e+03 1.69e+01
  " NE  ARG     1 " - " CZ  ARG     1 " 1.329  1.367 -0.038 5.10e+03 7.42e+00
  " CA  ARG     1 " - " N   ARG     1 " 1.458  1.507 -0.049 2.77e+03 6.52e+00
  " NE  ARG     1 " - "HE   ARG     1 " 0.970  1.010 -0.040 2.50e+03 4.09e+00
  " CB  ARG     1 " - " CA  ARG     1 " 1.530  1.559 -0.029 2.50e+03 2.14e+00
  ... (remaining 18 not shown)
  Histogram of nonbonded interaction distances:
        2.16 -     2.68: 27
        2.68 -     3.20: 30
        3.20 -     3.72: 34
        3.72 -     4.24: 26
        4.24 -     4.76: 31
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HD2  ARG     1 " - "HH12 ARG     1 "  2.158 2.400
  "HE   ARG     1 " - "HH21 ARG     1 "  2.266 2.400
  "HD1  ARG     1 " - "HG2  ARG     1 "  2.275 1.600
  "HE   ARG     1 " - "HD1  ARG     1 "  2.285 1.600
  "HH22 ARG     1 " - "HH11 ARG     1 "  2.294 2.400
  ... (remaining 143 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.15 -     5.55: 6
        5.55 -    10.96: 0
       10.96 -    16.37: 1
       16.37 -    21.78: 0
       21.78 -    27.18: 1
  Dihedral angle restraints sorted by residual:
  " OXT ARG     1 "
  " C   ARG     1 "
  " CA  ARG     1 "
  " N   ARG     1 "
      ideal   model   delta periodicty    weight residual
     160.00  132.82   27.18     2       1.11e-03 8.21e-01
  " CB  ARG     1 "
  " CG  ARG     1 "
  " CD  ARG     1 "
  " NE  ARG     1 "
      ideal   model   delta periodicty    weight residual
     180.00   71.06  -11.06     3       4.44e-03 5.44e-01
  " CG  ARG     1 "
  " CB  ARG     1 "
  " CA  ARG     1 "
  " N   ARG     1 "
      ideal   model   delta periodicty    weight residual
      60.00   58.02    1.98     3       4.44e-03 1.74e-02
  ... (remaining 5 not shown)
  target: 59.5404
    bond_residual_sum (n=23): 43.5818
    nonbonded_residual_sum (n=148): 0.401844
    angle_residual_sum (n=39): 13.8295
    dihedral_residual_sum (n=8): 1.39834
    chirality_residual_sum (n=1): 0.245561
    planarity_residual_sum (n=2): 0.0833694
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 59.5404
  bond_residual_sum (n=23): 43.5818
  nonbonded_residual_sum (n=148): 0.401844
  angle_residual_sum (n=39): 13.8295
  dihedral_residual_sum (n=8): 1.39834
  chirality_residual_sum (n=1): 0.245561
  planarity_residual_sum (n=2): 0.0833694
  norm of gradients: 782.779

Energies after minimization:
target: 2.16128
  bond_residual_sum (n=23): 0.0230452
  nonbonded_residual_sum (n=148): 1.44523
  angle_residual_sum (n=39): 0.534692
  dihedral_residual_sum (n=8): 0.13943
  chirality_residual_sum (n=1): 0.017907
  planarity_residual_sum (n=2): 0.00097234
  norm of gradients: 9.26042e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/lys.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 10
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 10
      Number of chains: 1
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 2.00

Residue name:  LYS%COO LYS
Missing hydrogen atoms:  ['HE2', 'HD2', 'HD1', 'H', 'HG2', 'HG1', 'HZ1', 'HZ3', 'HZ2', 'HE1', 'HA', 'HB1', 'HB2']

missing  HE2: bond:   CE  HE2 bond distance = 0.970
         HE2: angle:  HE1   CE  HE2 = 110.000
         HE2: angle:  HE2   CE   NZ = 108.000
         HE2: angle:   CD   CE  HE2 = 109.000
Building:  HE2  and  HE1
missing  HD2: bond:   CD  HD2 bond distance = 0.970
         HD2: angle:  HD1   CD  HD2 = 110.000
         HD2: angle:  HD2   CD   CE = 108.000
         HD2: angle:   CG   CD  HD2 = 109.000
Building:  HD2  and  HD1
Building:  HD2  and  HD1
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HG2: bond:   CG  HG2 bond distance = 0.970
         HG2: angle:  HG1   CG  HG2 = 110.000
         HG2: angle:  HG2   CG   CD = 108.000
         HG2: angle:   CB   CG  HG2 = 109.000
Building:  HG2  and  HG1
missing  HZ1: bond:   NZ  HZ1 bond distance = 0.960
         HZ1: angle:  HZ1   NZ  HZ2 = 109.000
         HZ1: angle:  HZ1   NZ  HZ3 = 109.000
         HZ1: angle:   CE   NZ  HZ1 = 110.000
Building: HZ1  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2
Building: HB1  ...

Still missing:  LYS ['H']
Build  12  from  13  % =  92.3076923077

('LYS', ['H'])
lys.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 25
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 25
      Number of chains: 1
        Number of residues, atoms: 1, 23
          Unexpected atoms: {'LYS%COO,HB3': 1}
          Duplicate atoms: {'LYS%COO,HB2': 1, 'LYS%COO,HB1': 1}
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of atoms with unknown scattering type symbols: 3
    "HB1  LYS     1 "
    "HB2  LYS     1 "
    "HB3  LYS     1 "
  Number of atoms with unknown nonbonded energy type symbols: 3
    "HB1  LYS     1 "
    "HB2  LYS     1 "
    "HB3  LYS     1 "
  Time building chain proxies: 0.01, per 1000 atoms: 0.40
  Number of scatterers: 25
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     O       2      8.00
     N       2      7.00
     C       6      6.00
     H      12      1.00
     ?       3      0.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.00 seconds
  Histogram of bond lengths:
        0.96 -     1.08: 12
        1.08 -     1.20: 0
        1.20 -     1.32: 2
        1.32 -     1.44: 0
        1.44 -     1.55: 7
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  LYS     1 " - " N   LYS     1 " 1.458  1.506 -0.048 2.77e+03 6.37e+00
  " CA  LYS     1 " - "HA   LYS     1 " 0.980  1.020 -0.040 2.50e+03 4.08e+00
  " CB  LYS     1 " - " CA  LYS     1 " 1.530  1.555 -0.025 2.50e+03 1.52e+00
  " C   LYS     1 " - " OXT LYS     1 " 1.231  1.250 -0.019 2.50e+03 8.82e-01
  " C   LYS     1 " - " O   LYS     1 " 1.231  1.249 -0.018 2.50e+03 8.33e-01
  ... (remaining 16 not shown)
  Histogram of nonbonded interaction distances:
        0.75 -     1.56: 9
        1.56 -     2.36: 25
        2.36 -     3.17: 59
        3.17 -     3.97: 48
        3.97 -     4.78: 41
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HB1  LYS     1 " - "HB2  LYS     1 "  0.754 1.000
  "HB2  LYS     1 " - "HB1  LYS     1 "  0.795 1.000
  " CB  LYS     1 " - "HB1  LYS     1 "  0.970 1.000
  " CB  LYS     1 " - "HB2  LYS     1 "  0.970 1.000
  " CB  LYS     1 " - "HB3  LYS     1 "  0.971 1.000
  ... (remaining 177 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.22 -     7.96: 1
        7.96 -    15.70: 3
       15.70 -    23.45: 0
       23.45 -    31.19: 1
       31.19 -    38.93: 1
  Dihedral angle restraints sorted by residual:
  " CD  LYS     1 "
  " CE  LYS     1 "
  " NZ  LYS     1 "
  "HZ3  LYS     1 "
      ideal   model   delta periodicty    weight residual
      60.00  141.07   38.93     3       1.11e-03 1.68e+00
  " OXT LYS     1 "
  " C   LYS     1 "
  " CA  LYS     1 "
  " N   LYS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.77   29.77     2       1.11e-03 9.85e-01
  " CA  LYS     1 "
  " CB  LYS     1 "
  " CG  LYS     1 "
  " CD  LYS     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -73.50   13.50     3       4.44e-03 8.10e-01
  ... (remaining 3 not shown)
  target: 27.5582
    bond_residual_sum (n=21): 14.692
    nonbonded_residual_sum (n=182): 0.0935827
    angle_residual_sum (n=39): 7.55969
    dihedral_residual_sum (n=6): 4.52202
    chirality_residual_sum (n=1): 0.690449
    planarity_residual_sum (n=1): 0.000506488
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 27.5582
  bond_residual_sum (n=21): 14.692
  nonbonded_residual_sum (n=182): 0.0935827
  angle_residual_sum (n=39): 7.55969
  dihedral_residual_sum (n=6): 4.52202
  chirality_residual_sum (n=1): 0.690449
  planarity_residual_sum (n=1): 0.000506488
  norm of gradients: 484.198

Energies after minimization:
target: 0.606765
  bond_residual_sum (n=21): 0.00276302
  nonbonded_residual_sum (n=182): 0.14388
  angle_residual_sum (n=39): 0.377241
  dihedral_residual_sum (n=6): 0.0617973
  chirality_residual_sum (n=1): 0.0210834
  planarity_residual_sum (n=1): 7.2611e-15
  norm of gradients: 1.56354e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/ala.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 6
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 6
      Number of chains: 1
        Number of residues, atoms: 1, 6
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 1.67

Residue name:  ALA%COO ALA
Missing hydrogen atoms:  ['H', 'HA', 'HB1', 'HB3', 'HB2']

missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.960
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB  HB3 = 110.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2
Building:  HB1  and  HB2
Building:  HB1  and  HB2
Building: HB1  ...

Still missing:  ALA ['H']
Build  4  from  5  % =  80.0

('ALA', ['H'])
ala.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 10
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 10
      Number of chains: 1
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.00, per 1000 atoms: 0.00
  Number of scatterers: 10
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       3      6.00
     H       4      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.96 -     1.07: 4
        1.07 -     1.19: 0
        1.19 -     1.30: 2
        1.30 -     1.42: 0
        1.42 -     1.53: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  ALA     1 " - "HA   ALA     1 " 0.980  1.050 -0.070 2.50e+03 1.23e+01
  " CA  ALA     1 " - " N   ALA     1 " 1.458  1.503 -0.045 2.77e+03 5.55e+00
  " C   ALA     1 " - " OXT ALA     1 " 1.231  1.250 -0.019 2.50e+03 9.41e-01
  " C   ALA     1 " - " O   ALA     1 " 1.231  1.249 -0.018 2.50e+03 7.81e-01
  " C   ALA     1 " - " CA  ALA     1 " 1.525  1.534 -0.009 2.27e+03 1.75e-01
  ... (remaining 4 not shown)
  Histogram of nonbonded interaction distances:
        2.30 -     2.68: 5
        2.68 -     3.05: 5
        3.05 -     3.43: 6
        3.43 -     3.81: 3
        3.81 -     4.19: 2
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HA   ALA     1 " - "HB3  ALA     1 "  2.298 1.600
  " OXT ALA     1 " - "HA   ALA     1 "  2.457 1.813
  "HA   ALA     1 " - "HB1  ALA     1 "  2.473 1.600
  " N   ALA     1 " - "HB1  ALA     1 "  2.586 1.833
  " C   ALA     1 " - "HB2  ALA     1 "  2.615 1.933
  ... (remaining 16 not shown)
  Histogram of dihedral angle deviations from ideal:
       16.71 -    19.19: 1
       19.19 -    21.67: 0
       21.67 -    24.15: 0
       24.15 -    26.63: 0
       26.63 -    29.11: 1
  Dihedral angle restraints sorted by residual:
  " N   ALA     1 "
  " CB  ALA     1 "
  " CA  ALA     1 "
  "HB3  ALA     1 "
      ideal   model   delta periodicty    weight residual
     -60.00  163.29   16.71     3       4.44e-03 1.24e+00
  " OXT ALA     1 "
  " C   ALA     1 "
  " CA  ALA     1 "
  " N   ALA     1 "
      ideal   model   delta periodicty    weight residual
     160.00  130.89   29.11     2       1.11e-03 9.42e-01
  target: 28.6918
    bond_residual_sum (n=9): 19.9062
    nonbonded_residual_sum (n=21): 0
    angle_residual_sum (n=15): 6.41999
    dihedral_residual_sum (n=2): 2.18223
    chirality_residual_sum (n=1): 0.183373
    planarity_residual_sum (n=1): 1.80044e-05
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 28.6918
  bond_residual_sum (n=9): 19.9062
  nonbonded_residual_sum (n=21): 0
  angle_residual_sum (n=15): 6.41999
  dihedral_residual_sum (n=2): 2.18223
  chirality_residual_sum (n=1): 0.183373
  planarity_residual_sum (n=1): 1.80044e-05
  norm of gradients: 591.226

Energies after minimization:
target: 0.306869
  bond_residual_sum (n=9): 0.00245699
  nonbonded_residual_sum (n=21): 0
  angle_residual_sum (n=15): 0.285572
  dihedral_residual_sum (n=2): 7.20081e-13
  chirality_residual_sum (n=1): 0.0188403
  planarity_residual_sum (n=1): 3.60129e-17
  norm of gradients: 8.87014e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/gly.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 5
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 5
      Number of chains: 1
        Number of residues, atoms: 1, 5
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.00, per 1000 atoms: 0.00

Residue name:  GLY%COO GLY
Missing hydrogen atoms:  ['H', 'HA2', 'HA1']

missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HA2: bond:   CA  HA2 bond distance = 0.970
         HA2: angle:  HA1   CA  HA2 = 109.000
         HA2: angle:  HA2   CA    C = 109.000
         HA2: angle:    N   CA  HA2 = 110.000
Building: HA1 and HA2

Still missing:  GLY ['H']
Build  2  from  3  % =  66.6666666667

('GLY', ['H'])
gly.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7
      Number of chains: 1
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of resolved scattering type symbol conflicts: 2
  Time building chain proxies: 0.01, per 1000 atoms: 1.43
  Number of scatterers: 7
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       2      6.00
     H       2      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.00 seconds
  Histogram of bond lengths:
        0.97 -     1.08: 2
        1.08 -     1.19: 0
        1.19 -     1.30: 2
        1.30 -     1.41: 0
        1.41 -     1.52: 2
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  GLY     1 " - " N   GLY     1 " 1.451  1.491 -0.040 3.91e+03 6.31e+00
  " C   GLY     1 " - " O   GLY     1 " 1.231  1.250 -0.019 2.50e+03 8.56e-01
  " OXT GLY     1 " - " C   GLY     1 " 1.231  1.249 -0.018 2.50e+03 7.95e-01
  " C   GLY     1 " - " CA  GLY     1 " 1.516  1.524 -0.008 3.09e+03 2.10e-01
  " CA  GLY     1 " - "HA2  GLY     1 " 0.970  0.970  0.000 2.50e+03 4.41e-04
  " CA  GLY     1 " - "HA1  GLY     1 " 0.970  0.970 -0.000 2.50e+03 3.54e-05
  Histogram of nonbonded interaction distances:
        2.43 -     2.63: 1
        2.63 -     2.83: 1
        2.83 -     3.03: 2
        3.03 -     3.22: 1
        3.22 -     3.42: 1
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " OXT GLY     1 " - "HA2  GLY     1 "  2.435 1.813
  " O   GLY     1 " - "HA1  GLY     1 "  2.646 1.813
  " O   GLY     1 " - " N   GLY     1 "  2.924 2.167
  " OXT GLY     1 " - "HA1  GLY     1 "  2.983 1.813
  " O   GLY     1 " - "HA2  GLY     1 "  3.158 1.813
  " OXT GLY     1 " - " N   GLY     1 "  3.421 2.167
  Histogram of dihedral angle deviations from ideal:
       39.17 -    39.17: 1
       39.17 -    39.17: 0
       39.17 -    39.17: 0
       39.17 -    39.17: 0
       39.17 -    39.17: 0
  Dihedral angle restraints sorted by residual:
  " OXT GLY     1 "
  " C   GLY     1 "
  " CA  GLY     1 "
  " N   GLY     1 "
      ideal   model   delta periodicty    weight residual
     160.00  120.83   39.17     2       1.11e-03 1.70e+00
  target: 16.1071
    bond_residual_sum (n=6): 8.17073
    nonbonded_residual_sum (n=6): 0
    angle_residual_sum (n=9): 6.23143
    dihedral_residual_sum (n=1): 1.7049
    chirality_residual_sum (n=0): 0
    planarity_residual_sum (n=1): 2.26356e-05
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 16.1071
  bond_residual_sum (n=6): 8.17073
  nonbonded_residual_sum (n=6): 0
  angle_residual_sum (n=9): 6.23143
  dihedral_residual_sum (n=1): 1.7049
  chirality_residual_sum (n=0): 0
  planarity_residual_sum (n=1): 2.26356e-05
  norm of gradients: 488.772

Energies after minimization:
target: 0.13971
  bond_residual_sum (n=6): 2.73651e-15
  nonbonded_residual_sum (n=6): 0
  angle_residual_sum (n=9): 0.13971
  dihedral_residual_sum (n=1): 1.01096e-14
  chirality_residual_sum (n=0): 0
  planarity_residual_sum (n=1): 5.29595e-16
  norm of gradients: 8.47466e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/his.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 11
      Number of chains: 1
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.82

Residue name:  HIS%COO HIS
Missing hydrogen atoms:  ['HE2', 'HE1', 'HD1', 'H', 'HD2', 'HA', 'HB1', 'HB2']

missing  HE2: bond:  NE2  HE2 bond distance = 0.860
         HE2: angle:  HE2  NE2  CD2 = 125.500
         HE2: angle:  CE1  NE2  HE2 = 125.500
Building: HE2  ...
missing  HE1: bond:  CE1  HE1 bond distance = 0.930
         HE1: angle:  HE1  CE1  NE2 = 125.800
         HE1: angle:  ND1  CE1  HE1 = 125.800
Building: HE1  ...
missing  HD1: bond:  ND1  HD1 bond distance = 0.860
         HD1: angle:  HD1  ND1  CE1 = 125.350
         HD1: angle:   CG  ND1  HD1 = 125.350
Building: HD1  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HD2: bond:  CD2  HD2 bond distance = 0.930
         HD2: angle:  NE2  CD2  HD2 = 126.400
         HD2: angle:   CG  CD2  HD2 = 126.400
Building: HD2  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2

Still missing:  HIS ['H']
Build  7  from  8  % =  87.5

('HIS', ['H'])
his.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 18
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 18
      Number of chains: 1
        Number of residues, atoms: 1, 18
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.11
  Number of scatterers: 18
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       3      7.00
     C       6      6.00
     H       7      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.00 seconds
  Histogram of bond lengths:
        0.86 -     1.00: 6
        1.00 -     1.14: 1
        1.14 -     1.28: 2
        1.28 -     1.42: 5
        1.42 -     1.56: 4
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  HIS     1 " - " N   HIS     1 " 1.458  1.505 -0.047 2.77e+03 6.20e+00
  " CA  HIS     1 " - "HA   HIS     1 " 0.980  1.028 -0.048 2.50e+03 5.66e+00
  " CB  HIS     1 " - " CA  HIS     1 " 1.530  1.557 -0.027 2.50e+03 1.76e+00
  " C   HIS     1 " - " OXT HIS     1 " 1.231  1.250 -0.019 2.50e+03 9.07e-01
  " C   HIS     1 " - " O   HIS     1 " 1.231  1.249 -0.018 2.50e+03 7.83e-01
  ... (remaining 13 not shown)
  Histogram of nonbonded interaction distances:
        2.36 -     2.85: 14
        2.85 -     3.33: 19
        3.33 -     3.82: 21
        3.82 -     4.30: 13
        4.30 -     4.79: 15
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HE1  HIS     1 " - "HD1  HIS     1 "  2.363 1.600
  "HE2  HIS     1 " - "HE1  HIS     1 "  2.364 1.600
  "HE2  HIS     1 " - "HD2  HIS     1 "  2.426 1.600
  " OXT HIS     1 " - "HA   HIS     1 "  2.462 1.813
  "HD1  HIS     1 " - "HB1  HIS     1 "  2.486 2.400
  ... (remaining 77 not shown)
  Histogram of dihedral angle deviations from ideal:
       19.37 -    21.37: 2
       21.37 -    23.36: 0
       23.36 -    25.35: 0
       25.35 -    27.35: 0
       27.35 -    29.34: 1
  Dihedral angle restraints sorted by residual:
  " CG  HIS     1 "
  " CB  HIS     1 "
  " CA  HIS     1 "
  " N   HIS     1 "
      ideal   model   delta periodicty    weight residual
     180.00 -160.63  -19.37     3       4.44e-03 1.67e+00
  " CA  HIS     1 "
  " CB  HIS     1 "
  " CG  HIS     1 "
  " ND1 HIS     1 "
      ideal   model   delta periodicty    weight residual
      90.00  110.09  -20.09     2       2.50e-03 1.01e+00
  " OXT HIS     1 "
  " C   HIS     1 "
  " CA  HIS     1 "
  " N   HIS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  130.66   29.34     2       1.11e-03 9.57e-01
  target: 27.8228
    bond_residual_sum (n=18): 16.2986
    nonbonded_residual_sum (n=82): 0
    angle_residual_sum (n=30): 7.23089
    dihedral_residual_sum (n=3): 3.63384
    chirality_residual_sum (n=1): 0.646547
    planarity_residual_sum (n=2): 0.0129392
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 27.8228
  bond_residual_sum (n=18): 16.2986
  nonbonded_residual_sum (n=82): 0
  angle_residual_sum (n=30): 7.23089
  dihedral_residual_sum (n=3): 3.63384
  chirality_residual_sum (n=1): 0.646547
  planarity_residual_sum (n=2): 0.0129392
  norm of gradients: 494.121

Energies after minimization:
target: 0.310556
  bond_residual_sum (n=18): 0.00295388
  nonbonded_residual_sum (n=82): 0.0216123
  angle_residual_sum (n=30): 0.253279
  dihedral_residual_sum (n=3): 0.0122131
  chirality_residual_sum (n=1): 0.0204814
  planarity_residual_sum (n=2): 1.70664e-05
  norm of gradients: 1.564e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/ile.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 9
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 9
      Number of chains: 1
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 2.22

Residue name:  ILE%COO ILE
Missing hydrogen atoms:  ['HG22', 'H', 'HG21', 'HG11', 'HG12', 'HD13', 'HB', 'HD12', 'HD11', 'HA', 'HG23']

missing HG22: bond:  CG2 HG22 bond distance = 0.960
        HG22: angle: HG21  CG2 HG22 = 110.000
        HG22: angle: HG22  CG2 HG23 = 110.000
        HG22: angle:   CB  CG2 HG22 = 109.000
Building: HG22  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing HG11: bond:  CG1 HG11 bond distance = 0.970
        HG11: angle: HG11  CG1 HG12 = 110.000
        HG11: angle: HG11  CG1  CD1 = 108.000
        HG11: angle:   CB  CG1 HG11 = 109.000
Building: HG11  ...
missing HD13: bond:  CD1 HD13 bond distance = 0.960
        HD13: angle: HD12  CD1 HD13 = 110.000
        HD13: angle: HD11  CD1 HD13 = 110.000
        HD13: angle:  CG1  CD1 HD13 = 109.000
Building: HD13  ...
missing   HB: bond:   CB   HB bond distance = 0.970
          HB: angle:   HB   CB  CG1 = 109.000
          HB: angle:   HB   CB  CG2 = 109.000
          HB: angle:   CA   CB   HB = 109.000
Building:  HB
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA

Still missing:  ILE ['H']
Build  10  from  11  % =  90.9090909091

('ILE', ['H'])
ile.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 20
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 20
      Number of chains: 1
        Number of residues, atoms: 1, 20
          Unexpected atoms: {'ILE%COO,HG13': 1}
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of atoms with unknown scattering type symbols: 1
    "HG13 ILE     1 "
  Number of atoms with unknown nonbonded energy type symbols: 1
    "HG13 ILE     1 "
  Time building chain proxies: 0.01, per 1000 atoms: 0.50
  Number of scatterers: 20
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       6      6.00
     H      10      1.00
     ?       1      0.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.96 -     1.09: 9
        1.09 -     1.21: 1
        1.21 -     1.34: 2
        1.34 -     1.46: 0
        1.46 -     1.59: 6
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  ILE     1 " - "HA   ILE     1 " 0.980  1.117 -0.137 2.50e+03 4.71e+01
  " CB  ILE     1 " - "HB   ILE     1 " 0.970  1.035 -0.065 2.50e+03 1.07e+01
  " CA  ILE     1 " - " N   ILE     1 " 1.458  1.506 -0.048 2.77e+03 6.33e+00
  " CB  ILE     1 " - " CA  ILE     1 " 1.540  1.588 -0.048 1.37e+03 3.18e+00
  " CB  ILE     1 " - " CG1 ILE     1 " 1.530  1.565 -0.035 2.50e+03 3.08e+00
  ... (remaining 13 not shown)
  Histogram of nonbonded interaction distances:
        0.97 -     1.74: 6
        1.74 -     2.50: 8
        2.50 -     3.27: 44
        3.27 -     4.04: 42
        4.04 -     4.80: 31
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " CG1 ILE     1 " - "HG13 ILE     1 "  0.970 1.000
  "HG12 ILE     1 " - "HD11 ILE     1 "  1.196 1.600
  "HG12 ILE     1 " - "HD12 ILE     1 "  1.284 1.600
  "HG12 ILE     1 " - "HD13 ILE     1 "  1.320 1.600
  "HG12 ILE     1 " - "HG13 ILE     1 "  1.577 1.000
  ... (remaining 126 not shown)
  Histogram of dihedral angle deviations from ideal:
        1.23 -     9.85: 1
        9.85 -    18.48: 2
       18.48 -    27.10: 1
       27.10 -    35.72: 0
       35.72 -    44.34: 1
  Dihedral angle restraints sorted by residual:
  " CB  ILE     1 "
  " CD1 ILE     1 "
  " CG1 ILE     1 "
  "HD13 ILE     1 "
      ideal   model   delta periodicty    weight residual
     -60.00  104.34  -44.34     3       1.11e-03 2.18e+00
  " CA  ILE     1 "
  " CB  ILE     1 "
  " CG1 ILE     1 "
  " CD1 ILE     1 "
      ideal   model   delta periodicty    weight residual
     180.00   74.80  -14.80     3       4.44e-03 9.73e-01
  " N   ILE     1 "
  " CB  ILE     1 "
  " CA  ILE     1 "
  " CG2 ILE     1 "
      ideal   model   delta periodicty    weight residual
    -180.00   73.35  -13.35     3       4.44e-03 7.92e-01
  ... (remaining 2 not shown)
  target: 1250.78
    bond_residual_sum (n=18): 73.4561
    nonbonded_residual_sum (n=131): 1.78373
    angle_residual_sum (n=33): 1170.92
    dihedral_residual_sum (n=5): 4.36609
    chirality_residual_sum (n=2): 0.254482
    planarity_residual_sum (n=1): 6.19818e-05
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 1250.78
  bond_residual_sum (n=18): 73.4561
  nonbonded_residual_sum (n=131): 1.78373
  angle_residual_sum (n=33): 1170.92
  dihedral_residual_sum (n=5): 4.36609
  chirality_residual_sum (n=2): 0.254482
  planarity_residual_sum (n=1): 6.19818e-05
  norm of gradients: 1975.1

Energies after minimization:
target: 468.73
  bond_residual_sum (n=18): 0.100701
  nonbonded_residual_sum (n=131): 3.04479
  angle_residual_sum (n=33): 463.605
  dihedral_residual_sum (n=5): 1.96075
  chirality_residual_sum (n=2): 0.0181844
  planarity_residual_sum (n=1): 0.000934329
  norm of gradients: 3.32362e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/leu.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 9
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 9
      Number of chains: 1
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 2.22

Residue name:  LEU%COO LEU
Missing hydrogen atoms:  ['HD22', 'HD23', 'HD21', 'H', 'HD13', 'HD12', 'HD11', 'HA', 'HB1', 'HG', 'HB2']

missing HD22: bond:  CD2 HD22 bond distance = 0.960
        HD22: angle: HD21  CD2 HD22 = 110.000
        HD22: angle: HD22  CD2 HD23 = 110.000
        HD22: angle:   CG  CD2 HD22 = 109.000
Building: HD22  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing HD13: bond:  CD1 HD13 bond distance = 0.960
        HD13: angle: HD12  CD1 HD13 = 110.000
        HD13: angle: HD11  CD1 HD13 = 110.000
        HD13: angle:   CG  CD1 HD13 = 109.000
Building: HD13  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2
Building: HB1  ...
missing   HG: bond:   CG   HG bond distance = 0.970
          HG: angle:   HG   CG  CD1 = 108.000
          HG: angle:   HG   CG  CD2 = 108.000
          HG: angle:   CB   CG   HG = 109.000
Building:  HG

Still missing:  LEU ['H']
Build  10  from  11  % =  90.9090909091

('LEU', ['H'])
leu.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 22
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 22
      Number of chains: 1
        Number of residues, atoms: 1, 20
          Unexpected atoms: {'LEU%COO,HB3': 1}
          Duplicate atoms: {'LEU%COO,HB1': 1, 'LEU%COO,HB2': 1}
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of resolved scattering type symbol conflicts: 10
  Number of atoms with unknown nonbonded energy type symbols: 3
    "HB1  LEU     1 "
    "HB2  LEU     1 "
    "HB3  LEU     1 "
  Time building chain proxies: 0.01, per 1000 atoms: 0.45
  Number of scatterers: 22
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       9      6.00
     H      10      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.96 -     1.08: 10
        1.08 -     1.20: 0
        1.20 -     1.32: 2
        1.32 -     1.44: 0
        1.44 -     1.56: 6
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CG  LEU     1 " - "HG   LEU     1 " 0.970  1.055 -0.085 2.50e+03 1.81e+01
  " CA  LEU     1 " - "HA   LEU     1 " 0.980  1.032 -0.052 2.50e+03 6.72e+00
  " CA  LEU     1 " - " N   LEU     1 " 1.458  1.503 -0.045 2.77e+03 5.52e+00
  " CB  LEU     1 " - " CG  LEU     1 " 1.530  1.565 -0.035 2.50e+03 2.99e+00
  " CB  LEU     1 " - " CA  LEU     1 " 1.530  1.563 -0.033 2.50e+03 2.68e+00
  ... (remaining 13 not shown)
  Histogram of nonbonded interaction distances:
        0.02 -     0.98: 6
        0.98 -     1.94: 10
        1.94 -     2.91: 57
        2.91 -     3.87: 63
        3.87 -     4.83: 30
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HB1  LEU     1 " - "HB2  LEU     1 "  0.021 1.000
  "HB2  LEU     1 " - "HB3  LEU     1 "  0.143 1.000
  " CG  LEU     1 " - "HB1  LEU     1 "  0.630 1.000
  " CB  LEU     1 " - "HB2  LEU     1 "  0.970 1.000
  " CB  LEU     1 " - "HB3  LEU     1 "  0.970 1.000
  ... (remaining 161 not shown)
  Histogram of dihedral angle deviations from ideal:
        1.70 -     7.51: 1
        7.51 -    13.31: 0
       13.31 -    19.11: 1
       19.11 -    24.92: 1
       24.92 -    30.72: 2
  Dihedral angle restraints sorted by residual:
  " CA  LEU     1 "
  " CB  LEU     1 "
  " CG  LEU     1 "
  " CD2 LEU     1 "
      ideal   model   delta periodicty    weight residual
     180.00   82.11  -22.11     3       4.44e-03 2.17e+00
  " CB  LEU     1 "
  " CG  LEU     1 "
  " CD2 LEU     1 "
  "HD23 LEU     1 "
      ideal   model   delta periodicty    weight residual
      60.00  149.28   30.72     3       1.11e-03 1.05e+00
  " OXT LEU     1 "
  " C   LEU     1 "
  " CA  LEU     1 "
  " N   LEU     1 "
      ideal   model   delta periodicty    weight residual
     160.00  130.57   29.43     2       1.11e-03 9.62e-01
  ... (remaining 2 not shown)
  target: 81.9297
    bond_residual_sum (n=18): 38.4452
    nonbonded_residual_sum (n=166): 24.0123
    angle_residual_sum (n=33): 14.3639
    dihedral_residual_sum (n=5): 4.4702
    chirality_residual_sum (n=2): 0.637222
    planarity_residual_sum (n=1): 0.000879497
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 81.9297
  bond_residual_sum (n=18): 38.4452
  nonbonded_residual_sum (n=166): 24.0123
  angle_residual_sum (n=33): 14.3639
  dihedral_residual_sum (n=5): 4.4702
  chirality_residual_sum (n=2): 0.637222
  planarity_residual_sum (n=1): 0.000879497
  norm of gradients: 807.361

Energies after minimization:
target: 3.70968
  bond_residual_sum (n=18): 0.026014
  nonbonded_residual_sum (n=166): 1.47424
  angle_residual_sum (n=33): 0.873991
  dihedral_residual_sum (n=5): 1.31309
  chirality_residual_sum (n=2): 0.0223345
  planarity_residual_sum (n=1): 1.58556e-15
  norm of gradients: 1.76535e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/phe.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 12
      Number of chains: 1
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.67

Residue name:  PHE%COO PHE
Missing hydrogen atoms:  ['HZ', 'HE2', 'HE1', 'HD1', 'H', 'HD2', 'HA', 'HB1', 'HB2']

missing   HZ: bond:   CZ   HZ bond distance = 0.930
          HZ: angle:   HZ   CZ  CE2 = 120.000
          HZ: angle:  CE1   CZ   HZ = 120.000
Building: HZ  ...
missing  HE2: bond:  CE2  HE2 bond distance = 0.930
         HE2: angle:  HE2  CE2  CD2 = 120.000
         HE2: angle:   CZ  CE2  HE2 = 120.000
Building: HE2  ...
missing  HE1: bond:  CE1  HE1 bond distance = 0.930
         HE1: angle:  HE1  CE1   CZ = 120.000
         HE1: angle:  CD1  CE1  HE1 = 120.000
Building: HE1  ...
missing  HD1: bond:  CD1  HD1 bond distance = 0.930
         HD1: angle:  HD1  CD1  CE1 = 119.650
         HD1: angle:   CG  CD1  HD1 = 119.650
Building: HD1  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HD2: bond:  CD2  HD2 bond distance = 0.930
         HD2: angle:   CG  CD2  HD2 = 119.650
         HD2: angle:  CE2  CD2  HD2 = 119.650
Building: HD2  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2

Still missing:  PHE ['H']
Build  8  from  9  % =  88.8888888889

('PHE', ['H'])
phe.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 20
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 20
      Number of chains: 1
        Number of residues, atoms: 1, 20
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.50
  Number of scatterers: 20
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       9      6.00
     H       8      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.92 -     1.05: 8
        1.05 -     1.17: 0
        1.17 -     1.29: 2
        1.29 -     1.41: 1
        1.41 -     1.53: 9
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  PHE     1 " - " N   PHE     1 " 1.458  1.491 -0.033 2.77e+03 3.05e+00
  " CD2 PHE     1 " - " CE2 PHE     1 " 1.382  1.430 -0.048 1.11e+03 2.53e+00
  " CD1 PHE     1 " - " CE1 PHE     1 " 1.382  1.430 -0.048 1.11e+03 2.51e+00
  " CG  PHE     1 " - " CD1 PHE     1 " 1.384  1.414 -0.030 2.27e+03 2.04e+00
  " CA  PHE     1 " - "HA   PHE     1 " 0.980  1.008 -0.028 2.50e+03 1.92e+00
  ... (remaining 15 not shown)
  Histogram of nonbonded interaction distances:
        2.34 -     2.83: 19
        2.83 -     3.32: 25
        3.32 -     3.81: 16
        3.81 -     4.31: 11
        4.31 -     4.80: 25
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HD2  PHE     1 " - "HB2  PHE     1 "  2.341 2.400
  "HZ   PHE     1 " - "HE1  PHE     1 "  2.353 1.600
  "HZ   PHE     1 " - "HE2  PHE     1 "  2.353 1.600
  "HE1  PHE     1 " - "HD1  PHE     1 "  2.354 1.600
  "HE2  PHE     1 " - "HD2  PHE     1 "  2.354 1.600
  ... (remaining 91 not shown)
  Histogram of dihedral angle deviations from ideal:
        1.50 -     9.03: 1
        9.03 -    16.57: 0
       16.57 -    24.10: 1
       24.10 -    31.64: 0
       31.64 -    39.17: 1
  Dihedral angle restraints sorted by residual:
  " OXT PHE     1 "
  " C   PHE     1 "
  " CA  PHE     1 "
  " N   PHE     1 "
      ideal   model   delta periodicty    weight residual
     160.00  120.83   39.17     2       1.11e-03 1.70e+00
  " CA  PHE     1 "
  " CB  PHE     1 "
  " CG  PHE     1 "
  " CD1 PHE     1 "
      ideal   model   delta periodicty    weight residual
      90.00   70.30   19.70     2       2.50e-03 9.71e-01
  " CG  PHE     1 "
  " CB  PHE     1 "
  " CA  PHE     1 "
  " N   PHE     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -61.50    1.50     3       4.44e-03 9.94e-03
  target: 30.4027
    bond_residual_sum (n=20): 19.3992
    nonbonded_residual_sum (n=96): 1.39216
    angle_residual_sum (n=33): 6.61389
    dihedral_residual_sum (n=3): 2.68534
    chirality_residual_sum (n=1): 0.311507
    planarity_residual_sum (n=2): 0.000673786
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 30.4027
  bond_residual_sum (n=20): 19.3992
  nonbonded_residual_sum (n=96): 1.39216
  angle_residual_sum (n=33): 6.61389
  dihedral_residual_sum (n=3): 2.68534
  chirality_residual_sum (n=1): 0.311507
  planarity_residual_sum (n=2): 0.000673786
  norm of gradients: 455.299

Energies after minimization:
target: 0.424633
  bond_residual_sum (n=20): 0.0121589
  nonbonded_residual_sum (n=95): 0.0862652
  angle_residual_sum (n=33): 0.269303
  dihedral_residual_sum (n=3): 0.0381779
  chirality_residual_sum (n=1): 0.0187277
  planarity_residual_sum (n=2): 3.11324e-14
  norm of gradients: 1.42258e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/tyr.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 13
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 13
      Number of chains: 1
        Number of residues, atoms: 1, 13
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.54

Residue name:  TYR%COO TYR
Missing hydrogen atoms:  ['HE2', 'HE1', 'HD1', 'H', 'HH', 'HD2', 'HA', 'HB1', 'HB2']

missing  HE2: bond:  CE2  HE2 bond distance = 0.930
         HE2: angle:  HE2  CE2  CD2 = 120.200
         HE2: angle:   CZ  CE2  HE2 = 120.200
Building: HE2  ...
missing  HE1: bond:  CE1  HE1 bond distance = 0.930
         HE1: angle:  HE1  CE1   CZ = 120.200
         HE1: angle:  CD1  CE1  HE1 = 120.200
Building: HE1  ...
missing  HD1: bond:  CD1  HD1 bond distance = 0.930
         HD1: angle:  HD1  CD1  CE1 = 119.400
         HD1: angle:   CG  CD1  HD1 = 119.400
Building: HD1  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing   HH: bond:   OH   HH bond distance = 0.820
          HH: angle:   CZ   OH   HH = 110.000
Building: HH  ...
missing  HD2: bond:  CD2  HD2 bond distance = 0.930
         HD2: angle:  HD2  CD2  CE2 = 119.400
         HD2: angle:   CG  CD2  HD2 = 119.400
Building: HD2  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2

Still missing:  TYR ['H']
Build  8  from  9  % =  88.8888888889

('TYR', ['H'])
tyr.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 21
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 21
      Number of chains: 1
        Number of residues, atoms: 1, 21
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 0.95
  Number of scatterers: 21
  At special positions: 0
  Unit cell: (72.24, 72.01, 86.99, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       3      8.00
     N       1      7.00
     C       9      6.00
     H       8      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.82 -     0.97: 5
        0.97 -     1.11: 3
        1.11 -     1.26: 2
        1.26 -     1.40: 1
        1.40 -     1.55: 10
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  TYR     1 " - " N   TYR     1 " 1.458  1.507 -0.049 2.77e+03 6.73e+00
  " CA  TYR     1 " - "HA   TYR     1 " 0.980  1.021 -0.041 2.50e+03 4.14e+00
  " CD2 TYR     1 " - " CG  TYR     1 " 1.389  1.429 -0.040 2.27e+03 3.69e+00
  " CG  TYR     1 " - " CD1 TYR     1 " 1.389  1.429 -0.040 2.27e+03 3.65e+00
  " CZ  TYR     1 " - " CE2 TYR     1 " 1.378  1.414 -0.036 1.74e+03 2.22e+00
  ... (remaining 16 not shown)
  Histogram of nonbonded interaction distances:
        2.27 -     2.77: 17
        2.77 -     3.28: 16
        3.28 -     3.78: 28
        3.78 -     4.28: 13
        4.28 -     4.78: 25
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HE2  TYR     1 " - "HH   TYR     1 "  2.274 2.400
  "HE1  TYR     1 " - "HD1  TYR     1 "  2.340 1.600
  "HE2  TYR     1 " - "HD2  TYR     1 "  2.341 1.600
  " CE2 TYR     1 " - "HH   TYR     1 "  2.402 1.933
  "HA   TYR     1 " - "HB2  TYR     1 "  2.442 1.600
  ... (remaining 94 not shown)
  Histogram of dihedral angle deviations from ideal:
        4.49 -    15.60: 2
       15.60 -    26.70: 0
       26.70 -    37.81: 1
       37.81 -    48.92: 0
       48.92 -    60.03: 1
  Dihedral angle restraints sorted by residual:
  " CE1 TYR     1 "
  " OH  TYR     1 "
  " CZ  TYR     1 "
  "HH   TYR     1 "
      ideal   model   delta periodicty    weight residual
     -60.00 -179.97  -60.03     2       1.11e-03 4.00e+00
  " OXT TYR     1 "
  " C   TYR     1 "
  " CA  TYR     1 "
  " N   TYR     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.67   29.67     2       1.11e-03 9.78e-01
  " CG  TYR     1 "
  " CB  TYR     1 "
  " CA  TYR     1 "
  " N   TYR     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -68.78    8.78     3       4.44e-03 3.42e-01
  " CA  TYR     1 "
  " CB  TYR     1 "
  " CG  TYR     1 "
  " CD1 TYR     1 "
      ideal   model   delta periodicty    weight residual
      90.00  -85.51   -4.49     2       2.50e-03 5.04e-02
  target: 40.7025
    bond_residual_sum (n=21): 28.8817
    nonbonded_residual_sum (n=99): 0.00767341
    angle_residual_sum (n=34): 5.73976
    dihedral_residual_sum (n=4): 5.37431
    chirality_residual_sum (n=1): 0.660392
    planarity_residual_sum (n=2): 0.0386784
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 40.7025
  bond_residual_sum (n=21): 28.8817
  nonbonded_residual_sum (n=99): 0.00767341
  angle_residual_sum (n=34): 5.73976
  dihedral_residual_sum (n=4): 5.37431
  chirality_residual_sum (n=1): 0.660392
  planarity_residual_sum (n=2): 0.0386784
  norm of gradients: 573.519

Energies after minimization:
target: 0.403008
  bond_residual_sum (n=21): 0.00376556
  nonbonded_residual_sum (n=99): 0.0746504
  angle_residual_sum (n=34): 0.274608
  dihedral_residual_sum (n=4): 0.0305242
  chirality_residual_sum (n=1): 0.0187801
  planarity_residual_sum (n=2): 0.000680611
  norm of gradients: 1.15053e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/trp.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 15
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 15
      Number of chains: 1
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.33

Residue name:  TRP%COO TRP
Missing hydrogen atoms:  ['HH2', 'HE1', 'HD1', 'HE3', 'H', 'HZ3', 'HZ2', 'HA', 'HB1', 'HB2']

missing  HH2: bond:  CH2  HH2 bond distance = 0.930
         HH2: angle:  HH2  CH2  CZ2 = 119.250
         HH2: angle:  CZ3  CH2  HH2 = 119.250
Building: HH2  ...
missing  HE1: bond:  NE1  HE1 bond distance = 0.860
         HE1: angle:  HE1  NE1  CE2 = 125.550
         HE1: angle:  CD1  NE1  HE1 = 125.550
Building: HE1  ...
missing  HD1: bond:  CD1  HD1 bond distance = 0.930
         HD1: angle:  HD1  CD1  NE1 = 124.900
         HD1: angle:   CG  CD1  HD1 = 124.900
Building: HD1  ...
missing  HE3: bond:  CE3  HE3 bond distance = 0.930
         HE3: angle:  HE3  CE3  CZ3 = 120.700
         HE3: angle:  CD2  CE3  HE3 = 120.700
Building: HE3  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HZ3: bond:  CZ3  HZ3 bond distance = 0.930
         HZ3: angle:  HZ3  CZ3  CH2 = 119.450
         HZ3: angle:  CE3  CZ3  HZ3 = 119.450
Building: HZ3  ...
missing  HZ2: bond:  CZ2  HZ2 bond distance = 0.930
         HZ2: angle:  CH2  CZ2  HZ2 = 121.250
         HZ2: angle:  CE2  CZ2  HZ2 = 121.250
Building: HZ2  ...
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   CG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2

Still missing:  TRP ['H']
Build  9  from  10  % =  90.0

('TRP', ['H'])
trp.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 24
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 24
      Number of chains: 1
        Number of residues, atoms: 1, 24
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.42
  Number of scatterers: 24
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       2      7.00
     C      11      6.00
     H       9      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.86 -     1.00: 8
        1.00 -     1.14: 1
        1.14 -     1.27: 2
        1.27 -     1.41: 4
        1.41 -     1.55: 10
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  TRP     1 " - " N   TRP     1 " 1.458  1.507 -0.049 2.77e+03 6.78e+00
  " CE3 TRP     1 " - " CD2 TRP     1 " 1.398  1.433 -0.035 3.91e+03 4.74e+00
  " CA  TRP     1 " - "HA   TRP     1 " 0.980  1.020 -0.040 2.50e+03 4.09e+00
  " CZ2 TRP     1 " - " CH2 TRP     1 " 1.368  1.403 -0.035 2.77e+03 3.34e+00
  " CZ2 TRP     1 " - " CE2 TRP     1 " 1.394  1.427 -0.033 2.27e+03 2.47e+00
  ... (remaining 20 not shown)
  Histogram of nonbonded interaction distances:
        2.34 -     2.83: 18
        2.83 -     3.32: 30
        3.32 -     3.81: 26
        3.81 -     4.30: 24
        4.30 -     4.79: 31
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HH2  TRP     1 " - "HZ2  TRP     1 "  2.339 1.600
  "HH2  TRP     1 " - "HZ3  TRP     1 "  2.347 1.600
  "HE3  TRP     1 " - "HZ3  TRP     1 "  2.349 1.600
  "HE1  TRP     1 " - "HD1  TRP     1 "  2.411 1.600
  "HA   TRP     1 " - "HB2  TRP     1 "  2.445 1.600
  ... (remaining 124 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.23 -     6.06: 1
        6.06 -    11.89: 1
       11.89 -    17.72: 0
       17.72 -    23.55: 0
       23.55 -    29.38: 1
  Dihedral angle restraints sorted by residual:
  " N   TRP     1 "
  " C   TRP     1 "
  " CA  TRP     1 "
  " OXT TRP     1 "
      ideal   model   delta periodicty    weight residual
    -160.00 -130.62  -29.38     2       1.11e-03 9.59e-01
  " CG  TRP     1 "
  " CB  TRP     1 "
  " CA  TRP     1 "
  " N   TRP     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -69.24    9.24     3       4.44e-03 3.79e-01
  " CA  TRP     1 "
  " CB  TRP     1 "
  " CG  TRP     1 "
  " CD1 TRP     1 "
      ideal   model   delta periodicty    weight residual
      90.00   90.23   -0.23     2       2.50e-03 1.27e-04
  target: 38.5693
    bond_residual_sum (n=25): 30.5434
    nonbonded_residual_sum (n=129): 0
    angle_residual_sum (n=42): 5.981
    dihedral_residual_sum (n=3): 1.33836
    chirality_residual_sum (n=1): 0.679262
    planarity_residual_sum (n=2): 0.0272789
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 38.5693
  bond_residual_sum (n=25): 30.5434
  nonbonded_residual_sum (n=129): 0
  angle_residual_sum (n=42): 5.981
  dihedral_residual_sum (n=3): 1.33836
  chirality_residual_sum (n=1): 0.679262
  planarity_residual_sum (n=2): 0.0272789
  norm of gradients: 676.859

Energies after minimization:
target: 0.278592
  bond_residual_sum (n=25): 0.00650554
  nonbonded_residual_sum (n=129): 0
  angle_residual_sum (n=42): 0.252833
  dihedral_residual_sum (n=3): 5.14472e-13
  chirality_residual_sum (n=1): 0.0192529
  planarity_residual_sum (n=2): 3.90508e-15
  norm of gradients: 1.01642e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/thr.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 8
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 8
      Number of chains: 1
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 1.25

Residue name:  THR%COO THR
Missing hydrogen atoms:  ['HA', 'H', 'HG1', 'HG21', 'HB', 'HG23', 'HG22']

missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing  HG1: bond:  OG1  HG1 bond distance = 0.820
         HG1: angle:   CB  OG1  HG1 = 110.000
Building:  HG1
Unknown hydrogen type:  HG1
missing HG21: bond:  CG2 HG21 bond distance = 0.960
        HG21: angle: HG21  CG2 HG22 = 109.000
        HG21: angle: HG21  CG2 HG23 = 109.000
        HG21: angle:   CB  CG2 HG21 = 110.000
Building: HG21  ...
missing   HB: bond:   CB   HB bond distance = 0.970
          HB: angle:   HB   CB  OG1 = 109.000
          HB: angle:   HB   CB  CG2 = 108.000
          HB: angle:   CA   CB   HB = 109.000
Building:  HB
Building:  HB

Still missing:  THR ['H', 'HG1']
Build  5  from  7  % =  71.4285714286

('THR', ['H', 'HG1'])
thr.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 13
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 13
      Number of chains: 1
        Number of residues, atoms: 1, 13
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.77
  Number of scatterers: 13
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       3      8.00
     N       1      7.00
     C       4      6.00
     H       5      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.00 seconds
  Histogram of bond lengths:
        0.96 -     1.08: 5
        1.08 -     1.20: 0
        1.20 -     1.32: 2
        1.32 -     1.44: 1
        1.44 -     1.56: 4
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CB  THR     1 " - "HB   THR     1 " 0.970  1.029 -0.059 2.50e+03 8.81e+00
  " CA  THR     1 " - " N   THR     1 " 1.458  1.508 -0.050 2.77e+03 6.87e+00
  " CA  THR     1 " - "HA   THR     1 " 0.980  1.031 -0.051 2.50e+03 6.60e+00
  " C   THR     1 " - " OXT THR     1 " 1.231  1.250 -0.019 2.50e+03 8.89e-01
  " C   THR     1 " - " O   THR     1 " 1.231  1.250 -0.019 2.50e+03 8.66e-01
  ... (remaining 7 not shown)
  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 8
        2.70 -     3.24: 15
        3.24 -     3.78: 8
        3.78 -     4.32: 4
        4.32 -     4.85: 9
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HG21 THR     1 " - "HB   THR     1 "  2.165 1.600
  "HA   THR     1 " - "HG22 THR     1 "  2.360 2.400
  " OG1 THR     1 " - "HG23 THR     1 "  2.377 1.813
  "HA   THR     1 " - "HB   THR     1 "  2.451 1.600
  " O   THR     1 " - "HA   THR     1 "  2.459 1.813
  ... (remaining 39 not shown)
  Histogram of dihedral angle deviations from ideal:
        8.60 -    15.06: 1
       15.06 -    21.53: 0
       21.53 -    28.00: 0
       28.00 -    34.47: 1
       34.47 -    40.94: 1
  Dihedral angle restraints sorted by residual:
  " CA  THR     1 "
  " CB  THR     1 "
  " CG2 THR     1 "
  "HG23 THR     1 "
      ideal   model   delta periodicty    weight residual
      60.00  100.94  -40.94     3       1.11e-03 1.86e+00
  " OXT THR     1 "
  " C   THR     1 "
  " CA  THR     1 "
  " N   THR     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.57   29.57     2       1.11e-03 9.72e-01
  " N   THR     1 "
  " CB  THR     1 "
  " CA  THR     1 "
  " CG2 THR     1 "
      ideal   model   delta periodicty    weight residual
    -180.00   68.60   -8.60     3       4.44e-03 3.28e-01
  target: 41.9888
    bond_residual_sum (n=12): 24.73
    nonbonded_residual_sum (n=44): 0.0634987
    angle_residual_sum (n=21): 13.1355
    dihedral_residual_sum (n=3): 3.16212
    chirality_residual_sum (n=2): 0.896754
    planarity_residual_sum (n=1): 0.000866164
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 41.9888
  bond_residual_sum (n=12): 24.73
  nonbonded_residual_sum (n=44): 0.0634987
  angle_residual_sum (n=21): 13.1355
  dihedral_residual_sum (n=3): 3.16212
  chirality_residual_sum (n=2): 0.896754
  planarity_residual_sum (n=1): 0.000866164
  norm of gradients: 845.041

Energies after minimization:
target: 0.307825
  bond_residual_sum (n=12): 0.00188959
  nonbonded_residual_sum (n=44): 0.00310892
  angle_residual_sum (n=21): 0.279099
  dihedral_residual_sum (n=3): 0.000232147
  chirality_residual_sum (n=2): 0.0234957
  planarity_residual_sum (n=1): 4.01819e-16
  norm of gradients: 9.01203e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/val.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 8
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 8
      Number of chains: 1
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 1.25

Residue name:  VAL%COO VAL
Missing hydrogen atoms:  ['HG22', 'H', 'HG21', 'HG11', 'HG12', 'HG13', 'HB', 'HG23', 'HA']

missing HG22: bond:  CG2 HG22 bond distance = 0.960
        HG22: angle: HG21  CG2 HG22 = 110.000
        HG22: angle: HG22  CG2 HG23 = 110.000
        HG22: angle:   CB  CG2 HG22 = 109.000
Building: HG22  ...
missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing HG11: bond:  CG1 HG11 bond distance = 0.960
        HG11: angle: HG11  CG1 HG12 = 110.000
        HG11: angle: HG11  CG1 HG13 = 110.000
        HG11: angle:   CB  CG1 HG11 = 109.000
Building: HG11  ...
missing   HB: bond:   CB   HB bond distance = 0.980
          HB: angle:   HB   CB  CG1 = 108.000
          HB: angle:   HB   CB  CG2 = 108.000
          HB: angle:   CA   CB   HB = 109.000
Building:  HB
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA

Still missing:  VAL ['H']
Build  8  from  9  % =  88.8888888889

('VAL', ['H'])
val.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 16
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 16
      Number of chains: 1
        Number of residues, atoms: 1, 16
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.25
  Number of scatterers: 16
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       2      8.00
     N       1      7.00
     C       5      6.00
     H       8      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.00 seconds
  Histogram of bond lengths:
        0.96 -     1.08: 7
        1.08 -     1.21: 1
        1.21 -     1.33: 2
        1.33 -     1.46: 0
        1.46 -     1.58: 5
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  VAL     1 " - "HA   VAL     1 " 0.980  1.091 -0.111 2.50e+03 3.07e+01
  " CA  VAL     1 " - " N   VAL     1 " 1.458  1.505 -0.047 2.77e+03 6.17e+00
  " CB  VAL     1 " - "HB   VAL     1 " 0.980  1.026 -0.046 2.50e+03 5.22e+00
  " CB  VAL     1 " - " CA  VAL     1 " 1.540  1.581 -0.041 1.37e+03 2.30e+00
  " C   VAL     1 " - " O   VAL     1 " 1.231  1.250 -0.019 2.50e+03 9.13e-01
  ... (remaining 10 not shown)
  Histogram of nonbonded interaction distances:
        2.05 -     2.60: 10
        2.60 -     3.15: 20
        3.15 -     3.71: 24
        3.71 -     4.26: 13
        4.26 -     4.81: 7
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HG23 VAL     1 " - "HG13 VAL     1 "  2.050 2.400
  "HG12 VAL     1 " - "HB   VAL     1 "  2.164 1.600
  "HG21 VAL     1 " - "HB   VAL     1 "  2.186 1.600
  "HG11 VAL     1 " - "HA   VAL     1 "  2.372 2.400
  " CG2 VAL     1 " - "HG13 VAL     1 "  2.458 1.933
  ... (remaining 69 not shown)
  Histogram of dihedral angle deviations from ideal:
        4.61 -    16.45: 2
       16.45 -    28.29: 1
       28.29 -    40.13: 0
       40.13 -    51.97: 0
       51.97 -    63.81: 1
  Dihedral angle restraints sorted by residual:
  " CA  VAL     1 "
  " CB  VAL     1 "
  " CG1 VAL     1 "
  "HG13 VAL     1 "
      ideal   model   delta periodicty    weight residual
      60.00  123.81  -63.81     2       1.11e-03 4.52e+00
  " OXT VAL     1 "
  " C   VAL     1 "
  " CA  VAL     1 "
  " N   VAL     1 "
      ideal   model   delta periodicty    weight residual
     160.00  135.14   24.86     2       1.11e-03 6.87e-01
  " CA  VAL     1 "
  " CB  VAL     1 "
  " CG2 VAL     1 "
  "HG23 VAL     1 "
      ideal   model   delta periodicty    weight residual
      60.00 -135.02   15.02     2       1.11e-03 2.51e-01
  " N   VAL     1 "
  " CB  VAL     1 "
  " CA  VAL     1 "
  " CG2 VAL     1 "
      ideal   model   delta periodicty    weight residual
    -180.00  -55.39   -4.61     3       4.44e-03 9.44e-02
  target: 64.4875
    bond_residual_sum (n=15): 47.3506
    nonbonded_residual_sum (n=74): 0.526769
    angle_residual_sum (n=27): 10.9254
    dihedral_residual_sum (n=4): 5.55583
    chirality_residual_sum (n=2): 0.128855
    planarity_residual_sum (n=1): 5.12181e-05
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 64.4875
  bond_residual_sum (n=15): 47.3506
  nonbonded_residual_sum (n=74): 0.526769
  angle_residual_sum (n=27): 10.9254
  dihedral_residual_sum (n=4): 5.55583
  chirality_residual_sum (n=2): 0.128855
  planarity_residual_sum (n=1): 5.12181e-05
  norm of gradients: 882.216

Energies after minimization:
target: 0.396236
  bond_residual_sum (n=15): 0.00109572
  nonbonded_residual_sum (n=74): 0.112962
  angle_residual_sum (n=27): 0.23705
  dihedral_residual_sum (n=4): 0.0290599
  chirality_residual_sum (n=2): 0.015864
  planarity_residual_sum (n=1): 0.000204325
  norm of gradients: 1.71926e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/cys.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7
      Number of chains: 1
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 1.43

Residue name:  CYS%COO CYS
Missing hydrogen atoms:  ['H', 'HA', 'HB1', 'HG', 'HB2']

missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   SG = 108.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2
Building:  HB1  and  HB2
Building:  HB1  and  HB2
missing   HG: bond:   HG   SG bond distance = 1.340
          HG: angle:   CB   SG   HG = 109.000
Building:  HG
Building: HG  ...

Still missing:  CYS ['H']
Build  4  from  5  % =  80.0

('CYS', ['H'])
cys.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 11
      Number of chains: 1
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.91
  Number of scatterers: 11
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       1     16.00
     O       2      8.00
     N       1      7.00
     C       3      6.00
     H       4      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.97 -     1.14: 3
        1.14 -     1.31: 2
        1.31 -     1.48: 1
        1.48 -     1.65: 3
        1.65 -     1.82: 1
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  CYS     1 " - "HA   CYS     1 " 0.980  1.072 -0.092 2.50e+03 2.12e+01
  " CA  CYS     1 " - " N   CYS     1 " 1.458  1.506 -0.048 2.77e+03 6.44e+00
  " CB  CYS     1 " - " CA  CYS     1 " 1.530  1.561 -0.031 2.50e+03 2.47e+00
  " C   CYS     1 " - " OXT CYS     1 " 1.231  1.250 -0.019 2.50e+03 9.05e-01
  " C   CYS     1 " - " O   CYS     1 " 1.231  1.249 -0.018 2.50e+03 8.46e-01
  ... (remaining 5 not shown)
  Histogram of nonbonded interaction distances:
        2.37 -     2.78: 6
        2.78 -     3.19: 5
        3.19 -     3.60: 12
        3.60 -     4.01: 1
        4.01 -     4.42: 5
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HA   CYS     1 " - "HB1  CYS     1 "  2.369 1.600
  "HA   CYS     1 " - "HB2  CYS     1 "  2.402 1.600
  " OXT CYS     1 " - "HA   CYS     1 "  2.467 1.813
  " O   CYS     1 " - "HG   CYS     1 "  2.593 2.720
  " C   CYS     1 " - "HB2  CYS     1 "  2.721 1.933
  ... (remaining 24 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.69 -    12.55: 1
       12.55 -    24.41: 0
       24.41 -    36.27: 1
       36.27 -    48.13: 0
       48.13 -    59.99: 1
  Dihedral angle restraints sorted by residual:
  " CA  CYS     1 "
  " CB  CYS     1 "
  " SG  CYS     1 "
  "HG   CYS     1 "
      ideal   model   delta periodicty    weight residual
     180.00   -0.01  -59.99     3       4.44e-03 1.60e+01
  " OXT CYS     1 "
  " C   CYS     1 "
  " CA  CYS     1 "
  " N   CYS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  133.17   26.83     2       1.11e-03 8.00e-01
  " N   CYS     1 "
  " CB  CYS     1 "
  " CA  CYS     1 "
  " SG  CYS     1 "
      ideal   model   delta periodicty    weight residual
    -180.00  -59.31   -0.69     3       4.44e-03 2.14e-03
  target: 60.0107
    bond_residual_sum (n=10): 32.5394
    nonbonded_residual_sum (n=29): 0.0383642
    angle_residual_sum (n=16): 10.4642
    dihedral_residual_sum (n=3): 16.7978
    chirality_residual_sum (n=1): 0.170388
    planarity_residual_sum (n=1): 0.000445961
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 60.0107
  bond_residual_sum (n=10): 32.5394
  nonbonded_residual_sum (n=29): 0.0383642
  angle_residual_sum (n=16): 10.4642
  dihedral_residual_sum (n=3): 16.7978
  chirality_residual_sum (n=1): 0.170388
  planarity_residual_sum (n=1): 0.000445961
  norm of gradients: 705.66

Energies after minimization:
target: 0.298138
  bond_residual_sum (n=10): 0.00162971
  nonbonded_residual_sum (n=29): 6.56403e-05
  angle_residual_sum (n=16): 0.277211
  dihedral_residual_sum (n=3): 1.73645e-06
  chirality_residual_sum (n=1): 0.0192296
  planarity_residual_sum (n=1): 2.14662e-08
  norm of gradients: 1.25602e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/rosie/scratch1/rwgk/dist/regression/hydrogens/ser.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7
      Number of chains: 1
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 1.43

Residue name:  SER%COO SER
Missing hydrogen atoms:  ['H', 'HA', 'HB1', 'HG', 'HB2']

missing    H: bond:    N    H bond distance = 0.860
           H: angle:    H    N   CA = 114.000
Unknown hydrogen type:  H
missing   HA: bond:   CA   HA bond distance = 0.980
          HA: angle:   HA   CA   CB = 109.000
          HA: angle:   HA   CA    C = 109.000
          HA: angle:    N   CA   HA = 110.000
Building:  HA
missing  HB1: bond:   CB  HB1 bond distance = 0.970
         HB1: angle:  HB1   CB  HB2 = 110.000
         HB1: angle:  HB1   CB   OG = 109.000
         HB1: angle:   CA   CB  HB1 = 109.000
Building:  HB1  and  HB2
Building:  HB1  and  HB2
missing   HG: bond:   OG   HG bond distance = 0.820
          HG: angle:   CB   OG   HG = 110.000
Building:  HG
Building: HG  ...

Still missing:  SER ['H']
Build  4  from  5  % =  80.0

('SER', ['H'])
ser.pdb_h
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 11
      Number of chains: 1
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 0.91
  Number of scatterers: 11
  At special positions: 0
  Unit cell: (10, 10, 10, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O       3      8.00
     N       1      7.00
     C       3      6.00
     H       4      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.01 seconds
  Histogram of bond lengths:
        0.82 -     0.96: 1
        0.96 -     1.11: 3
        1.11 -     1.26: 2
        1.26 -     1.40: 0
        1.40 -     1.55: 4
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " CA  SER     1 " - " N   SER     1 " 1.458  1.504 -0.046 2.77e+03 5.86e+00
  " CA  SER     1 " - "HA   SER     1 " 0.980  1.027 -0.047 2.50e+03 5.50e+00
  " C   SER     1 " - " OXT SER     1 " 1.231  1.249 -0.018 2.50e+03 8.06e-01
  " C   SER     1 " - " O   SER     1 " 1.231  1.249 -0.018 2.50e+03 7.75e-01
  " CB  SER     1 " - " CA  SER     1 " 1.530  1.545 -0.015 2.50e+03 5.78e-01
  ... (remaining 5 not shown)
  Histogram of nonbonded interaction distances:
        2.35 -     2.71: 11
        2.71 -     3.07: 4
        3.07 -     3.42: 9
        3.42 -     3.78: 1
        3.78 -     4.14: 4
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  "HA   SER     1 " - "HB1  SER     1 "  2.352 1.600
  " CA  SER     1 " - "HG   SER     1 "  2.363 1.933
  "HA   SER     1 " - "HB2  SER     1 "  2.400 1.600
  " O   SER     1 " - "HG   SER     1 "  2.419 2.720
  " OXT SER     1 " - "HA   SER     1 "  2.458 1.813
  ... (remaining 24 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.03 -     5.75: 2
        5.75 -    11.46: 0
       11.46 -    17.17: 0
       17.17 -    22.88: 0
       22.88 -    28.59: 1
  Dihedral angle restraints sorted by residual:
  " N   SER     1 "
  " C   SER     1 "
  " CA  SER     1 "
  " OXT SER     1 "
      ideal   model   delta periodicty    weight residual
    -160.00 -131.41  -28.59     2       1.11e-03 9.08e-01
  " OG  SER     1 "
  " CB  SER     1 "
  " CA  SER     1 "
  " N   SER     1 "
      ideal   model   delta periodicty    weight residual
     180.00   57.04    2.96     3       4.44e-03 3.89e-02
  " CA  SER     1 "
  " OG  SER     1 "
  " CB  SER     1 "
  "HG   SER     1 "
      ideal   model   delta periodicty    weight residual
    -180.00   -0.03    0.03     2       1.11e-03 1.32e-06
  target: 21.3981
    bond_residual_sum (n=10): 13.8342
    nonbonded_residual_sum (n=29): 0.29357
    angle_residual_sum (n=16): 5.87119
    dihedral_residual_sum (n=3): 0.947303
    chirality_residual_sum (n=1): 0.451758
    planarity_residual_sum (n=1): 5.48188e-05
  Time first energy calculation (mainly nonbonded setup): 0.00

Energies at start of minimization:
target: 21.3981
  bond_residual_sum (n=10): 13.8342
  nonbonded_residual_sum (n=29): 0.29357
  angle_residual_sum (n=16): 5.87119
  dihedral_residual_sum (n=3): 0.947303
  chirality_residual_sum (n=1): 0.451758
  planarity_residual_sum (n=1): 5.48188e-05
  norm of gradients: 480.26

Energies after minimization:
target: 0.36904
  bond_residual_sum (n=10): 0.000845077
  nonbonded_residual_sum (n=29): 0.110287
  angle_residual_sum (n=16): 0.235222
  dihedral_residual_sum (n=3): 0.00655037
  chirality_residual_sum (n=1): 0.0161358
  planarity_residual_sum (n=1): 9.05847e-12
  norm of gradients: 7.63484e-06

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/max_lik/tst_maxlik.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import max_lik
u+s,u,s: 22.24 22.16 0.08

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/masks/tst_masks.py
/net/rosie/scratch1/rwgk/dist/mmtbx/masks/tst_masks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import masks
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import maptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
P 1
P -1
P 1 2 1
C 1 2/c 1
P 2 2 2
I m m a
P 4
P 41
I 41/a c d :2
P 3
P 31
P 3 1 m
R -3 c :H
P 6
P 63/m m c
P 2 3
I a -3 d
Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4)
u+s,u,s: 2.95 2.62 0.33

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py
/net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/max_lik/tst_max_lik.py:14: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.max_lik import max_like_non_uniform
P 1
P -1
P 1 2 1
C 1 2/c 1
P 2 2 2
I m m a
P 4
P 41
I 41/a c d :2
P 3
P 31
P 3 1 m
R -3 c :H
P 6
P 63/m m c
P 2 3
I a -3 d
Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4)
u+s,u,s: 10.63 10.43 0.20
P 1
P -1
P 1 2 1
C 1 2/c 1
P 2 2 2
I m m a
P 4
P 41
I 41/a c d :2
P 3
P 31
P 3 1 m
R -3 c :H
P 6
P 63/m m c
P 2 3
I a -3 d
Hall: -I 4 2c (1/2*x+1/2*y+1/12,-1/2*x+1/2*y-1/12,z-1/4)
u+s,u,s: 34.39 32.79 1.60
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/tst_cartesian_dynamics.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/tst_cartesian_dynamics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.restraints
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/restraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.adp_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/dynamics/cartesian_dynamics.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
u+s,u,s: 1.88 1.78 0.10

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
|-----------------------------------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   40.4770   20.8090   77.3260                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   16.2750   -1.2230   59.5040                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.1100 L22=  2.2200 L33=  2.3300 L12=  2.1200 L13=  2.1300 L23=  2.2300|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|

TLS from Uaniso:

|-----------------------------------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   40.4765   20.8088   77.3262                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   16.2748   -1.2233   59.5036                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.1100 L22=  2.2200 L33=  2.3300 L12=  2.1200 L13=  2.1300 L23=  2.2300|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|
u+s,u,s: 12.54 12.22 0.32

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/tls/tst_tls_refinement_fft.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
random_seed: 461690984
|-----------------------------------------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 17.09    max = 53.74    mean = 35.10   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       17.095 -   20.759:      12      |
|    -78.957 -  -78.957:       0      |       20.759 -   24.423:       0      |
|    -78.957 -  -78.957:       0      |       24.423 -   28.088:       0      |
|    -78.957 -  -78.957:       0      |       28.088 -   31.752:       0      |
|    -78.957 -  -78.957:       0      |       31.752 -   35.416:       8      |
|    -78.957 -  -78.957:       0      |       35.416 -   39.080:       4      |
|    -78.957 -  -78.957:       0      |       39.080 -   42.744:       0      |
|    -78.957 -  -78.957:       0      |       42.744 -   46.409:       0      |
|    -78.957 -  -78.957:       0      |       46.409 -   50.073:       0      |
|    -78.957 -  -78.957:       0      |       50.073 -   53.737:      12      |
|-----------------------------------------------------------------------------|
|-ANSWER----------------------------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.2200 L22=  2.4400 L33=  2.6600 L12=  2.2400 L13=  2.2600 L23=  2.4600|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.3300 T22=  0.6600 T33=  0.9900 T12=  0.3600 T13=  0.3900 T23=  0.6900|
|L11=  2.3300 L22=  2.6600 L33=  2.9900 L12=  2.3600 L13=  2.3900 L23=  2.6900|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                                                                             |
| all data [11.8-1.50] high resolution [6.0-1.50] low resolution [11.8-6.00]  |
| r_work = 0.0000      r_work = 0.0000            r_work = 0.0000             |
| r_free = 0.0000      r_free = 0.0000            r_free = 0.0000             |
|                                                                             |
| scale (work) = 1.0000  scale (free) = 1.0000  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ls_wunit_k1:  work = 0.000000E+00  free = 0.000000E+00               |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 11.8227 -  1.5003 1.00    909   48 0.0000 0.0000  0.0000E+00  0.0000E+00|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 11.8227 -  1.5003   909    48 1.000   0.000   0.000   1.000       0.000 |
|alpha:            min =       1.0000 max =       1.0000 mean =       1.0000  |
|beta:             min =       0.0000 max =       0.0000 mean =       0.0000  |
|figures of merit: min =       1.0000 max =       1.0000 mean =       1.0000  |
|phase err.(work): min =       0.0000 max =       0.0000 mean =       0.0000  |
|phase err.(test): min =       0.0000 max =       0.0000 mean =       0.0000  |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                                                                             |
| all data [11.8-1.50] high resolution [6.0-1.50] low resolution [11.8-6.00]  |
| r_work = 0.4848      r_work = 0.5116            r_work = 0.0741             |
| r_free = 0.4934      r_free = 0.5628            r_free = 0.0000             |
|                                                                             |
| scale (work) = 1.0714  scale (free) = 0.9195  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ls_wunit_k1:  work = 1.615700E-01  free = 2.171270E-01               |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 11.8227 -  1.5003 1.00    909   48 0.4848 0.4934  1.6157E-01  2.1713E-01|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 11.8227 -  1.5003   909    48 0.356  62.347  64.114   0.863      30.521 |
|alpha:            min =       0.8633 max =       0.8633 mean =       0.8633  |
|beta:             min =      30.5215 max =      30.5215 mean =      30.5215  |
|figures of merit: min =       0.0003 max =       0.9992 mean =       0.3564  |
|phase err.(work): min =       0.0000 max =      89.9818 mean =      62.3466  |
|phase err.(test): min =       0.0000 max =      89.9620 mean =      64.1145  |
|-----------------------------------------------------------------------------|
********************************************************************************
 
 0.0 
 
|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 1.615700e-01  r_work = 0.4848  r_free = 0.4934   |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 25.00    max = 25.00    mean = 25.00   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       25.000 -   25.000:      36      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.0000 T22=  0.0000 T33=  0.0000 T12=  0.0000 T13=  0.0000 T23=  0.0000|
|L11=  0.0000 L22=  0.0000 L33=  0.0000 L12=  0.0000 L13=  0.0000 L23=  0.0000|
|S11=  0.0000 S22=  0.0000 S33=  0.0000 S12=  0.0000 S13=  0.0000 S21=  0.0000|
|S23=  0.0000 S31=  0.0000 S32=  0.0000                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.0000 T22=  0.0000 T33=  0.0000 T12=  0.0000 T13=  0.0000 T23=  0.0000|
|L11=  0.0000 L22=  0.0000 L33=  0.0000 L12=  0.0000 L13=  0.0000 L23=  0.0000|
|S11=  0.0000 S22=  0.0000 S33=  0.0000 S12=  0.0000 S13=  0.0000 S21=  0.0000|
|S23=  0.0000 S31=  0.0000 S32=  0.0000                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.0000 T22=  0.0000 T33=  0.0000 T12=  0.0000 T13=  0.0000 T23=  0.0000|
|L11=  0.0000 L22=  0.0000 L33=  0.0000 L12=  0.0000 L13=  0.0000 L23=  0.0000|
|S11=  0.0000 S22=  0.0000 S33=  0.0000 S12=  0.0000 S13=  0.0000 S21=  0.0000|
|S23=  0.0000 S31=  0.0000 S32=  0.0000                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 16.96    max = 31.03    mean = 24.35   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       16.961 -   18.368:      12      |
|    -78.957 -  -78.957:       0      |       18.368 -   19.775:       0      |
|    -78.957 -  -78.957:       0      |       19.775 -   21.183:       0      |
|    -78.957 -  -78.957:       0      |       21.183 -   22.590:       0      |
|    -78.957 -  -78.957:       0      |       22.590 -   23.997:       0      |
|    -78.957 -  -78.957:       0      |       23.997 -   25.404:      12      |
|    -78.957 -  -78.957:       0      |       25.404 -   26.811:       0      |
|    -78.957 -  -78.957:       0      |       26.811 -   28.218:       0      |
|    -78.957 -  -78.957:       0      |       28.218 -   29.625:       0      |
|    -78.957 -  -78.957:       0      |       29.625 -   31.032:      12      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.0707 T22=  0.2304 T33=  0.3306 T12=  0.1272 T13=  0.1685 T23=  0.2761|
|L11=  0.0010 L22=  0.0002 L33=  0.0000 L12= -0.0006 L13= -0.0001 L23=  0.0001|
|S11=  0.0032 S22= -0.0022 S33= -0.0010 S12=  0.0087 S13=  0.0100 S21=  0.0046|
|S23= -0.0027 S31=  0.0068 S32=  0.0014                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.1903 T22=  0.3382 T33=  0.4254 T12=  0.1696 T13=  0.1536 T23=  0.2781|
|L11=  0.0010 L22=  0.0006 L33=  0.0002 L12= -0.0010 L13=  0.0002 L23=  0.0001|
|S11=  0.0061 S22= -0.0005 S33= -0.0056 S12=  0.0102 S13=  0.0090 S21= -0.0040|
|S23= -0.0090 S31= -0.0006 S32=  0.0047                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2950 T22=  0.4147 T33=  0.4667 T12=  0.1318 T13=  0.1894 T23=  0.2388|
|L11=  0.0010 L22=  0.0008 L33=  0.0003 L12= -0.0010 L13=  0.0003 L23=  0.0002|
|S11=  0.0036 S22= -0.0028 S33= -0.0007 S12=  0.0115 S13=  0.0084 S21= -0.0056|
|S23= -0.0076 S31= -0.0007 S32=  0.0043                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 1.381012e-02  r_work = 0.1294  r_free = 0.1581   |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.0707 T22=  0.2304 T33=  0.3306 T12=  0.1272 T13=  0.1685 T23=  0.2761|
|L11=  0.0010 L22=  0.0002 L33=  0.0000 L12= -0.0006 L13= -0.0001 L23=  0.0001|
|S11=  0.0032 S22= -0.0022 S33= -0.0010 S12=  0.0087 S13=  0.0100 S21=  0.0046|
|S23= -0.0027 S31=  0.0068 S32=  0.0014                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.1903 T22=  0.3382 T33=  0.4254 T12=  0.1696 T13=  0.1536 T23=  0.2781|
|L11=  0.0010 L22=  0.0006 L33=  0.0002 L12= -0.0010 L13=  0.0002 L23=  0.0001|
|S11=  0.0061 S22= -0.0005 S33= -0.0056 S12=  0.0102 S13=  0.0090 S21= -0.0040|
|S23= -0.0090 S31= -0.0006 S32=  0.0047                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2950 T22=  0.4147 T33=  0.4667 T12=  0.1318 T13=  0.1894 T23=  0.2388|
|L11=  0.0010 L22=  0.0008 L33=  0.0003 L12= -0.0010 L13=  0.0003 L23=  0.0002|
|S11=  0.0036 S22= -0.0028 S33= -0.0007 S12=  0.0115 S13=  0.0084 S21= -0.0056|
|S23= -0.0076 S31= -0.0007 S32=  0.0043                                       |
|-----------------------------------------------------------------------------|
 
 [<mmtbx_tls_ext.tlso object at 0x2b0dd929afc8>, <mmtbx_tls_ext.tlso object at 0x2b0dd936f050>, <mmtbx_tls_ext.tlso object at 0x2b0dd936f0a8>] 
 
|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 1.615700e-01  r_work = 0.4848  r_free = 0.4934   |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 25.00    max = 25.00    mean = 25.00   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       25.000 -   25.000:      36      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.2200 L22=  2.4400 L33=  2.6600 L12=  2.2400 L13=  2.2600 L23=  2.4600|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.3300 T22=  0.6600 T33=  0.9900 T12=  0.3600 T13=  0.3900 T23=  0.6900|
|L11=  2.3300 L22=  2.6600 L33=  2.9900 L12=  2.3600 L13=  2.3900 L23=  2.6900|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 17.09    max = 53.74    mean = 35.10   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       17.095 -   20.759:      12      |
|    -78.957 -  -78.957:       0      |       20.759 -   24.423:       0      |
|    -78.957 -  -78.957:       0      |       24.423 -   28.088:       0      |
|    -78.957 -  -78.957:       0      |       28.088 -   31.752:       0      |
|    -78.957 -  -78.957:       0      |       31.752 -   35.416:       8      |
|    -78.957 -  -78.957:       0      |       35.416 -   39.080:       4      |
|    -78.957 -  -78.957:       0      |       39.080 -   42.744:       0      |
|    -78.957 -  -78.957:       0      |       42.744 -   46.409:       0      |
|    -78.957 -  -78.957:       0      |       46.409 -   50.073:       0      |
|    -78.957 -  -78.957:       0      |       50.073 -   53.737:      12      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.2200 L22=  2.4400 L33=  2.6600 L12=  2.2400 L13=  2.2600 L23=  2.4600|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.3300 T22=  0.6600 T33=  0.9900 T12=  0.3600 T13=  0.3900 T23=  0.6900|
|L11=  2.3300 L22=  2.6600 L33=  2.9900 L12=  2.3600 L13=  2.3900 L23=  2.6900|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 2.277375e-23  r_work = 0.0000  r_free = 0.0000   |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1100 T22=  0.2200 T33=  0.3300 T12=  0.1200 T13=  0.1300 T23=  0.2300|
|L11=  1.1100 L22=  1.2200 L33=  1.3300 L12=  1.1200 L13=  1.1300 L23=  1.2300|
|S11=  0.1100 S22=  0.2200 S33= -0.3300 S12=  0.1200 S13=  0.1300 S21=  0.2100|
|S23=  0.2300 S31=  0.3100 S32=  0.3200                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2200 T22=  0.4400 T33=  0.6600 T12=  0.2400 T13=  0.2600 T23=  0.4600|
|L11=  2.2200 L22=  2.4400 L33=  2.6600 L12=  2.2400 L13=  2.2600 L23=  2.4600|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.3300 T22=  0.6600 T33=  0.9900 T12=  0.3600 T13=  0.3900 T23=  0.6900|
|L11=  2.3300 L22=  2.6600 L33=  2.9900 L12=  2.3600 L13=  2.3900 L23=  2.6900|
|S11=  0.2200 S22=  0.4400 S33= -0.6600 S12=  0.2400 S13=  0.2600 S21=  0.4200|
|S23=  0.4600 S31=  0.6200 S32=  0.6400                                       |
|-----------------------------------------------------------------------------|
 
 None 
 
|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 1.615700e-01  r_work = 0.4848  r_free = 0.4934   |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 25.00    max = 25.00    mean = 25.00   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       25.000 -   25.000:      36      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|    -78.957 -  -78.957:       0      |       25.000 -   25.000:       0      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.3162 T22=  0.3165 T33=  0.3165 T12=  0.0002 T13=  0.0001 T23= -0.0001|
|L11=  0.1757 L22=  0.6063 L33=  0.4083 L12=  0.3586 L13= -0.1743 L23= -0.4231|
|S11=  0.0002 S22= -0.0006 S33=  0.0004 S12= -0.0004 S13=  0.0001 S21= -0.0006|
|S23= -0.0008 S31= -0.0000 S32=  0.0012                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.3160 T22=  0.3162 T33=  0.3166 T12=  0.0005 T13=  0.0001 T23= -0.0000|
|L11=  0.3007 L22=  0.5603 L33=  0.9046 L12=  0.4413 L13= -0.2863 L23= -0.4669|
|S11= -0.0022 S22= -0.0007 S33=  0.0029 S12= -0.0004 S13= -0.0024 S21= -0.0022|
|S23= -0.0033 S31=  0.0014 S32=  0.0004                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.3158 T22=  0.3163 T33=  0.3168 T12=  0.0008 T13=  0.0001 T23=  0.0002|
|L11=  0.1960 L22=  0.6095 L33=  0.9342 L12=  0.5735 L13= -0.2105 L23= -0.3654|
|S11= -0.0034 S22= -0.0005 S33=  0.0039 S12=  0.0002 S13= -0.0041 S21= -0.0021|
|S23= -0.0046 S31=  0.0011 S32= -0.0013                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 17.53    max = 23.17    mean = 20.48   |
| Isotropic B only:              min = -78.96   max = -78.96   mean = -78.96  |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|    -78.957 -  -78.957:      36      |       17.533 -   18.096:      12      |
|    -78.957 -  -78.957:       0      |       18.096 -   18.660:       0      |
|    -78.957 -  -78.957:       0      |       18.660 -   19.223:       0      |
|    -78.957 -  -78.957:       0      |       19.223 -   19.787:       0      |
|    -78.957 -  -78.957:       0      |       19.787 -   20.350:       0      |
|    -78.957 -  -78.957:       0      |       20.350 -   20.914:      12      |
|    -78.957 -  -78.957:       0      |       20.914 -   21.477:       0      |
|    -78.957 -  -78.957:       0      |       21.477 -   22.041:       0      |
|    -78.957 -  -78.957:       0      |       22.041 -   22.605:       0      |
|    -78.957 -  -78.957:       0      |       22.605 -   23.168:      12      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1597 T22=  0.2327 T33=  0.2741 T12=  0.0929 T13=  0.0747 T23=  0.1712|
|L11=  0.1757 L22=  0.6061 L33=  0.4081 L12=  0.3584 L13= -0.1744 L23= -0.4234|
|S11=  0.0020 S22= -0.0018 S33= -0.0002 S12= -0.0012 S13=  0.0005 S21=  0.0048|
|S23= -0.0013 S31=  0.0059 S32=  0.0002                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2146 T22=  0.2645 T33=  0.3075 T12=  0.1196 T13=  0.0507 T23=  0.1842|
|L11=  0.3008 L22=  0.5602 L33=  0.9045 L12=  0.4409 L13= -0.2864 L23= -0.4673|
|S11= -0.0009 S22= -0.0011 S33=  0.0020 S12= -0.0009 S13= -0.0012 S21= -0.0005|
|S23= -0.0046 S31=  0.0034 S32= -0.0002                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2567 T22=  0.2922 T33=  0.3294 T12=  0.1004 T13=  0.0492 T23=  0.1729|
|L11=  0.1961 L22=  0.6094 L33=  0.9340 L12=  0.5732 L13= -0.2106 L23= -0.3656|
|S11= -0.0031 S22= -0.0015 S33=  0.0046 S12= -0.0000 S13= -0.0029 S21= -0.0005|
|S23= -0.0054 S31=  0.0027 S32= -0.0018                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 3.598349e-02  r_work = 0.2268  r_free = 0.3000   |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1597 T22=  0.2327 T33=  0.2741 T12=  0.0929 T13=  0.0747 T23=  0.1712|
|L11=  0.1757 L22=  0.6061 L33=  0.4081 L12=  0.3584 L13= -0.1744 L23= -0.4234|
|S11=  0.0020 S22= -0.0018 S33= -0.0002 S12= -0.0012 S13=  0.0005 S21=  0.0048|
|S23= -0.0013 S31=  0.0059 S32=  0.0002                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2146 T22=  0.2645 T33=  0.3075 T12=  0.1196 T13=  0.0507 T23=  0.1842|
|L11=  0.3008 L22=  0.5602 L33=  0.9045 L12=  0.4409 L13= -0.2864 L23= -0.4673|
|S11= -0.0009 S22= -0.0011 S33=  0.0020 S12= -0.0009 S13= -0.0012 S21= -0.0005|
|S23= -0.0046 S31=  0.0034 S32= -0.0002                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2567 T22=  0.2922 T33=  0.3294 T12=  0.1004 T13=  0.0492 T23=  0.1729|
|L11=  0.1961 L22=  0.6094 L33=  0.9340 L12=  0.5732 L13= -0.2106 L23= -0.3656|
|S11= -0.0031 S22= -0.0015 S33=  0.0046 S12= -0.0000 S13= -0.0029 S21= -0.0005|
|S23= -0.0054 S31=  0.0027 S32= -0.0018                                       |
|-----------------------------------------------------------------------------|
u+s,u,s: 8.46 8.34 0.12

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.development import random_structure
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/examples/f_model_manager.py:46: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  import mmtbx.f_model
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/masks.py:11: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
f_calc          =  <cctbx.miller.array object at 0x2ad137087410>
f_obs           =  <cctbx.miller.array object at 0x2ad13610ae10>
f_mask          =  <cctbx.miller.array object at 0x2ad137080f90>
r_free_flags    =  <cctbx.miller.array object at 0x2ad13610aed0>
b_cart         =  [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
k_sol           =  0.0
b_sol           =  0.0
sf_algorithm    =  fft
target_name     =  None
0.276185393827
0.286931074917
 Bin     Resolution       No. Refl.      R-factors      
number     range         work   test     work   test    
  1: 36.8046 -  3.8248    974    130   0.2596 0.3110
  2:  3.8248 -  3.0363    918    122   0.2678 0.2499
  3:  3.0363 -  2.6526    912    108   0.2726 0.2858
  4:  2.6526 -  2.4101    909     95   0.2820 0.2624
  5:  2.4101 -  2.2374    924     78   0.2917 0.2728
  6:  2.2374 -  2.1055    907    100   0.2866 0.3145
  7:  2.1055 -  2.0001    907     84   0.2945 0.3079
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 36.8046 -  3.8248   974   130 0.820  22.852  22.017   0.948    7166.714 |
|  2:  3.8248 -  3.0363   918   122 0.775  27.795  27.712   0.944    6402.645 |
|  3:  3.0363 -  2.6526   912   108 0.797  26.300  25.441   0.935    4110.440 |
|  4:  2.6526 -  2.4101   909    95 0.789  27.739  22.867   0.940    3546.703 |
|  5:  2.4101 -  2.2374   924    78 0.802  26.508  23.350   0.944    2982.966 |
|  6:  2.2374 -  2.1055   907   100 0.784  28.145  25.305   0.969    2583.097 |
|  7:  2.1055 -  2.0001   907    84 0.760  29.998  29.866   0.977    2446.075 |
|alpha:            min =       0.9351 max =       0.9772 mean =       0.9509  |
|beta:             min =    2446.0747 max =    7166.7138 mean =    4232.4934  |
|figures of merit: min =       0.0000 max =       1.0000 mean =       0.7899  |
|phase err.(work): min =       0.0000 max =      89.9980 mean =      27.0040  |
|phase err.(test): min =       0.0000 max =      89.7514 mean =      25.1376  |
|-----------------------------------------------------------------------------|
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import max_lik
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076152 r_work= 0.2097     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9623  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000075 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   5.0718  10.0454 -14.9289   0.0000   6.9997  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.063                                      |
| mean alpha:  1.0018  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000075 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   5.0718  10.0454 -14.9289   0.0000   6.9997  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.063                                      |
| mean alpha:  1.0018  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0002 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS min.&grid s.:  u+s,u,s: 1.78 1.64 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076152 r_work= 0.2097     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9623  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 4: k & b: minimization; T= ls_wunit_k1-------------------------|
| k_sol= 0.35 b_sol=  65.20 target_w =            0.047005 r_work= 0.1866     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0013  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 4: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.35 b_sol=  65.20 target_w =            0.000050 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   5.0227   9.9880 -14.9766   0.0000   6.9958  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.011                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0006  10.0006 -15.0003   0.0000   7.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0002 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS minimization:  u+s,u,s: 2.48 2.34 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076152 r_work= 0.2097     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9623  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS fix_ksolbsol:  u+s,u,s: 2.62 2.48 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.047067 r_work= 0.1864     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0013  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS fix_ksolbsol:  u+s,u,s: 2.76 2.62 0.14
OK: LS fix_all 1:     u+s,u,s: 2.80 2.66 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076152 r_work= 0.2097     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9623  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS fix_all 2:     u+s,u,s: 2.86 2.72 0.14
OK: LS fix_all 3:     u+s,u,s: 2.91 2.77 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0000  10.0000 -15.0000   0.0000   7.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: LS fix_all 4:     u+s,u,s: 3.51 3.37 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.047067 r_work= 0.1864     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0013  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0003  10.0001 -15.0005   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_7:       u+s,u,s: 3.62 3.48 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.042954 r_work= 0.1808     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0008  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0002  10.0000 -15.0006   0.0000   7.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_8:       u+s,u,s: 3.72 3.58 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.026255 r_work= 0.0847     |
| B(11,22,33,12,13,23)=   5.0000  10.0000 -15.0000   0.0000   7.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9676  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000007 r_work= 0.0011     |
| B(11,22,33,12,13,23)=   5.0000  10.0000 -15.0000   0.0000   7.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9997  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   5.0000  10.0000 -15.0000   0.0000   7.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_9:       u+s,u,s: 4.12 3.98 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.028906 r_work= 0.0895     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9634  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000083 r_work= 0.0043     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_10:      u+s,u,s: 4.37 4.23 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.028917 r_work= 0.1189     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9693  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.25 b_sol=  10.00 target_w =            0.000003 r_work= 0.0017     |
| B(11,22,33,12,13,23)=   1.8969   3.8342  -6.0896   0.0000   2.9813  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.119                                     |
| mean alpha:  0.9971  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.25 b_sol=  10.00 target_w =            0.000000 r_work= 0.0006     |
| B(11,22,33,12,13,23)=   2.0101   4.0156  -5.9923   0.0000   3.0020  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.011                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.25 b_sol=  10.40 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.25 b_sol=  10.40 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.075532 r_work= 0.1729     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9395  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.50 b_sol=  20.00 target_w =            0.000120 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   1.9302   3.8424  -6.0407   0.0000   2.9732  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.089                                     |
| mean alpha:  0.9986  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.50 b_sol=  20.00 target_w =            0.000115 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   2.0600   4.0817  -5.9341   0.0000   3.0036  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.069                                      |
| mean alpha:  1.0024  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.48 b_sol=  18.90 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0000  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.48 b_sol=  18.90 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0000  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.074578 r_work= 0.1771     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9215  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.80 b_sol=  45.00 target_w =            0.000000 r_work= 0.0004     |
| B(11,22,33,12,13,23)=   2.0011   4.0045  -6.0007   0.0000   3.0009  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.002                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.80 b_sol=  45.00 target_w =            0.000000 r_work= 0.0004     |
| B(11,22,33,12,13,23)=   2.0011   4.0045  -6.0007   0.0000   3.0009  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.002                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.80 b_sol=  45.20 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.80 b_sol=  45.20 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.067056 r_work= 0.1505     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9256  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.70 b_sol=  70.00 target_w =            0.000080 r_work= 0.0049     |
| B(11,22,33,12,13,23)=   2.0790   4.0845  -5.9175   0.0000   3.0073  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.082                                      |
| mean alpha:  1.0026  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.70 b_sol=  70.00 target_w =            0.000079 r_work= 0.0051     |
| B(11,22,33,12,13,23)=   2.1231   4.1720  -5.8722   0.0000   3.0153  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.141                                      |
| mean alpha:  1.0040  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.72 b_sol=  77.10 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.72 b_sol=  77.10 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.039174 r_work= 0.1302     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9617  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.30 b_sol=  15.00 target_w =            0.000031 r_work= 0.0034     |
| B(11,22,33,12,13,23)=   1.7725   3.6882  -6.2223   0.0000   2.9736  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.254                                     |
| mean alpha:  0.9932  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.30 b_sol=  15.00 target_w =            0.000028 r_work= 0.0022     |
| B(11,22,33,12,13,23)=   1.8900   3.8770  -6.1205   0.0000   2.9947  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.118                                     |
| mean alpha:  0.9964  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.31 b_sol=  16.01 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0003   3.9998  -6.0007   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.31 b_sol=  16.01 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0003   3.9998  -6.0007   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.070098 r_work= 0.1495     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9340  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.65 b_sol=  75.00 target_w =            0.000073 r_work= 0.0035     |
| B(11,22,33,12,13,23)=   1.8823   3.8243  -6.1240   0.0000   2.9849  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.139                                     |
| mean alpha:  0.9964  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.65 b_sol=  75.00 target_w =            0.000072 r_work= 0.0031     |
| B(11,22,33,12,13,23)=   1.9332   3.9112  -6.0703   0.0000   2.9915  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.075                                     |
| mean alpha:  0.9980  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.63 b_sol=  70.45 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0007   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.63 b_sol=  70.45 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0001  -6.0007   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: closest to real:  u+s,u,s: 10.58 10.43 0.15
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013796 r_work= 0.1211     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8413  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013796 r_work= 0.1211     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8413  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.8876   7.7038   7.1928  -0.1093   0.2703   0.3535 |
| trace(B) = (B11 + B22 + B33)/3 = 7.595                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.012946 r_work= 0.1161     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8242  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000018 r_work= 0.0039     |
| B(11,22,33,12,13,23)=   9.5846   8.6554   5.6714   0.0000  -0.3820   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.970                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000018 r_work= 0.0039     |
| B(11,22,33,12,13,23)=   9.5846   8.6554   5.6714   0.0000  -0.3820   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.970                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.5519   9.0844   5.9949  -0.1109  -0.3483  -0.5996 |
| trace(B) = (B11 + B22 + B33)/3 = 8.210                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013514 r_work= 0.1193     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8193  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.5519   9.0844   5.9949   0.0000  -0.3483   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.210                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.5519   9.0844   5.9949   0.0000  -0.3483   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.210                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.5519   9.0844   5.9949   0.0000  -0.3483   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.210                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010237 r_work= 0.1052     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8640  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000127 r_work= 0.0106     |
| B(11,22,33,12,13,23)=   7.1491   7.2739   5.5949   0.0000  -1.0254   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.673                                      |
| mean alpha:  0.9994  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000127 r_work= 0.0106     |
| B(11,22,33,12,13,23)=   7.1491   7.2739   5.5949   0.0000  -1.0254   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.673                                      |
| mean alpha:  0.9994  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.8469   6.8954   5.5875  -1.2783  -0.3653   0.3518 |
| trace(B) = (B11 + B22 + B33)/3 = 6.443                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009349 r_work= 0.1007     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8691  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.8469   6.8954   5.5875   0.0000  -0.3653   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.443                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.8469   6.8954   5.5875   0.0000  -0.3653   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.443                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.8469   6.8954   5.5875   0.0000  -0.3653   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.443                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.012438 r_work= 0.1155     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7996  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000020 r_work= 0.0040     |
| B(11,22,33,12,13,23)=   6.9758   7.0023   8.2485   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.409                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000020 r_work= 0.0040     |
| B(11,22,33,12,13,23)=   6.9758   7.0023   8.2485   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.409                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.3538   6.7230   8.2391  -0.1385  -0.5272   0.6033 |
| trace(B) = (B11 + B22 + B33)/3 = 7.439                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.012525 r_work= 0.1158     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7988  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.3538   6.7230   8.2391   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.439                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.3538   6.7230   8.2391   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.439                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.3538   6.7230   8.2391  -0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.439                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006040 r_work= 0.0816     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8396  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000010 r_work= 0.0031     |
| B(11,22,33,12,13,23)=   5.5741   5.5431   5.1311   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.416                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000010 r_work= 0.0031     |
| B(11,22,33,12,13,23)=   5.5741   5.5431   5.1311   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.416                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4620   5.5699   5.3731   0.3988  -0.2103  -0.3390 |
| trace(B) = (B11 + B22 + B33)/3 = 5.468                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006186 r_work= 0.0827     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8382  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4620   5.5699   5.3731   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.468                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4620   5.5699   5.3731   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.468                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4620   5.5699   5.3731   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.468                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010109 r_work= 0.1046     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8055  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000031 r_work= 0.0051     |
| B(11,22,33,12,13,23)=   7.1289   6.5922   6.5176   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.746                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000031 r_work= 0.0051     |
| B(11,22,33,12,13,23)=   7.1289   6.5922   6.5176   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.746                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.5773   6.7188   6.1764  -0.8598   0.0200   0.6227 |
| trace(B) = (B11 + B22 + B33)/3 = 6.824                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010344 r_work= 0.1056     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8037  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.5773   6.7188   6.1764   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.824                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.5773   6.7188   6.1764   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.824                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.5773   6.7188   6.1764   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.824                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009562 r_work= 0.0980     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8083  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000026 r_work= 0.0048     |
| B(11,22,33,12,13,23)=   8.4657   5.7985   5.4881   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.584                                      |
| mean alpha:  1.0012  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000026 r_work= 0.0048     |
| B(11,22,33,12,13,23)=   8.4657   5.7985   5.4881   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.584                                      |
| mean alpha:  1.0012  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.1210   5.9846   5.6871  -0.4486  -0.6196   0.1577 |
| trace(B) = (B11 + B22 + B33)/3 = 6.931                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010579 r_work= 0.1036     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7986  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.1210   5.9846   5.6871   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.931                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.1210   5.9846   5.6871   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.931                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.1210   5.9846   5.6871   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.931                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009107 r_work= 0.1033     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8127  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000112 r_work= 0.0105     |
| B(11,22,33,12,13,23)=   6.1075   6.1075   7.7428   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.653                                      |
| mean alpha:  0.9971  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000112 r_work= 0.0105     |
| B(11,22,33,12,13,23)=   6.1075   6.1075   7.7428   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.653                                      |
| mean alpha:  0.9971  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.1727   7.2458   7.2068   0.3352   0.5118   0.7445 |
| trace(B) = (B11 + B22 + B33)/3 = 6.542                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.008647 r_work= 0.1013     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8175  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.2093   6.2093   7.2068   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.542                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.2093   6.2093   7.2068   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.542                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.2093   6.2093   7.2068   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.542                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.016877 r_work= 0.1410     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7767  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0006     |
| B(11,22,33,12,13,23)=   8.4545   8.4545   8.3400   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.416                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0006     |
| B(11,22,33,12,13,23)=   8.4545   8.4545   8.3400   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.416                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.5600   8.5670   8.3593  -0.1351  -0.0554   0.0333 |
| trace(B) = (B11 + B22 + B33)/3 = 8.495                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.017150 r_work= 0.1423     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7748  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.5635   8.5635   8.3593   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.495                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.5635   8.5635   8.3593   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.495                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.5635   8.5635   8.3593   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.495                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.008726 r_work= 0.1020     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8023  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000086 r_work= 0.0093     |
| B(11,22,33,12,13,23)=   6.6775   6.6775   7.4541   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.936                                      |
| mean alpha:  0.9973  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000086 r_work= 0.0093     |
| B(11,22,33,12,13,23)=   6.6775   6.6775   7.4541   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.936                                      |
| mean alpha:  0.9973  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.9267   8.5394   7.1572  -0.9879  -0.0395   1.1474 |
| trace(B) = (B11 + B22 + B33)/3 = 7.208                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009182 r_work= 0.1047     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7970  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2331   7.2331   7.1572   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.208                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2331   7.2331   7.1572   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.208                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2331   7.2331   7.1572   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.208                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.014291 r_work= 0.1270     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7664  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000009 r_work= 0.0030     |
| B(11,22,33,12,13,23)=   8.4841   8.4841   8.0971  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.355                                      |
| mean alpha:  0.9998  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000009 r_work= 0.0030     |
| B(11,22,33,12,13,23)=   8.4841   8.4841   8.0971  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.355                                      |
| mean alpha:  0.9998  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.1645   8.3733   8.0462   0.2081  -0.2029   0.4660 |
| trace(B) = (B11 + B22 + B33)/3 = 8.195                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013789 r_work= 0.1246     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7703  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2689   8.2689   8.0462  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.195                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2689   8.2689   8.0462  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.195                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2689   8.2689   8.0462  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.195                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.005417 r_work= 0.0814     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8553  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000001 r_work= 0.0009     |
| B(11,22,33,12,13,23)=   5.1653   5.1653   5.1653   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.165                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000001 r_work= 0.0009     |
| B(11,22,33,12,13,23)=   5.1653   5.1653   5.1653   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.165                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.2701   5.2409   5.9655   0.0543  -0.1968  -0.3110 |
| trace(B) = (B11 + B22 + B33)/3 = 5.492                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006089 r_work= 0.0866     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8470  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4922   5.4922   5.4922   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.492                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4922   5.4922   5.4922   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.492                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4922   5.4922   5.4922   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.492                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013699 r_work= 0.1293     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7834  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000014 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   8.0887   8.0887   8.0887   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.089                                      |
| mean alpha:  1.0007  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000014 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   8.0887   8.0887   8.0887   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.089                                      |
| mean alpha:  1.0007  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.9523   8.1336   9.5178  -0.0406   0.3017  -0.6763 |
| trace(B) = (B11 + B22 + B33)/3 = 8.868                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.016250 r_work= 0.1422     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7654  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8679   8.8679   8.8679   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.868                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8679   8.8679   8.8679   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.868                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8679   8.8679   8.8679   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.868                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.011457 r_work= 0.1170     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8094  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000169 r_work= 0.0126     |
| B(11,22,33,12,13,23)=   6.9874   6.9874   6.9874   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.987                                      |
| mean alpha:  0.9978  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000169 r_work= 0.0126     |
| B(11,22,33,12,13,23)=   6.9874   6.9874   6.9874   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.987                                      |
| mean alpha:  0.9978  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.5330   8.3048   7.9826  -0.9643  -1.1388  -0.7708 |
| trace(B) = (B11 + B22 + B33)/3 = 7.940                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.014344 r_work= 0.1318     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7893  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.9402   7.9402   7.9402   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.940                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.9402   7.9402   7.9402   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.940                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.9402   7.9402   7.9402   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.940                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013957 r_work= 0.1191     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7587  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.013957 r_work= 0.1191     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7587  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.2343   8.8299   7.0174  -0.8081  -1.5322  -1.4553 |
| trace(B) = (B11 + B22 + B33)/3 = 8.027                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006746 r_work= 0.0859     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8202  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000016 r_work= 0.0039     |
| B(11,22,33,12,13,23)=   6.1458   6.2690   5.1110   0.0000  -0.2329   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.842                                      |
| mean alpha:  0.9996  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000016 r_work= 0.0039     |
| B(11,22,33,12,13,23)=   6.1458   6.2690   5.1110   0.0000  -0.2329   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.842                                      |
| mean alpha:  0.9996  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.0569   6.1086   5.1268  -0.4919  -0.0477   0.1139 |
| trace(B) = (B11 + B22 + B33)/3 = 5.764                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006572 r_work= 0.0846     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8223  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.0569   6.1086   5.1268   0.0000  -0.0477   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.764                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.0569   6.1086   5.1268   0.0000  -0.0477   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.764                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.0569   6.1086   5.1268  -0.0000  -0.0477   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.764                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.008106 r_work= 0.0959     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8122  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0006     |
| B(11,22,33,12,13,23)=   6.3164   5.8219   6.2481   0.0000   0.0750   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.129                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0006     |
| B(11,22,33,12,13,23)=   6.3164   5.8219   6.2481   0.0000   0.0750   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.129                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.3042   5.8650   6.2902  -0.0485   0.0967  -0.0741 |
| trace(B) = (B11 + B22 + B33)/3 = 6.153                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.008160 r_work= 0.0962     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8116  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.3042   5.8650   6.2902   0.0000   0.0967   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.153                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.3042   5.8650   6.2902   0.0000   0.0967   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.153                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.3042   5.8650   6.2902   0.0000   0.0967   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.153                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.011804 r_work= 0.1271     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7735  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000058 r_work= 0.0079     |
| B(11,22,33,12,13,23)=   8.6139   8.6818   6.4113   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.902                                      |
| mean alpha:  1.0006  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000058 r_work= 0.0079     |
| B(11,22,33,12,13,23)=   8.6139   8.6818   6.4113   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.902                                      |
| mean alpha:  1.0006  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8145   8.6359   6.8993   0.8687  -1.0731  -0.4080 |
| trace(B) = (B11 + B22 + B33)/3 = 8.117                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.012323 r_work= 0.1307     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7679  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8145   8.6359   6.8993   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.117                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8145   8.6359   6.8993   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.117                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8145   8.6359   6.8993   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.117                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.008852 r_work= 0.1076     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8005  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000022 r_work= 0.0050     |
| B(11,22,33,12,13,23)=   5.2979   6.5849   8.2008   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.695                                      |
| mean alpha:  0.9985  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000022 r_work= 0.0050     |
| B(11,22,33,12,13,23)=   5.2979   6.5849   8.2008   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.695                                      |
| mean alpha:  0.9985  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.0790   6.0597   7.6333   0.2289   0.2566   0.7610 |
| trace(B) = (B11 + B22 + B33)/3 = 6.257                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.007755 r_work= 0.0995     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8128  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.0790   6.0597   7.6333   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.257                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.0790   6.0597   7.6333   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.257                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.0790   6.0597   7.6333   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.257                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015933 r_work= 0.1318     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7467  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000014 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   8.9958   8.4030   9.3134   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.904                                      |
| mean alpha:  0.9989  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000014 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   8.9958   8.4030   9.3134   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.904                                      |
| mean alpha:  0.9989  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8352   8.0349   9.0082   0.1639   0.1234   0.5310 |
| trace(B) = (B11 + B22 + B33)/3 = 8.626                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015015 r_work= 0.1272     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7539  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8352   8.0349   9.0082   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.626                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8352   8.0349   9.0082   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.626                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.8352   8.0349   9.0082   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.626                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009962 r_work= 0.1050     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7884  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000026 r_work= 0.0046     |
| B(11,22,33,12,13,23)=   5.9067   6.2200   8.6700   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.932                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000026 r_work= 0.0046     |
| B(11,22,33,12,13,23)=   5.9067   6.2200   8.6700   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.932                                      |
| mean alpha:  0.9999  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.1226   6.0781   8.2641  -0.5259   0.1813   0.6015 |
| trace(B) = (B11 + B22 + B33)/3 = 6.822                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009533 r_work= 0.1029     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7913  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.1226   6.0781   8.2641   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.822                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.1226   6.0781   8.2641   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.822                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.1226   6.0781   8.2641   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.822                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009387 r_work= 0.0992     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8170  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000041 r_work= 0.0063     |
| B(11,22,33,12,13,23)=   5.6597   5.6597   7.2900   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.203                                      |
| mean alpha:  1.0012  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000041 r_work= 0.0063     |
| B(11,22,33,12,13,23)=   5.6597   5.6597   7.2900   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.203                                      |
| mean alpha:  1.0012  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.9391   7.6049   7.1274  -1.4817   0.4860  -0.2503 |
| trace(B) = (B11 + B22 + B33)/3 = 6.890                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010866 r_work= 0.1104     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7985  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.7720   6.7720   7.1274   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.890                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.7720   6.7720   7.1274   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.890                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.7720   6.7720   7.1274   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.890                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015043 r_work= 0.1365     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7599  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000009 r_work= 0.0029     |
| B(11,22,33,12,13,23)=   8.4648   8.4648   8.5600   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.497                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000009 r_work= 0.0029     |
| B(11,22,33,12,13,23)=   8.4648   8.4648   8.5600   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.497                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4788   8.4142   8.7917   0.2418   0.0353  -0.8204 |
| trace(B) = (B11 + B22 + B33)/3 = 8.562                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015253 r_work= 0.1375     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7584  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4465   8.4465   8.7917   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.562                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4465   8.4465   8.7917   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.562                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4465   8.4465   8.7917   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.562                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010938 r_work= 0.1192     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7783  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000078 r_work= 0.0089     |
| B(11,22,33,12,13,23)=   8.1105   8.1105   6.6422  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.621                                      |
| mean alpha:  0.9982  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000078 r_work= 0.0089     |
| B(11,22,33,12,13,23)=   8.1105   8.1105   6.6422  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.621                                      |
| mean alpha:  0.9982  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.4034   9.0210   6.6581   1.0701   0.0484   0.0416 |
| trace(B) = (B11 + B22 + B33)/3 = 7.028                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.009413 r_work= 0.1092     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7935  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2122   7.2122   6.6581  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.028                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2122   7.2122   6.6581  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.028                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2122   7.2122   6.6581  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.028                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010448 r_work= 0.1072     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7938  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000115 r_work= 0.0113     |
| B(11,22,33,12,13,23)=   5.9975   5.9975   8.8174  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.937                                      |
| mean alpha:  0.9994  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000115 r_work= 0.0113     |
| B(11,22,33,12,13,23)=   5.9975   5.9975   8.8174  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.937                                      |
| mean alpha:  0.9994  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.8529   7.6654   8.8904  -1.3320  -0.7881  -0.1526 |
| trace(B) = (B11 + B22 + B33)/3 = 7.803                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.012447 r_work= 0.1194     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7723  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2592   7.2592   8.8904  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.803                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2592   7.2592   8.8904  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.803                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   7.2592   7.2592   8.8904  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.803                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010826 r_work= 0.1128     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7988  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0004     |
| B(11,22,33,12,13,23)=   6.9484   6.9484   6.9484   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.948                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0004     |
| B(11,22,33,12,13,23)=   6.9484   6.9484   6.9484   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.948                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.9244   6.9246   6.9212  -0.1257   0.1063   0.0601 |
| trace(B) = (B11 + B22 + B33)/3 = 6.923                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.010754 r_work= 0.1124     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7994  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.9234   6.9234   6.9234   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.923                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.9234   6.9234   6.9234   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.923                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.9234   6.9234   6.9234   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 6.923                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006565 r_work= 0.0900     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8334  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000001 r_work= 0.0010     |
| B(11,22,33,12,13,23)=   5.4785   5.4785   5.4785   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.479                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000001 r_work= 0.0010     |
| B(11,22,33,12,13,23)=   5.4785   5.4785   5.4785   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.479                                      |
| mean alpha:  1.0001  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   6.0054   5.5042   5.3567   0.0212   0.0060  -0.0449 |
| trace(B) = (B11 + B22 + B33)/3 = 5.622                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.006895 r_work= 0.0924     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.8294  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.6221   5.6221   5.6221   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.622                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.6221   5.6221   5.6221   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.622                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   5.6221   5.6221   5.6221   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 5.622                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015921 r_work= 0.1357     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7533  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000006 r_work= 0.0020     |
| B(11,22,33,12,13,23)=   8.6640   8.6640   8.6640   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.664                                      |
| mean alpha:  0.9995  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000006 r_work= 0.0020     |
| B(11,22,33,12,13,23)=   8.6640   8.6640   8.6640   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.664                                      |
| mean alpha:  0.9995  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   9.0761   8.3930   7.8696  -0.3029   0.2675   0.5716 |
| trace(B) = (B11 + B22 + B33)/3 = 8.446                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.015183 r_work= 0.1320     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.7589  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4463   8.4463   8.4463   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.446                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4463   8.4463   8.4463   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.446                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0000     |
| B(11,22,33,12,13,23)=   8.4463   8.4463   8.4463  -0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.446                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: uaniso constr.:   u+s,u,s: 33.15 32.79 0.36
OK: scale_from_ls():  u+s,u,s: 33.15 32.79 0.36

libtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import max_lik
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076303 r_work= 0.2074     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9722  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000075 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   4.0695   5.0422  -8.9193   0.0000  12.0058  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.064                                      |
| mean alpha:  1.0018  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000075 r_work= 0.0044     |
| B(11,22,33,12,13,23)=   4.0695   5.0422  -8.9193   0.0000  12.0058  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.064                                      |
| mean alpha:  1.0018  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 20: k_sol & b_sol min.; T= ls_wunit_k1-------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 20: anisotropic scale; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 20: k_sol & b_sol min.; T= ml----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML min.&grid s.:  u+s,u,s: 7.17 7.04 0.13
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076303 r_work= 0.2074     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9722  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k & b: minimization; T= ls_wunit_k1-------------------------|
| k_sol= 0.34 b_sol=  62.19 target_w =            0.046887 r_work= 0.1827     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0113  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.34 b_sol=  62.19 target_w =            0.000041 r_work= 0.0032     |
| B(11,22,33,12,13,23)=   4.0551   5.0355  -8.9365   0.0000  12.0047  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.051                                      |
| mean alpha:  1.0014  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 4: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0004   5.0003  -9.0004   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 4: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0002  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 4: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0002  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML minimization:  u+s,u,s: 7.83 7.70 0.13
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076303 r_work= 0.2074     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9722  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML fix_ksolbsol:  u+s,u,s: 8.24 8.10 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.046935 r_work= 0.1827     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0111  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML fix_ksolbsol:  u+s,u,s: 8.64 8.50 0.14
OK: ML fix_all 1:     u+s,u,s: 8.69 8.55 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.076303 r_work= 0.2074     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9722  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML fix_all 2:     u+s,u,s: 8.74 8.60 0.14
OK: ML fix_all 3:     u+s,u,s: 8.79 8.65 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0000   5.0000  -9.0000   0.0000  12.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0003   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: ML fix_all 4:     u+s,u,s: 9.42 9.28 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.046935 r_work= 0.1827     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0111  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0005   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_7:       u+s,u,s: 9.82 9.68 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.042917 r_work= 0.1773     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0108  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0002   5.0001  -9.0006   0.0000  12.0002  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_8:       u+s,u,s: 9.93 9.79 0.14
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.026148 r_work= 0.0844     |
| B(11,22,33,12,13,23)=   4.0000   5.0000  -9.0000   0.0000  12.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9668  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000007 r_work= 0.0011     |
| B(11,22,33,12,13,23)=   4.0000   5.0000  -9.0000   0.0000  12.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9997  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0000   5.0000  -9.0000   0.0000  12.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   4.0000   5.0000  -9.0000   0.0000  12.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_9:       u+s,u,s: 10.43 10.28 0.15
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.028906 r_work= 0.0895     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9634  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 1: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.35 b_sol=  65.00 target_w =            0.000083 r_work= 0.0043     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0002  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.33 b_sol=  55.00 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: exercise_10:      u+s,u,s: 10.77 10.62 0.15
|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.075532 r_work= 0.1729     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.9395  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.50 b_sol=  20.00 target_w =            0.000115 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   2.0600   4.0817  -5.9341   0.0000   3.0036  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.069                                      |
| mean alpha:  1.0024  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 5: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.50 b_sol=  20.00 target_w =            0.000115 r_work= 0.0036     |
| B(11,22,33,12,13,23)=   2.0600   4.0817  -5.9341   0.0000   3.0036  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.069                                      |
| mean alpha:  1.0024  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 10: k_sol & b_sol min.; T= ls_wunit_k1-------------------------|
| k_sol= 0.48 b_sol=  18.90 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0000  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 10: anisotropic scale; T= ls_wunit_k1--------------------------|
| k_sol= 0.48 b_sol=  18.90 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0000  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 10: k_sol & b_sol min.; T= ml----------------------------------|
| k_sol= 0.48 b_sol=  18.90 target_w =            0.000000 r_work= 0.0001     |
| B(11,22,33,12,13,23)=   2.0004   4.0000  -6.0006   0.0000   3.0001  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = -0.000                                     |
| mean alpha:  1.0000  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
OK: closest to real:  u+s,u,s: 13.87 13.72 0.15
OK: scale_from_ml():  u+s,u,s: 13.87 13.72 0.15

libtbx.show_dist_paths mmtbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_all_cif_files.py
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/tst_all_cif_files.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import server
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
srv.root_path: /net/rosie/scratch1/rwgk/dist/mon_lib
Mixed case: i/Ir.cif
number of cif files read successfully: 2452
writing file table_of_contents
mmtbx.monomer_library.comp_as_motif GLU
grep description
libtbx.assert_stdin   description = "GLUTAMIC-ACID"
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/monomer_library.comp_as_motif.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import server
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
libtbx.show_dist_paths mmtbx
grep ^  Number of atoms
libtbx.assert_stdin   Number of atoms with unknown nonbonded energy type symbols: 8
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
mmtbx.python /net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb139l.ent
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:6: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import server
mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb103l.ent
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/pdb_interpretation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import pdb_interpretation
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/regression/pdb/pdb103l.ent
  Monomer Library directory:
    "/net/rosie/scratch1/rwgk/dist/mon_lib"
  Total number of atoms: 1404
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 1404
      Number of chains: 2
        Number of residues, atoms: 159, 1270
          Classifications: {'peptide': 159}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 155}
          Chain breaks: 1
        Number of residues, atoms: 131, 134
          Unusual residues: {'SEO': 1, ' CL': 2}
          Classifications: {'undetermined': 3, 'water': 128}
          Link IDs: {None: 130}
  Number of atoms with unknown nonbonded energy type symbols: 4
    " OB1 SEO   900 "
    " CB1 SEO   900 "
    " CB  SEO   900 "
    " SG  SEO   900 "
  Time building chain proxies: 0.85, per 1000 atoms: 0.61
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.07 seconds
  Histogram of bond lengths:
        1.18 -     1.31: 246
        1.31 -     1.44: 347
        1.44 -     1.57: 683
        1.57 -     1.70: 2
        1.70 -     1.83: 10
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " C   TYR   161 " - " N   LYS   162 " 1.329  1.259  0.070 5.10e+03 2.49e+01
  " CG  ASP   159 " - " OD1 ASP   159 " 1.249  1.324 -0.075 2.77e+03 1.57e+01
  " C   TYR    24 " - " N   TYR    25 " 1.329  1.275  0.054 5.10e+03 1.51e+01
  " CD  GLU   108 " - " OE1 GLU   108 " 1.249  1.320 -0.071 2.77e+03 1.40e+01
  " CA  TYR    24 " - " C   TYR    24 " 1.525  1.448  0.077 2.27e+03 1.36e+01
  ... (remaining 1283 not shown)
  Histogram of nonbonded interaction distances:
        1.39 -     2.10: 5
        2.10 -     2.80: 471
        2.80 -     3.50: 2282
        3.50 -     4.20: 4362
        4.20 -     4.90: 6791
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OB1 SEO   900 " - " CB1 SEO   900 "  1.394 1.000
  " CB1 SEO   900 " - " CB  SEO   900 "  1.525 1.000
  "CL    CL   173 " - " O   HOH   291 "  1.682 3.270 y+1,x,-z
  " SG  SEO   900 " - " SG  SEO   900 "  1.755 1.000 x-y,-y,-z+1/3
  " CB  SEO   900 " - " SG  SEO   900 "  1.829 1.000
  ... (remaining 13906 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.74: 369
       17.74 -    35.48: 69
       35.48 -    53.22: 25
       53.22 -    70.95: 12
       70.95 -    88.69: 4
  Dihedral angle restraints sorted by residual:
  " CB  LYS    19 "
  " CG  LYS    19 "
  " CD  LYS    19 "
  " CE  LYS    19 "
      ideal   model   delta periodicty    weight residual
     180.00 -119.76   59.76     3       4.44e-03 1.59e+01
  " CA  GLU    22 "
  " CB  GLU    22 "
  " CG  GLU    22 "
  " CD  GLU    22 "
      ideal   model   delta periodicty    weight residual
     180.00 -120.27  -59.73     3       4.44e-03 1.59e+01
  " CB  LYS    16 "
  " CG  LYS    16 "
  " CD  LYS    16 "
  " CE  LYS    16 "
      ideal   model   delta periodicty    weight residual
     180.00 -120.48  -59.52     3       4.44e-03 1.57e+01
  ... (remaining 476 not shown)
  target: 7776.5
    bond_residual_sum (n=1288): 1150.69
    nonbonded_residual_sum (n=13911): 1379.45
    angle_residual_sum (n=1736): 4266.02
    dihedral_residual_sum (n=479): 608.911
    chirality_residual_sum (n=194): 207.005
    planarity_residual_sum (n=222): 164.43
  Time first energy calculation (mainly nonbonded setup): 0.00
  Number of scatterers: 1404
  At special positions: 0
  Unit cell: (60.9, 60.9, 95.6, 90, 90, 120)
  Space group: P 32 2 1 (No. 154)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S       6     16.00
     O     364      8.00
     N     230      7.00
     C     802      6.00
    sf(0) = scattering factor at diffraction angle 0.
mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/ot1_ot2.pdb
grep Unexpected atoms
libtbx.assert_stdin 
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/pdb_interpretation.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.monomer_library import pdb_interpretation
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
mmtbx.pdb_interpretation /net/rosie/scratch1/rwgk/dist/regression/pdb/large_bond.pdb
tail -1
libtbx.assert_stdin Sorry: Number of bonds with excessive lengths: 1
mmtbx.geometry_minimization /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb1etn.ent /net/rosie/scratch1/rwgk/dist/regression/misc/multiple_monomers.cif --max_iterations=20
tail -2
head -1
libtbx.assert_stdin Writing: pdb1etn_geometry_minimized.ent
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/geometry_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx import monomer_library
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/cif_types.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import geometry_restraints
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/monomer_library/pdb_interpretation.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
libtbx.show_dist_paths iotbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py --Quick
/net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_wildcard.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_wildcard.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import wildcard
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/wildcard.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_simple_parser.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_simple_parser.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import simple_parser
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/phil/__init__.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phil.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phil.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.phil
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/phil.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_crystal_symmetry_from_any.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_crystal_symmetry_from_any.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/tst_strudat.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/tst_strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/kriber/strudat.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/pdb/tst_ext.py
/net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/pdb/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
u+s,u,s: 0.74 0.66 0.08

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/tst_pdb.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/tst_pdb.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/space_group_symbols.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/space_group_symbols.py:248: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/tst_cns.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/tst_cns.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.cns.xray_structure
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/sdb_writer.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import adptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py P31
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.scalepack import merge
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.51 0.44 0.07

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/no_merge_original_index.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/no_merge_original_index.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py
/net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/extract_from_symop_lib.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/extract_from_symop_lib.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py P31
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
u+s,u,s: 0.70 0.58 0.12

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_reflection_file_utils.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_reflection_file_utils.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_adsc.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_adsc.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.detectors import adsc
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import os,math
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import os,math
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/detectors/tst_debug_write.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.detectors import adsc
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/tst_xplormap.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/tst_xplormap.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/map.py:32: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py P31
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb.xray_structure
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Writing tmp.pdb
Writing: tmp.phs
OK

libtbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py Fdd2 P31m
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.command_line import reflection_statistics
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
F d d 2
P 3 1 m
u+s,u,s: 3.96 3.82 0.14
OK

iotbx.lattice_symmetry --unit_cell=12.7923,12.7923,29.4356,102.846,102.846,22.7475
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.option_parser import iotbx_option_parser

Input
=====

Unit cell: (12.7923, 12.7923, 29.4356, 102.846, 102.846, 22.7475)
Space group: P 1 (No. 1)

Angular tolerance: 3.000 degrees

Similar symmetries
==================

Symmetry in minimum-lengths cell: Hall: -C 2y (x+y,z,2*x-z) (No. 12)
      Input minimum-lengths cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374)
           Symmetry-adapted cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374)
            Conventional setting: C 1 2/m 1 (No. 12)
                       Unit cell: (25.0822, 5.04549, 29.4356, 90, 103.108, 90)
                 Change of basis: 1/2*x+1/2*y,-1/2*x+1/2*y,z
                         Inverse: x-y,x+y,z
      Maximal angular difference: 0.000 degrees

Symmetry in minimum-lengths cell: P -1 (No. 2)
      Input minimum-lengths cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374)
           Symmetry-adapted cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374)
            Conventional setting: P -1 (No. 2)
                       Unit cell: (5.04549, 12.7923, 29.3711, 100.302, 94.9273, 101.374)
                 Change of basis: y-z,x+y-z,-z
                         Inverse: -x+y,x-z,-z
      Maximal angular difference: 0.000 degrees

iotbx.lattice_symmetry --unit_cell=12,12,12.1,89,90,92 F
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.option_parser import iotbx_option_parser
cctbx.lattice_symmetry
diff lattice_symmetry_py_out lattice_symmetry_cpp_out
libtbx.assert_stdin 
iotbx.lattice_symmetry --unit_cell=78.9 82.3 57.0 90 93.4 90 C --delta=1.4
grep Maximal angular difference:
wc -l
sed s/ //g
libtbx.assert_stdin 5
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/lattice_symmetry.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.option_parser import iotbx_option_parser
iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=EUO --distance_cutoff=3.5
wc -l
sed s/ //g
libtbx.assert_stdin 71
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal import coordination_sequences
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=NAT --cs=10
tail -2
head -1
libtbx.assert_stdin TD10: 1661.40
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal import coordination_sequences
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
iotbx.show_distances /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb --show_cartesian
tail -2
head -1
libtbx.assert_stdin Pair counts: [14, 14, 13, 11, 10, 8, 7, 11, 10, 9, 12, 10, 12, 14, 13]
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal import coordination_sequences
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/show_distances.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
iotbx.distance_least_squares /net/rosie/scratch1/rwgk/dist/regression/misc/strudat_zeolite_atlas --tag=AFX
grep Final
cut -c-36
libtbx.assert_stdin Final target value (i_trial=0): 0.00
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/distance_least_squares.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.geometry_restraints import distance_least_squares
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/distance_least_squares.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.kriber import strudat
if ( 1 ) then
tail -2
libtbx.show_dist_paths iotbx
head -1
libtbx.assert_stdin     FOM    17711 100.00%   0.00    0.97 W: weight (of some sort)
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py /net/cci-filer1/vol1/share/structure-lib/nsf-n/resolve-dm/phase_noanom.mtz
/net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
grep ^    H    
libtbx.show_dist_paths iotbx
tail -1
wc -l
sed s/ //g
libtbx.assert_stdin 1
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py --walk /net/cci-filer1/vol1/share/structure-lib --verbose
/net/rosie/scratch1/rwgk/dist/iotbx/include/iotbx/mtz/tst_ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
endif
iotbx.reflection_file_reader /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx=hklf3 /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp
file_type: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz
file_type: ccp4_mtz

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Frem,SIGFrem,DANOrem,SIGDANOrem
Observation type: xray.reconstructed_amplitude
Type of data: double, size=272
Type of sigmas: double, size=272
Number of Miller indices: 272
Anomalous flag: True
Unit cell: (84.511, 104.308, 174.103, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 54
Resolution range: 19.853 15.0015
Completeness in resolution range: 0.989091
Completeness with d_max=infinity: 0.572632
Bijvoet pairs: 109
Lone Bijvoet mates: 0
Anomalous signal: 0.0293

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMrem
Observation type: None
Type of data: int, size=163
Type of sigmas: None
Number of Miller indices: 163
Anomalous flag: False
Unit cell: (84.511, 104.308, 174.103, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 54
Resolution range: 19.853 15.0015
Completeness in resolution range: 0.981928
Completeness with d_max=infinity: 0.537954

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Finf,SIGFinf,DANOinf,SIGDANOinf
Observation type: xray.reconstructed_amplitude
Type of data: double, size=273
Type of sigmas: double, size=273
Number of Miller indices: 273
Anomalous flag: True
Unit cell: (84.577, 104.408, 174.249, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 56
Resolution range: 19.8687 15.0137
Completeness in resolution range: 0.992727
Completeness with d_max=infinity: 0.574737
Bijvoet pairs: 108
Lone Bijvoet mates: 1
Anomalous signal: 0.0281

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMinf
Observation type: None
Type of data: int, size=165
Type of sigmas: None
Number of Miller indices: 165
Anomalous flag: False
Unit cell: (84.577, 104.408, 174.249, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 56
Resolution range: 19.8687 15.0137
Completeness in resolution range: 0.993976
Completeness with d_max=infinity: 0.544554

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:Fabs,SIGFabs,DANOabs,SIGDANOabs
Observation type: xray.reconstructed_amplitude
Type of data: double, size=273
Type of sigmas: double, size=273
Number of Miller indices: 273
Anomalous flag: True
Unit cell: (84.572, 104.489, 174.424, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 56
Resolution range: 19.87 15.0207
Completeness in resolution range: 0.992727
Completeness with d_max=infinity: 0.574737
Bijvoet pairs: 108
Lone Bijvoet mates: 1
Anomalous signal: 0.0354

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz:ISYMabs
Observation type: None
Type of data: int, size=165
Type of sigmas: None
Number of Miller indices: 165
Anomalous flag: False
Unit cell: (84.572, 104.489, 174.424, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 56
Resolution range: 19.87 15.0207
Completeness in resolution range: 0.993976
Completeness with d_max=infinity: 0.544554

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns
file_type: cns_reflection_file

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:PA_MOD,PB_MOD,PC_MOD,PD_MOD
Observation type: None
Type of data: hendrickson_lattman, size=100
Type of sigmas: None
Number of Miller indices: 100
Anomalous flag: True
Unit cell: None
Space group: None

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:FULL_MOD
Observation type: None
Type of data: complex_double, size=100
Type of sigmas: None
Number of Miller indices: 100
Anomalous flag: True
Unit cell: None
Space group: None

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/density_modify.cns:FOM_MOD
Observation type: None
Type of data: double, size=100
Type of sigmas: None
Number of Miller indices: 100
Anomalous flag: True
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref
file_type: dtrek_reflnlist

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref:Intensity,SigmaI
Observation type: xray.intensity
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: False
Unit cell: (83.0345, 89.9715, 94.9243, 90, 90, 90)
Space group: P 2 2 2 (No. 16)
Systematic absences: 0
Centric reflections: 100
Resolution range: 32.6501 2.36571
Completeness in resolution range: 0.00336508
Completeness with d_max=infinity: 0.00336293

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref:Intensity+-,SigmaI+-
Observation type: xray.intensity
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: True
Unit cell: (83.0345, 89.9715, 94.9243, 90, 90, 90)
Space group: P 2 2 2 (No. 16)
Systematic absences: 0
Centric reflections: 100
Resolution range: 32.6501 2.36571
Completeness in resolution range: 0.00178253
Completeness with d_max=infinity: 0.0017818
Bijvoet pairs: 0
Lone Bijvoet mates: 0
Anomalous signal: 0.0000

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns
file_type: cns_reflection_file

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: True
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns
file_type: cns_index_fobs_sigma

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_no_header.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: False
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz
file_type: ccp4_mtz

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fp_phi_fom.mtz:foo,PHIfoo
Observation type: xray.amplitude
Type of data: complex_double, size=23
Type of sigmas: None
Number of Miller indices: 23
Anomalous flag: False
Unit cell: (54.723, 76.075, 50.884, 90, 90, 90)
Space group: P 21 21 2 (No. 18)
Systematic absences: 0
Centric reflections: 17
Resolution range: 50.884 20.3569
Completeness in resolution range: 1
Completeness with d_max=infinity: 1

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb
file_type: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx=hklf3
file_type: shelx_hklf

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3.shelx:Fobs,SigFobs
Observation type: xray.amplitude
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: False
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx=hklf3
file_type: shelx_hklf

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx:Fobs,SigFobs
Observation type: xray.amplitude
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: False
Unit cell: None
Space group: None

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_alpha.shelx:alphas
Observation type: None
Type of data: int, size=100
Type of sigmas: None
Number of Miller indices: 100
Anomalous flag: False
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx=hklf3
file_type: shelx_hklf

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hklf_3_anom.shelx:Fobs,SigFobs
Observation type: xray.amplitude
Type of data: double, size=101
Type of sigmas: double, size=101
Number of Miller indices: 101
Anomalous flag: True
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb
file_type: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz
file_type: ccp4_mtz

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz:i_anomalous(+),SIGi_anomalous(+),i_anomalous(-),SIGi_anomalous(-)
Observation type: xray.intensity
Type of data: double, size=183
Type of sigmas: double, size=183
Number of Miller indices: 183
Anomalous flag: True
Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
Space group: P 6 (No. 168)
Systematic absences: 0
Centric reflections: 10
Resolution range: 100.447 2.43475
Completeness in resolution range: 0.00735176
Completeness with d_max=infinity: 0.00735176
Bijvoet pairs: 83
Lone Bijvoet mates: 7
Anomalous signal: 0.0773

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor
file_type: cns_index_fobs_sigma

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/madbst.xplor:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: False
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca
file_type: scalepack_merge

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca:i_obs,sigma
Observation type: xray.intensity
Type of data: double, size=183
Type of sigmas: double, size=183
Number of Miller indices: 183
Anomalous flag: True
Unit cell: (115.986, 115.986, 44.151, 90, 90, 120)
Space group: P 6 (No. 168)
Systematic absences: 0
Centric reflections: 10
Resolution range: 100.447 2.43475
Completeness in resolution range: 0.00735176
Completeness with d_max=infinity: 0.00735176
Bijvoet pairs: 83
Lone Bijvoet mates: 7
Anomalous signal: 0.0773

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca
file_type: scalepack_no_merge_original_index

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca:i_obs,sigma,merged
Observation type: xray.intensity
Type of data: double, size=52
Type of sigmas: double, size=52
Number of Miller indices: 52
Anomalous flag: True
Unit cell: None
Space group: P 2 2 2 (No. 16)
Systematic absences: 0
Centric reflections: 52
Bijvoet pairs: 0
Lone Bijvoet mates: 0
Anomalous signal: 0.0000

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins
file_type: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup
file_type: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt
file_type: solve_fpfm

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve_fpfm.fmt:fpfm,sigma_fpfm
Observation type: xray.amplitude
Type of data: double, size=160
Type of sigmas: double, size=160
Number of Miller indices: 160
Anomalous flag: True
Unit cell: None
Space group: None

file_name: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl
file_type: xds_ascii

Miller array info: /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl:iobs,sigma_iobs
Observation type: xray.intensity
Type of data: double, size=100
Type of sigmas: double, size=100
Number of Miller indices: 100
Anomalous flag: True
Unit cell: (131.92, 134.49, 203.83, 90, 90, 90)
Space group: P 2 2 2 (No. 16)
Systematic absences: 0
Centric reflections: 26
Resolution range: 29.3029 24.1946
Completeness in resolution range: 0.877193
Completeness with d_max=infinity: 0.361011
Bijvoet pairs: 35
Lone Bijvoet mates: 4
Anomalous signal: 0.0577

iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/fobs_sigma_anomalous.cns --unit_cell=12,12,12.1,89,90,92
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_statistics /net/rosie/scratch1/rwgk/dist/regression/reflection_files/gpd_nat_resolution_8.mtz
grep l,-k,h
libtbx.assert_stdin   l,-k,h
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
if ( 1 ) then
iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz --resolution 4 --bins 8
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/rnase-s/data/rnase25.mtz --quick
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/p9/data/infl.sca --unit_cell=114,114,32,90,90,90 --space_group=I4 --weak_symmetry --resolution=4
grep Space group: 
libtbx.assert_stdin Space group: I 41 (No. 80)
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_statistics /net/cci-filer1/vol1/share/structure-lib/p9/data/infl.sca --unit_cell=114,114,32,90,90,90 --space_group=I4 --resolution=4
grep Space group: 
libtbx.assert_stdin Space group: I 4 (No. 79)
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.reflection_file_converter /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca --unit_cell=113.949,113.949,32.474,90,90,90 --mtz=tmpf --write_mtz_amplitudes --non_anomalous --mtz_root_label=FPEAK
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional

file_name: /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca
file_type: scalepack_no_merge_original_index

Miller array info: /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca:i_obs,sigma
Observation type: xray.intensity
Type of data: double, size=145453
Type of sigmas: double, size=145453
Number of Miller indices: 145453
Anomalous flag: True
Unit cell: None
Space group: I 41 (No. 80)

Selected data:
  /net/cci-filer1/vol1/share/structure-lib/p9/data/peak.sca:i_obs,sigma
  Observation type: xray.intensity

Input crystal symmetry:
  Unit cell: (113.949, 113.949, 32.474, 90, 90, 90)
  Space group: I 41 (No. 80)

Merging symmetry-equivalent values:
  R-linear = sum(abs(data - mean(data))) / sum(abs(data))
  R-square = sum((data - mean(data))**2) / sum(data**2)
  In these sums single measurements are excluded.
                               Redundancy       Mean      Mean
                             Min  Max   Mean  R-linear  R-square
  unused:         - 28.4910
  bin  1: 28.4910 -  3.7555    1    8  3.782    0.0549    0.0105
  bin  2:  3.7555 -  2.9819    1    8  3.781    0.0796    0.0253
  bin  3:  2.9819 -  2.6052    1    8  3.753    0.1007    0.0343
  bin  4:  2.6052 -  2.3672    1    8  3.719    0.1366    0.0554
  bin  5:  2.3672 -  2.1976    1    8  3.644    0.1559    0.0685
  bin  6:  2.1976 -  2.0680    1    8  3.534    0.1904    0.0906
  bin  7:  2.0680 -  1.9645    1    8  3.410    0.2253    0.1156
  bin  8:  1.9645 -  1.8790    1    6  3.297    0.2793    0.1542
  bin  9:  1.8790 -  1.8067    1    6  3.209    0.3637    0.2270
  bin 10:  1.8067 -  1.7443    1    7  3.166    0.4207    0.2714
  unused:  1.7443 -

  Miller array info: None
  Observation type: xray.intensity
  Type of data: double, size=41181
  Type of sigmas: double, size=41181
  Number of Miller indices: 41181
  Anomalous flag: True
  Unit cell: (113.949, 113.949, 32.474, 90, 90, 90)
  Space group: I 41 (No. 80)
  Systematic absences: 0
  Centric reflections: 1668
  Resolution range: 28.4872 1.74434
  Completeness in resolution range: 0.990714
  Completeness with d_max=infinity: 0.990547
  Bijvoet pairs: 19624
  Lone Bijvoet mates: 265
  Anomalous signal: 0.0835

Converting data array from anomalous to non-anomalous.
Writing MTZ file: tmpf.mtz
  Converting intensities to amplitudes.

endif
iotbx.cns.sdb_reader /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.sdb_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.cns import sdb_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/cns/sdb_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
file: heavy_search_1.sdb
unit cell: (116.09699999999999, 116.09699999999999, 44.174999999999997, 90.0, 90.0, 120.0)
space group: P 6
Number of scatterers: 6
At special positions: 0
Unit cell: (116.097, 116.097, 44.175, 90, 90, 120)
Space group: P 6 (No. 168)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
SE_SE Se     6 ( 0.2221  0.1206  0.0037) 1.00 0.8314
SE_SE Se     6 ( 0.2286  0.1400  0.2089) 1.00 0.4283
SE_SE Se     6 ( 0.3687  0.2845  0.2254) 1.00 0.9112
SE_SE Se     6 ( 0.1766  0.0992  0.2504) 1.00 0.5232
SE_SE Se     6 ( 0.3813  0.2748  0.3024) 1.00 0.8433
SE_SE Se     6 ( 0.2107  0.0698  0.9259) 1.00 0.8796

cp /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp .
iotbx.cns.transfer_crystal_symmetry /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz cns.inp
libtbx.assert_stdin Info: 5 changes (sg, a, b, c, gamma), writing modified file "cns.inp".
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.transfer_crystal_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import cns
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.cns.transfer_crystal_symmetry /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dano.mtz cns.inp
libtbx.assert_stdin Info: no changes, "cns.inp" was not modified.
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/cns.transfer_crystal_symmetry.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import cns
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
foreach file ( merge.sca no_merge.sca xds_ascii_merge.hkl dtscale.ref i_anomalous.mtz shelx.ins cns.inp heavy_search_1.sdb hyss.pdb solve.setup ../misc/cns.map )
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/merge.sca
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(115.986, 115.986, 44.151, 90, 90, 120),
  space_group_symbol='P 6')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/no_merge.sca
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=None,
  space_group_symbol='P 2 2 2')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/xds_ascii_merge.hkl
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(131.92, 134.49, 203.83, 90, 90, 90),
  space_group_symbol='P 2 2 2')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/dtscale.ref
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(83.0345, 89.9715, 94.9243, 90, 90, 90),
  space_group_symbol='P 2 2 2')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/i_anomalous.mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(115.986, 115.986, 44.151, 90, 90, 120),
  space_group_symbol='P 6')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(87.8432, 155.426, 209.866, 90, 99.2821, 90),
  space_group_symbol='P 1 21 1')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/cns.inp
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(116.097, 116.097, 44.175, 90, 90, 120),
  space_group_symbol='P 6')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/heavy_search_1.sdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(116.097, 116.097, 44.175, 90, 90, 120),
  space_group_symbol='P 6')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/hyss.pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(115.986, 115.986, 44.151, 90, 90, 120),
  space_group_symbol='P 6')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/solve.setup
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(131.919, 134.489, 203.834, 90, 90, 90),
  space_group_symbol='P 21 21 21')
end
iotbx.crystal_symmetry_from_any /net/rosie/scratch1/rwgk/dist/regression/reflection_files/../misc/cns.map
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/crystal_symmetry_from_any.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
crystal.symmetry(
  unit_cell=(7.4141, 7.4141, 12.604, 90, 90, 120),
  space_group_symbol=None)
end
libtbx.assert_stdin P 1 21 1
libtbx.show_dist_paths iotbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.shelx.crystal_symmetry_from_ins import read_shelx_latt
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/crystal_symmetry_from_ins.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
libtbx.assert_stdin P 1 21 1
libtbx.show_dist_paths iotbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py /net/rosie/scratch1/rwgk/dist/regression/reflection_files/shelx.ins
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/shelx_latt_sym_to_space_group_symbol.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.shelx.crystal_symmetry_from_ins import read_shelx_latt
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/shelx/crystal_symmetry_from_ins.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
libtbx.show_dist_paths iotbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/direct_methods_light.py /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132Isup2.hkl /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132sup1.cif
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/examples/direct_methods_light.py:13: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import acta_c
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/acta_c.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/acta_c.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/PyCifRW': missing __init__.py
  from PyCifRW.CifFile import CifFile
Miller array info: /net/rosie/scratch1/rwgk/dist/regression/misc/vj1132Isup2.hkl:F_meas,F_sigma
Observation type: xray.amplitude
Type of data: double, size=422
Type of sigmas: double, size=422
Number of Miller indices: 422
Anomalous flag: False
Unit cell: (12.0263, 6.0321, 5.8293, 90, 90, 90)
Space group: P n a 21 (No. 33)
Systematic absences: 0
Centric reflections: 83
Resolution range: 6.01315 0.83382
Completeness in resolution range: 1
Completeness with d_max=infinity: 1

unused:        - 6.0133 [ 0/0 ]
bin  1: 6.0133 - 1.6574 [57/57]
bin  2: 1.6574 - 1.3201 [55/55]
bin  3: 1.3201 - 1.1546 [55/55]
bin  4: 1.1546 - 1.0496 [45/45]
bin  5: 1.0496 - 0.9747 [55/55]
bin  6: 0.9747 - 0.9175 [55/55]
bin  7: 0.9175 - 0.8717 [48/48]
bin  8: 0.8717 - 0.8338 [52/52]
unused: 0.8338 -        [ 0/0 ]

number of large_e_values: 111

triplets per reflection: min,max,mean: 34, 216, 98.40
total number of triplets: 10922

e_map max 11.9186
e_map min -2.87961
e_map mean -2.29868e-17
e_map sigma 1

e_map peak list
       fractional coordinates       peak height
  ( 0.185597,  0.796808,  0.966541)     12.159
  ( 0.093150,  0.511063,  0.086868)      9.072
  ( 0.144450,  0.689052,  0.127853)      8.099
  ( 0.168054,  0.788814,  0.355261)      6.019
  ( 0.136866,  0.605904,  0.547503)      4.943
  ( 0.052046, -0.012755,  0.950492)      4.702
  ( 0.091541,  0.981652,  0.394957)      4.641
  ( 0.137974,  0.656793,  0.767546)      3.277
  ( 0.180290,  0.231704,  0.968437)      2.905
  (-0.003727,  0.232895,  0.460465)      2.618

Number of scatterers: 13
At special positions: 0
Unit cell: (12.0263, 6.0321, 5.829, 90, 90, 90)
Space group: P n a 21 (No. 33)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso
O1   O      4 ( 0.5896  0.4862  0.6045) 1.00 0.0356
O2   O      4 ( 0.6861  0.2009  0.7409) 1.00 0.0328
C2   C      4 ( 0.6636  0.2231  0.3380) 1.00 0.0224
H2   H      4 ( 0.7419  0.1804  0.3237) 1.00 0.0270
C1   C      4 ( 0.6443  0.3133  0.5818) 1.00 0.0222
C3   C      4 ( 0.5923  0.0216  0.2916) 1.00 0.0347
H3A  H      4 ( 0.6060 -0.0308  0.1387) 1.00 0.0520
H3B  H      4 ( 0.5153  0.0605  0.3069) 1.00 0.0520
H3C  H      4 ( 0.6104 -0.0930  0.3997) 1.00 0.0520
N1   N      4 ( 0.6395  0.3976  0.1659) 1.00 0.0258
H1A  H      4 ( 0.6815  0.5160  0.1942) 1.00 0.0390
H1B  H      4 ( 0.5680  0.4351  0.1741) 1.00 0.0390
H1C  H      4 ( 0.6544  0.3463  0.0261) 1.00 0.0390

correlation of f_obs and f_calc: 0.9943

Match summary:
  Operator:
       rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}}
    translation: {1.98612e-34, 0.5, 0.21909}
  rms coordinate differences: 0.39
  Pairs: 8
    O1 peak01 0.168
    O2 peak00 0.070
    C2 peak03 0.175
    C1 peak02 0.057
    C3 peak06 0.191
    H3B peak05 0.949
    N1 peak04 0.050
    H1C peak07 0.478
  Singles model 1: 5
    H2   H3A   H3C   H1A   H1B
  Singles model 2: 2
    peak08   peak09

if ( -d /net/cci/srv/html/cci/cctbx_downloads && /net/rosie/scratch1/rwgk/dist/htdocs != None ) then
libtbx.python /net/rosie/scratch1/rwgk/dist/htdocs/siena2005/sort_merge.py /net/cci/srv/html/cci/cctbx_downloads/regression/siena2005_gms_sort_merge_exercise_in_info_and_hkl.data
grep Centric reflections
libtbx.assert_stdin Centric reflections: 4354
/net/rosie/scratch1/rwgk/dist/htdocs/siena2005/sort_merge.py:15: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
endif
grep -i error
libtbx.show_dist_paths cctbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
cctbx.python /net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py --Verbose
/net/rosie/scratch1/rwgk/dist/cctbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_krivy_gruber.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.uctbx import reduction_base
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sgtbx_denominators.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import sgtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_adp_constraints.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 3
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_direct_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.crystal import close_packing
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_crystal_close_packing.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb
R -3 m :R
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.development import random_structure
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
I 41/a c d :2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_reciprocal_space_asu.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 3 1 2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx.test_utils import approx_equal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_triplet_generator.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import dmtbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 41
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import euclidean_model_matching as emma
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_find_centre_of_inversion.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import find_centre_of_inversion
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_expand_to_p1.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_change_basis.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.xray import minimization
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_wilson_plot.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import statistics
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math.gaussian # base class for gaussian
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_derivatives.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_fast_gradients.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_xray_minimization.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_maptbx_structure_factors.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import maptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_merge_equivalents.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_miller_fft_map.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import crystal
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_sampled_model_density.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/regression/tst_fast_nv1995.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import translation_search
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
F 2 2 2
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/make_cns_input.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.eltbx.xray_scattering
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/eltbx/xray_scattering.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.math.gaussian # base class for gaussian
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/math/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
P 31
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_epsilon.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.cns import reflection_reader
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/tst_cns_hl.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.cns import reflection_reader
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import adptbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/development/run_shelx.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.shelx.write_ins import LATT_SYMM
sh: shelxl: command not found
mean_weighted_phase_error: 1.10
direct/fft_regression mean weighted phase error: 0.04
direct/fft_xray mean weighted phase error: 0.04
direct/fft_regression mean weighted phase error: 0.31
direct/fft_xray mean weighted phase error: 0.31
direct/fft_regression mean weighted phase error: 0.09
direct/fft_xray mean weighted phase error: 0.09
direct/fft_regression mean weighted phase error: 0.26
direct/fft_xray mean weighted phase error: 0.26
direct/fft_regression mean weighted phase error: 0.10
direct/fft_xray mean weighted phase error: 0.10
direct/fft_regression mean weighted phase error: 0.05
direct/fft_xray mean weighted phase error: 0.04
direct/fft_regression mean weighted phase error: 0.68
direct/fft_xray mean weighted phase error: 0.68
direct/fft_regression mean weighted phase error: 0.15
direct/fft_xray mean weighted phase error: 0.14
direct/fft_regression mean weighted phase error: 0.04
direct/fft_xray mean weighted phase error: 0.04
direct/fft_regression mean weighted phase error: 0.05
direct/fft_xray mean weighted phase error: 0.05
direct/fft_regression mean weighted phase error: 0.21
direct/fft_xray mean weighted phase error: 0.21
direct/fft_regression mean weighted phase error: 0.03
direct/fft_xray mean weighted phase error: 0.04
direct/fft_regression mean weighted phase error: 0.42
direct/fft_xray mean weighted phase error: 0.42
direct/fft_regression mean weighted phase error: 0.17
direct/fft_xray mean weighted phase error: 0.16
direct/fft_regression mean weighted phase error: 0.71
direct/fft_xray mean weighted phase error: 0.71
direct/fft_regression mean weighted phase error: 0.10
direct/fft_xray mean weighted phase error: 0.10
grep -i error
libtbx.show_dist_paths iotbx
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
iotbx.python /net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py --Verbose
/net/rosie/scratch1/rwgk/dist/iotbx/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/tst_merge.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.scalepack import merge
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/tst.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
P 31
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/tst_phases.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.pdb.xray_structure
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/regression/tst_reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx.command_line import reflection_statistics
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
F d d 2
P 3 1 m
/net/rosie/scratch1/rwgk/dist/regression/misc/tst_iotbx_emma.csh
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/emma.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import crystal_symmetry_from_any
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/scalepack/merge.py:12: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import uctbx
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK
/net/rosie/scratch1/rwgk/dist/regression/misc/tst_iotbx_reflection_file.csh
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_build_path.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/find_in_repositories.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_statistics.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_converter.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_converter
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/mtz.dump.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import mtz
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
OK
iotbx.pdb.hierarchy /net/rosie/scratch1/rwgk/dist/regression/pdb/pdb13gs.ent --details=conformer --prefix=T@
grep -v ^T@
libtbx.assert_stdin 
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.hierarchy.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
libtbx.show_dist_paths phenix
grep -i error
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
phenix.python /net/rosie/scratch1/rwgk/dist/phenix/run_tests.py --Verbose
/net/rosie/scratch1/rwgk/dist/phenix/run_tests.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import test_utils
/net/rosie/scratch1/rwgk/dist/phenix/phenix/regression/tst_heavy_search.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
C 1 2 1
if ( 1 ) then
mmtbx.xtriage file=/net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz obs_labels=SEpeak log=gre_MAD.log
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/xtriage.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.scaling import xtriage
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/xtriage.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.phil
#############################################################
##                        mmtbx.xtriage                    ##
##                                                         ##
##      P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams     ##
##                                                         ##
#############################################################
Date 2006-06-25 Time 20:09:04 PDT -0700

##-------------------------------------------##
## WARNING:                                  ##
## Number of residues unspecified            ##
##-------------------------------------------##

Effective parameters: 
scaling.input {
  parameters {
    asu_contents {
      n_residues = None
      n_bases = None
      n_copies_per_asu = None
    }
    misc_twin_parameters {
      missing_symmetry {
        tanh_location = 0.08
        tanh_slope = 50
      }
      twinning_with_ncs {
        perform_analyses = False
        n_bins = 7
      }
      twin_test_cuts {
        low_resolution = 10
        high_resolution = None
        isigi_cut = 3
        completeness_cut = 0.85
      }
    }
    reporting {
      verbose = 1
      log = "gre_MAD.log"
      ccp4_style_graphs = True
    }
  }
  xray_data {
    file_name = "/net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz"
    obs_labels = SEpeak
    calc_labels = None
    unit_cell = 108.7419968 61.67900085 71.65200043 90 97.15100098 90
    space_group = "C 1 2 1"
    high_resolution = None
    low_resolution = None
  }
}
<scitbx_array_family_flex_ext.double object at 0xc2a570>

Symmetry, cell and reflection file content summary

Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak
Observation type: xray.amplitude
Type of data: double, size=23010
Type of sigmas: double, size=23010
Number of Miller indices: 23010
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 766
Resolution range: 29.664 2.74731
Completeness in resolution range: 0.955763
Completeness with d_max=infinity: 0.955049
Bijvoet pairs: 11010
Lone Bijvoet mates: 224
Anomalous signal: 0.1207

##----------------------------------------------------##
##                    Basic statistics                ##
##----------------------------------------------------##

Matthews coefficient and Solvent content statistics

Number of residues unknown, assuming 50% solvent content

----------------------------------------------------------------
|              Best guess :  436  residues in the asu          |
----------------------------------------------------------------

Completeness and data strength analyses 

  The following table lists the completeness in various resolution
  ranges, after applying a I/sigI cut. Miller indices for which
  individual I/sigI values are larger than the value specified in
  the top row of the table, are retained, while other intensities
  are discarded. The resulting completeness profiles are an indication
  of the strength of the data.

----------------------------------------------------------------------------------------
| Res. Range   | I/sigI>1  | I/sigI>2  | I/sigI>3  | I/sigI>5  | I/sigI>10 | I/sigI>15 |
----------------------------------------------------------------------------------------
| 29.67 - 6.75 | 93.3%     | 91.2%     | 90.0%     | 87.4%     | 81.7%     | 74.7%     |
|  6.75 - 5.37 | 96.1%     | 89.3%     | 86.9%     | 80.5%     | 63.7%     | 45.5%     |
|  5.37 - 4.69 | 97.0%     | 90.0%     | 87.4%     | 81.0%     | 63.8%     | 40.8%     |
|  4.69 - 4.27 | 97.7%     | 92.8%     | 90.8%     | 87.2%     | 75.2%     | 58.9%     |
|  4.27 - 3.96 | 98.2%     | 90.5%     | 87.1%     | 81.0%     | 65.4%     | 48.2%     |
|  3.96 - 3.73 | 97.9%     | 87.9%     | 84.1%     | 76.4%     | 58.5%     | 35.5%     |
|  3.73 - 3.54 | 97.3%     | 86.8%     | 82.6%     | 73.5%     | 48.2%     | 16.7%     |
|  3.54 - 3.39 | 97.5%     | 81.2%     | 74.9%     | 62.1%     | 41.2%     | 23.8%     |
|  3.39 - 3.26 | 99.0%     | 79.2%     | 70.9%     | 56.6%     | 31.2%     | 13.7%     |
|  3.26 - 3.14 | 97.5%     | 71.1%     | 62.1%     | 46.4%     | 20.8%     | 7.7%      |
|  3.14 - 3.05 | 97.0%     | 66.8%     | 58.2%     | 40.3%     | 15.6%     | 4.0%      |
|  3.05 - 2.96 | 98.5%     | 61.1%     | 50.1%     | 33.0%     | 7.5%      | 0.4%      |
|  2.96 - 2.88 | 96.3%     | 54.1%     | 43.2%     | 26.9%     | 8.9%      | 2.5%      |
|  2.88 - 2.81 | 94.1%     | 45.0%     | 35.6%     | 22.0%     | 6.9%      | 2.4%      |
----------------------------------------------------------------------------------------

Maximum likelihood isotropic Wilson scaling 
ML estimate of overall B value of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak:
37.29 A**(-2)
Estimated -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak:
-0.44

Maximum likelihood anisotropic Wilson scaling 
ML estimate of overall B_cart value of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak:
35.85,  0.00,  7.66
       36.31,  0.00
              41.02
Equivalent representation as U_cif: 
 0.48, -0.00,  0.16
        0.46,  0.00
               0.52

ML estimate of  -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak:
-0.44
Correcting for anisotropy in the data

Some basic intensity statistics follow.

Low resolution completeness analyses 

 The following table shows the completeness
 of the data to 5 Angstrom.
unused:         - 29.6645 [  0/18 ] 0.000
bin  1: 29.6645 - 10.6221 [368/402] 0.915
bin  2: 10.6221 -  8.4963 [383/408] 0.939
bin  3:  8.4963 -  7.4416 [368/388] 0.948
bin  4:  7.4416 -  6.7701 [367/389] 0.943
bin  5:  6.7701 -  6.2898 [381/396] 0.962
bin  6:  6.2898 -  5.9221 [392/409] 0.958
bin  7:  5.9221 -  5.6276 [375/382] 0.982
bin  8:  5.6276 -  5.3841 [417/434] 0.961
bin  9:  5.3841 -  5.1780 [367/371] 0.989
bin 10:  5.1780 -  5.0002 [389/407] 0.956
unused:  5.0002 -         [  0/0  ]

Mean intensity analyses 
 Analyses of the mean intensity. 
 Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59.
 The following resolution shells are worrisome: 
------------------------------------------------
| d_spacing | z_score | compl. | <Iobs>/<Iexp> |
------------------------------------------------
|    8.445  |   4.76  |   0.96 |     1.463     |
|    5.771  |   6.23  |   0.98 |     0.713     |
|    5.422  |   5.85  |   0.97 |     0.742     |
|    5.128  |   9.65  |   0.97 |     0.626     |
|    4.878  |   7.50  |   0.99 |     0.689     |
|    3.676  |   6.04  |   0.99 |     1.304     |
------------------------------------------------

 Possible reasons for the presence of the reported
 unexpected low or elevated mean intensity in
 a given resolution bin are : 
 - missing overloaded or weak reflections
 - suboptimal data processing
 - satelite (ice) crystals
 - NCS
 - translational pseudo symmetry (detected elsewhere)
 - outliers (detected elsewhere)
 - ice rings (detected elsewhere)
 - other problems
 Note that the presence of abnormalities 
 in a certain region of reciprocal space might
 confuse the data validation algorithm throughout
 a large region of reciprocal space, even though
 the data is acceptable in those areas. 

Possible outliers 
  Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764

 Acentric reflections:

            None 

 Centric reflections:

            None 

Ice ring related problems

 The following statistics were obtained from ice-ring 
 insensitive resolution ranges 
  mean bin z_score      : 2.54
      ( rms deviation   : 2.47 )
  mean bin completeness : 0.92
     ( rms deviation   : 0.18 )

 The following table shows the z-scores 
 and completeness in ice-ring sensitive areas.
 Large z-scores and high completeness in these 
 resolution ranges might be a reason to re-assess
 your data processsing if ice rings were present.

------------------------------------------------
| d_spacing | z_score | compl. | Rel. Ice int. |
------------------------------------------------
|    3.897  |   0.45  |   0.98 |     1.000     |
|    3.669  |   1.13  |   0.97 |     0.750     |
|    3.441  |   2.48  |   0.97 |     0.530     |
------------------------------------------------

 Abnormalities in mean intensity or completeness at
 resolution ranges with a relative ice ring intensity
 lower then 0.10 will be ignored.

 No ice ring related problems detected.
 If ice rings were present, the data does not look
 worse at ice ring related d_spacings as compared
 to the rest of the data set 

Analyses of anomalous differences

  Table of measurability as a function of resolution

  The measurability is defined as the fraction of 
  Bijvoet related intensity differences for which 
  |delta_I|/sigma_delta_I > 3.0
  min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 
  holds. 
  The measurability provides an intuitive feeling
  of the quality of the data, as it is related to the 
  number of reliable Bijvoet differences.
  When the data is processed properly and the standard 
  deviations have been estimated accurately, values larger
  than 0.05 are encouraging. 

unused:         - 29.6657 [   0/18  ]
bin  1: 29.6657 -  5.9049 [2279/2412]  0.3837
bin  2:  5.9049 -  4.6929 [2342/2404]  0.2224
bin  3:  4.6929 -  4.1014 [2356/2397]  0.1292
bin  4:  4.1014 -  3.7272 [2394/2432]  0.0857
bin  5:  3.7272 -  3.4605 [2341/2380]  0.0451
bin  6:  3.4605 -  3.2567 [2375/2403]  0.0373
bin  7:  3.2567 -  3.0938 [2396/2428]  0.0138
bin  8:  3.0938 -  2.9593 [2348/2390]  0.0035
bin  9:  2.9593 -  2.8454 [2334/2396]  0.0124
bin 10:  2.8454 -  2.7473 [1845/2433]  0.0059
unused:  2.7473 -         [   0/0   ]

 The anomalous signal seems to extend to about 3.7 A
 (or to 3.5 A, from a more optimistic point of view)
 The quoted resolution limits can be used as a guideline
 to decide where to cut the resolution for phenix.hyss

Basic analyses completed

##----------------------------------------------------##
##                   Twinning Analyses                ##
##----------------------------------------------------##

Using data between 10.00 to 3.96 Angstrom.

Determining possible twin laws.

  0 merohedral twin operators found
  0 pseudo-merohedral twin operators found
In total,   0 twin operator were found

Number of centrics  : 315
Number of acentrics : 7022

 Largest patterson peak with length larger then 15 Angstrom 

 Frac. coord.        :   0.086    0.000   -0.475
 Distance to origin  :  36.425
 Height (origin=100) :   7.995
 p_value(height)     :   3.396e-01

   The reported p_value has the following meaning: 
     The probability that a peak of the specified height 
     or larger is found in a Patterson function of a 
     macro molecule that does not have any translational
     pseudo symmetry is equal to  3.396e-01 
     p_values smaller then 0.05 might indicate 
     weak translation pseudo symmetry, or the self vector of 
     a large anomalous scatterer such as Hg, whereas values 
     smaller then 1e-3 are a very strong indication for 
     the presence of translational pseudo symmetry.

Wilson ratio and moments 

Acentric reflections 
   <I^2>/<I>^2    :1.992   (untwinned: 2.000; perfect twin 1.500)
   <F>^2/<F^2>    :0.787   (untwinned: 0.785; perfect twin 0.885)
   <|E^2 - 1|>    :0.736   (untwinned: 0.736; perfect twin 0.541)

Centric reflections 
   <I^2>/<I>^2    :2.726   (untwinned: 3.000; perfect twin 2.000)
   <F>^2/<F^2>    :0.690   (untwinned: 0.637; perfect twin 0.785)
   <|E^2 - 1|>    :0.946   (untwinned: 0.968; perfect twin 0.736)

NZ test (0<=z<1) to detect twinning and possible translational NCS

-----------------------------------------------
|  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
-----------------------------------------------
| 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
| 0.1 |   0.096 |    0.095 |  0.187 |   0.248 |
| 0.2 |   0.183 |    0.181 |  0.254 |   0.345 |
| 0.3 |   0.260 |    0.259 |  0.317 |   0.419 |
| 0.4 |   0.330 |    0.330 |  0.384 |   0.474 |
| 0.5 |   0.390 |    0.394 |  0.444 |   0.520 |
| 0.6 |   0.451 |    0.451 |  0.508 |   0.561 |
| 0.7 |   0.507 |    0.503 |  0.540 |   0.597 |
| 0.8 |   0.557 |    0.551 |  0.587 |   0.629 |
| 0.9 |   0.599 |    0.593 |  0.629 |   0.657 |
| 1.0 |   0.639 |    0.632 |  0.660 |   0.683 |
-----------------------------------------------
| Maximum deviation acentric      :  0.007    |
| Maximum deviation centric       :  0.101    |
|                                             |
| <NZ(obs)-NZ(twinned)>_acentric  : +0.002    |
| <NZ(obs)-NZ(twinned)>_centric   : -0.057    |
-----------------------------------------------

 L test for acentric data

 using difference vectors (dh,dk,dl) of the form: 
(2hp,2kp,2lp)
  where hp, kp, and lp are random signed integers such that 
  2 <= |dh| + |dk| + |dl| <= 8 

  Mean |L|   :0.496  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.328  (untwinned: 0.333; perfect twin: 0.200)

  The distribution of |L| values indicates a twin fraction of
  0.01. Note that this estimate is not as reliable as obtained
  via a Britton plot or H-test if twin laws are available. 

-------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
  - <I^2>/<I>^2 : 1.992
  - <F>^2/<F^2> : 0.787
  - <|E^2-1|>   : 0.736
  - 
, <L^2>: 0.496, 0.328
       Multivariate Z score L-test: 1.059 
       The multivariate Z score is a quality measure of the given
       spread in intensities. Good to reasonable data is expected
       to have a Z score lower than 3.5. 
       Large values can indicate twinning, but small values do not
       neccesarily exclude it. 

No (pseudo)merohedral twin laws were found.

Patterson analyses
  - Largest peak height   : 7.995
   (correpsonding p value : 3.396e-01)

The largest off-origin peak in the Patterson function is 8.00% of the 
height of the origin peak. No significant pseudotranslation is detected.

The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.

-------------------------------------------------------------------------------
mmtbx.xtriage file=/net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca log=sec17.log
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/command_line/xtriage.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/mmtbx': missing __init__.py
  from mmtbx.scaling import xtriage
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/mmtbx/mmtbx/scaling/xtriage.py:9: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.phil
#############################################################
##                        mmtbx.xtriage                    ##
##                                                         ##
##      P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams     ##
##                                                         ##
#############################################################
Date 2006-06-25 Time 20:09:08 PDT -0700

##-------------------------------------------##
## WARNING:                                  ##
## Number of residues unspecified            ##
##-------------------------------------------##

Effective parameters: 
scaling.input {
  parameters {
    asu_contents {
      n_residues = None
      n_bases = None
      n_copies_per_asu = None
    }
    misc_twin_parameters {
      missing_symmetry {
        tanh_location = 0.08
        tanh_slope = 50
      }
      twinning_with_ncs {
        perform_analyses = False
        n_bins = 7
      }
      twin_test_cuts {
        low_resolution = 10
        high_resolution = None
        isigi_cut = 3
        completeness_cut = 0.85
      }
    }
    reporting {
      verbose = 1
      log = "sec17.log"
      ccp4_style_graphs = True
    }
  }
  xray_data {
    file_name = "/net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca"
    obs_labels = None
    calc_labels = None
    unit_cell = 108.18 108.18 46.509 90 90 90
    space_group = "P 41"
    high_resolution = None
    low_resolution = None
  }
}
<scitbx_array_family_flex_ext.double object at 0xca1f80>

Symmetry, cell and reflection file content summary

Miller array info: /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma
Observation type: xray.amplitude
Type of data: double, size=15372
Type of sigmas: double, size=15372
Number of Miller indices: 15372
Anomalous flag: True
Unit cell: (108.18, 108.18, 46.509, 90, 90, 90)
Space group: P 41 (No. 76)
Systematic absences: 0
Centric reflections: 763
Resolution range: 19.8701 3.3032
Completeness in resolution range: 0.975319
Completeness with d_max=infinity: 0.971129
Bijvoet pairs: 7171
Lone Bijvoet mates: 267
Anomalous signal: 0.1071

##----------------------------------------------------##
##                    Basic statistics                ##
##----------------------------------------------------##

Matthews coefficient and Solvent content statistics

Number of residues unknown, assuming 50% solvent content

----------------------------------------------------------------
|              Best guess :  498  residues in the asu          |
----------------------------------------------------------------

Completeness and data strength analyses 

  The following table lists the completeness in various resolution
  ranges, after applying a I/sigI cut. Miller indices for which
  individual I/sigI values are larger than the value specified in
  the top row of the table, are retained, while other intensities
  are discarded. The resulting completeness profiles are an indication
  of the strength of the data.

----------------------------------------------------------------------------------------
| Res. Range   | I/sigI>1  | I/sigI>2  | I/sigI>3  | I/sigI>5  | I/sigI>10 | I/sigI>15 |
----------------------------------------------------------------------------------------
| 19.87 - 7.98 | 96.4%     | 95.3%     | 94.5%     | 93.6%     | 91.7%     | 89.3%     |
|  7.98 - 6.40 | 99.2%     | 98.2%     | 97.1%     | 95.5%     | 90.9%     | 84.7%     |
|  6.40 - 5.61 | 97.8%     | 95.4%     | 93.3%     | 87.1%     | 76.6%     | 66.8%     |
|  5.61 - 5.11 | 98.2%     | 95.9%     | 94.0%     | 87.9%     | 74.1%     | 58.0%     |
|  5.11 - 4.75 | 97.9%     | 96.2%     | 94.5%     | 91.1%     | 79.2%     | 62.5%     |
|  4.75 - 4.47 | 97.4%     | 95.4%     | 93.1%     | 88.9%     | 76.6%     | 56.9%     |
|  4.47 - 4.25 | 96.5%     | 94.5%     | 92.1%     | 88.0%     | 75.3%     | 56.5%     |
|  4.25 - 4.07 | 96.6%     | 94.0%     | 91.2%     | 85.4%     | 69.3%     | 44.9%     |
|  4.07 - 3.91 | 95.6%     | 92.1%     | 87.8%     | 80.1%     | 61.9%     | 34.8%     |
|  3.91 - 3.78 | 94.3%     | 89.6%     | 83.7%     | 71.1%     | 48.7%     | 20.5%     |
|  3.78 - 3.66 | 95.7%     | 90.9%     | 85.6%     | 71.5%     | 42.4%     | 14.8%     |
|  3.66 - 3.56 | 91.6%     | 85.0%     | 78.0%     | 63.3%     | 34.1%     | 9.5%      |
|  3.56 - 3.46 | 89.8%     | 80.4%     | 70.2%     | 52.8%     | 22.2%     | 3.8%      |
|  3.46 - 3.38 | 87.4%     | 76.3%     | 64.6%     | 46.7%     | 15.5%     | 1.7%      |
----------------------------------------------------------------------------------------

Maximum likelihood isotropic Wilson scaling 
ML estimate of overall B value of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma:
75.85 A**(-2)
Estimated -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma:
-2.43

Maximum likelihood anisotropic Wilson scaling 
ML estimate of overall B_cart value of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma:
68.92,  0.00,  0.00
       68.92,  0.00
              91.87
Equivalent representation as U_cif: 
 0.87, -0.00, -0.00
        0.87,  0.00
               1.16

ML estimate of  -log of scale factor of /net/cci-filer1/vol1/share/structure-lib/sec17/data/peak.sca:i_obs,sigma:
-2.42
Correcting for anisotropy in the data

Some basic intensity statistics follow.

Low resolution completeness analyses 

 The following table shows the completeness
 of the data to 5 Angstrom.
unused:         - 19.8702 [  0/68 ] 0.000
bin  1: 19.8702 - 10.3027 [425/455] 0.934
bin  2: 10.3027 -  8.3766 [443/446] 0.993
bin  3:  8.3766 -  7.3796 [446/447] 0.998
bin  4:  7.3796 -  6.7336 [447/449] 0.996
bin  5:  6.7336 -  6.2673 [450/454] 0.991
bin  6:  6.2673 -  5.9080 [428/429] 0.998
bin  7:  5.9080 -  5.6192 [459/466] 0.985
bin  8:  5.6192 -  5.3796 [446/450] 0.991
bin  9:  5.3796 -  5.1763 [437/440] 0.993
bin 10:  5.1763 -  5.0006 [460/462] 0.996
unused:  5.0006 -         [  0/0  ]

Mean intensity analyses 
 Analyses of the mean intensity. 
 Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59.
 The following resolution shells are worrisome: 
------------------------------------------------
| d_spacing | z_score | compl. | <Iobs>/<Iexp> |
------------------------------------------------
|    5.773  |   7.95  |   0.99 |     0.658     |
|    5.423  |   8.62  |   0.99 |     0.654     |
|    5.130  |   6.31  |   0.99 |     0.744     |
|    4.879  |   5.36  |   0.99 |     0.775     |
|    4.662  |   4.52  |   0.99 |     0.803     |
|    3.676  |   5.45  |   0.99 |     1.248     |
------------------------------------------------

 Possible reasons for the presence of the reported
 unexpected low or elevated mean intensity in
 a given resolution bin are : 
 - missing overloaded or weak reflections
 - suboptimal data processing
 - satelite (ice) crystals
 - NCS
 - translational pseudo symmetry (detected elsewhere)
 - outliers (detected elsewhere)
 - ice rings (detected elsewhere)
 - other problems
 Note that the presence of abnormalities 
 in a certain region of reciprocal space might
 confuse the data validation algorithm throughout
 a large region of reciprocal space, even though
 the data is acceptable in those areas. 

Possible outliers 
  Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764

 Acentric reflections:

            None 

 Centric reflections:

            None 

Ice ring related problems

 The following statistics were obtained from ice-ring 
 insensitive resolution ranges 
  mean bin z_score      : 3.47
      ( rms deviation   : 2.83 )
  mean bin completeness : 0.99
     ( rms deviation   : 0.00 )

 The following table shows the z-scores 
 and completeness in ice-ring sensitive areas.
 Large z-scores and high completeness in these 
 resolution ranges might be a reason to re-assess
 your data processsing if ice rings were present.

------------------------------------------------
| d_spacing | z_score | compl. | Rel. Ice int. |
------------------------------------------------
|    3.897  |   0.12  |   0.97 |     1.000     |
|    3.669  |   0.96  |   0.95 |     0.750     |
|    3.441  |   2.14  |   0.94 |     0.530     |
------------------------------------------------

 Abnormalities in mean intensity or completeness at
 resolution ranges with a relative ice ring intensity
 lower then 0.10 will be ignored.

 At 3.67 A there is an lower occupancy
  then expected from the rest of the data set.
  Even though the completeness is lower as expected,
  the mean instensity is still reasonable at this resolution

 At 3.44 A there is an lower occupancy
  then expected from the rest of the data set.
  Even though the completeness is lower as expected,
  the mean instensity is still reasonable at this resolution

 There were  2 ice ring related warnings
 This could indicate the presence of ice rings.

Analyses of anomalous differences

  Table of measurability as a function of resolution

  The measurability is defined as the fraction of 
  Bijvoet related intensity differences for which 
  |delta_I|/sigma_delta_I > 3.0
  min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 
  holds. 
  The measurability provides an intuitive feeling
  of the quality of the data, as it is related to the 
  number of reliable Bijvoet differences.
  When the data is processed properly and the standard 
  deviations have been estimated accurately, values larger
  than 0.05 are encouraging. 

unused:         - 19.8704 [   0/68  ]
bin  1: 19.8704 -  7.0211 [1551/1585]  0.1924
bin  2:  7.0211 -  5.6142 [1560/1575]  0.0814
bin  3:  5.6142 -  4.9168 [1546/1555]  0.0261
bin  4:  4.9168 -  4.4729 [1563/1582]  0.0081
bin  5:  4.4729 -  4.1554 [1557/1577]  0.0095
bin  6:  4.1554 -  3.9124 [1531/1570]  0.0083
bin  7:  3.9124 -  3.7178 [1541/1585]  0.0069
bin  8:  3.7178 -  3.5569 [1509/1552]  0.0028
bin  9:  3.5569 -  3.4207 [1522/1606]  0.0085
bin 10:  3.4207 -  3.3032 [1492/1574]  0.0044
unused:  3.3032 -         [   0/0   ]

 The anomalous signal seems to extend to about 5.9 A
 (or to 5.2 A, from a more optimistic point of view)
 The quoted resolution limits can be used as a guideline
 to decide where to cut the resolution for phenix.hyss
 As the anomalous signal is not very strong in this dataset
 substructire solution via SAD might prove to be a challenge.
 Especially if only low resolution reflections are used,
 the resulting substructures could contain a significant amount of
 of false positives.

Basic analyses completed

##----------------------------------------------------##
##                   Twinning Analyses                ##
##----------------------------------------------------##

Using data between 10.00 to 3.66 Angstrom.

Determining possible twin laws.

The following twin laws have been found:

-------------------------------------------------------------------------------
| Type | Axis   | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law |
-------------------------------------------------------------------------------
|   M  | 2-fold | 0.000        | 0.000           | 0.000           | -h,k,-l  |
-------------------------------------------------------------------------------
M:  Merohedral twin law
PM: Pseudomerohedral twin law

  1 merohedral twin operators found
  0 pseudo-merohedral twin operators found
In total,   1 twin operator were found

Number of centrics  : 559
Number of acentrics : 10332

 Largest patterson peak with length larger then 15 Angstrom 

 Frac. coord.        :   0.027    0.057    0.345
 Distance to origin  :  17.444
 Height (origin=100) :   3.886
 p_value(height)     :   9.982e-01

   The reported p_value has the following meaning: 
     The probability that a peak of the specified height 
     or larger is found in a Patterson function of a 
     macro molecule that does not have any translational
     pseudo symmetry is equal to  9.982e-01 
     p_values smaller then 0.05 might indicate 
     weak translation pseudo symmetry, or the self vector of 
     a large anomalous scatterer such as Hg, whereas values 
     smaller then 1e-3 are a very strong indication for 
     the presence of translational pseudo symmetry.

Wilson ratio and moments 

Acentric reflections 
   <I^2>/<I>^2    :1.969   (untwinned: 2.000; perfect twin 1.500)
   <F>^2/<F^2>    :0.792   (untwinned: 0.785; perfect twin 0.885)
   <|E^2 - 1|>    :0.732   (untwinned: 0.736; perfect twin 0.541)

Centric reflections 
   <I^2>/<I>^2    :2.442   (untwinned: 3.000; perfect twin 2.000)
   <F>^2/<F^2>    :0.698   (untwinned: 0.637; perfect twin 0.785)
   <|E^2 - 1|>    :0.889   (untwinned: 0.968; perfect twin 0.736)

NZ test (0<=z<1) to detect twinning and possible translational NCS

-----------------------------------------------
|  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
-----------------------------------------------
| 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
| 0.1 |   0.086 |    0.095 |  0.179 |   0.248 |
| 0.2 |   0.171 |    0.181 |  0.301 |   0.345 |
| 0.3 |   0.251 |    0.259 |  0.363 |   0.419 |
| 0.4 |   0.322 |    0.330 |  0.438 |   0.474 |
| 0.5 |   0.395 |    0.394 |  0.488 |   0.520 |
| 0.6 |   0.452 |    0.451 |  0.537 |   0.561 |
| 0.7 |   0.505 |    0.503 |  0.576 |   0.597 |
| 0.8 |   0.553 |    0.551 |  0.608 |   0.629 |
| 0.9 |   0.591 |    0.593 |  0.635 |   0.657 |
| 1.0 |   0.632 |    0.632 |  0.664 |   0.683 |
-----------------------------------------------
| Maximum deviation acentric      :  0.011    |
| Maximum deviation centric       :  0.069    |
|                                             |
| <NZ(obs)-NZ(twinned)>_acentric  : -0.003    |
| <NZ(obs)-NZ(twinned)>_centric   : -0.031    |
-----------------------------------------------

 L test for acentric data

 using difference vectors (dh,dk,dl) of the form: 
(2hp,2kp,2lp)
  where hp, kp, and lp are random signed integers such that 
  2 <= |dh| + |dk| + |dl| <= 8 

  Mean |L|   :0.485  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.318  (untwinned: 0.333; perfect twin: 0.200)

  The distribution of |L| values indicates a twin fraction of
  0.00. Note that this estimate is not as reliable as obtained
  via a Britton plot or H-test if twin laws are available. 

---------------------------------------------
 Analysing possible twin law :  -h,k,-l
---------------------------------------------

Results of the H-test on a-centric data: 

 (Only 50.0% of the strongest twin pairs were used)

mean |H| : 0.458   (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.299   (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.042
Estimation of twin fraction via cum. dist. of H: 0.034

Britton analyses

  Extrapolation performed on  0.00 < alpha < 0.495 
  Estimated twin fraction: 0.011
  Correlation: 0.9990

R vs R statistic:
  R_abs_twin = <|I1-I2|>/<|I1+I2|>
  Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

   R_abs_twin observed data   : 0.457

  R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
   R_sq_twin observed data    : 0.297
  No calculated data available.
  R_twin for calculated data not determined.

Maximum Likelihood twin fraction determination
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.

   The estimated twin fraction is equal to 0.022

Exploring higher metric symmetry

The point group of data as dictated by the space group is P 4
  the point group in the niggli setting is Hall:  P 4 (z,x,y)
The point group of the lattice is Hall:  P 4 2 (z,x,y)
A summary of R values for various possible point groups follow.

-------------------------------------------------------------------------------------------
| Point group          | mean R_used | max R_used | mean R_unused | min R_unused | choice |
-------------------------------------------------------------------------------------------
| Hall:  P 4 (z,x,y)   | None        | None       | 0.457         | 0.457        | <---   |
| Hall:  P 4 2 (z,x,y) | 0.457       | 0.457      | None          | None         |        |
-------------------------------------------------------------------------------------------

R_used: mean and maximum R value for symmetry operators *used* in this point group
R_unused: mean and minimum R value for symmetry operators *not used* in this point group
 The likely point group of the data is:  Hall:  P 4 (z,x,y)

Possible space groups in this point groups are:
   Unit cell: (108.18, 108.18, 46.509, 90, 90, 90)
   Space group: P 41 (No. 76)

   Unit cell: (108.18, 108.18, 46.509, 90, 90, 90)
   Space group: P 43 (No. 78)

Note that this analyses does not take into account the effects of twinning.
If the data is (allmost) perfectly twinned, the symmetry will appear to be
higher than it actually is.

-------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
  - <I^2>/<I>^2 : 1.969
  - <F>^2/<F^2> : 0.792
  - <|E^2-1|>   : 0.732
  - 
, <L^2>: 0.485, 0.318
       Multivariate Z score L-test: 0.983 
       The multivariate Z score is a quality measure of the given
       spread in intensities. Good to reasonable data is expected
       to have a Z score lower than 3.5. 
       Large values can indicate twinning, but small values do not
       neccesarily exclude it. 

Statistics depending on twin laws
-----------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
-----------------------------------------------------------------
| -h,k,-l  |   M  | 0.457  | 0.011         | 0.034   | 0.022    |
-----------------------------------------------------------------

Patterson analyses
  - Largest peak height   : 3.886
   (correpsonding p value : 9.982e-01)

The largest off-origin peak in the Patterson function is 3.89% of the 
height of the origin peak. No significant pseudotranslation is detected.

The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.
Even though no twinning is suspected, it might be worthwhile carrying out 
a refinement using a dedicated twin target anyway, as twinned structures with
low twin fractions are difficult to distinguish from non-twinned structures.

-------------------------------------------------------------------------------
phenix.hyss /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz 2 se --molecular_weight=8000 --solvent_content=0.70
/net/rosie/scratch1/rwgk/dist/phenix/phenix/command_line/hyss.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx.array_family import flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
/net/rosie/scratch1/rwgk/dist/phenix/phenix/command_line/hyss.py:8: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
Command line arguments: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz 2 se --molecular_weight=8000 --solvent_content=0.70

------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: rwgk
------------------------------------------------------------------------------

                       HySS: Hybrid Substructure Search

------------------------------------------------------------------------------
Phenix developers include:
  P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung,
  T.R. Ioerger, A.J. McCoy, E.W. McKee, N.W. Moriarty, R.K. Pai, R.J. Read,
  T.D. Romo, J.C. Sacchettini, N.K. Sauter, J.N. Smith, L.C. Storoni,
  T.C. Terwilliger, P.H. Zwart
Phenix home page:
  http://www.phenix-online.org/
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library,
    CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
------------------------------------------------------------------------------

Reading reflection file: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEinfl,SIGFSEinfl,DSEinfl,SIGDSEinfl
Observation type: xray.reconstructed_amplitude
Type of data: double, size=22062
Type of sigmas: double, size=22062
Number of Miller indices: 22062
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 722
Resolution range: 28.2923 2.74876
Completeness in resolution range: 0.91753
Completeness with d_max=infinity: 0.916691
Bijvoet pairs: 10497
Lone Bijvoet mates: 346
Anomalous signal: 0.1065

Removing systematic absences:
Number of reflections: 22062

Removing zero or negative observations:
Number of reflections: 22062

************************
Anomalous signal: 0.1065
************************

Applying resolution limits: 15 3.24876
Number of reflections: 13427

Applying sigma cutoff: 1
Number of reflections: 13427

Computing anomalous differences
Number of reflections: 6391

Applying difference sigma cutoff: 0.5
Number of reflections: 5647

Applying rms outlier cutoff: 4
Number of reflections: 5641

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=5641
Type of sigmas: double, size=5641
Number of Miller indices: 5641
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24877
Completeness in resolution range: 0.753842
Completeness with d_max=infinity: 0.745277
Fraction of original data: 1/1.96 = 51.1%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEinfl,SIGF(+)SEinfl,F(-)SEinfl,SIGF(-)SEinfl
Observation type: xray.amplitude
Type of data: double, size=22062
Type of sigmas: double, size=22062
Number of Miller indices: 22062
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 722
Resolution range: 28.2923 2.74876
Completeness in resolution range: 0.91753
Completeness with d_max=infinity: 0.916691
Bijvoet pairs: 10497
Lone Bijvoet mates: 346
Anomalous signal: 0.1018

Removing systematic absences:
Number of reflections: 22062

Removing zero or negative observations:
Number of reflections: 22062

************************
Anomalous signal: 0.1018
************************

Applying resolution limits: 15 3.24876
Number of reflections: 13427

Applying sigma cutoff: 1
Number of reflections: 13427

Computing anomalous differences
Number of reflections: 6391

Applying difference sigma cutoff: 0.5
Number of reflections: 4511

Applying rms outlier cutoff: 4
Number of reflections: 4508

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=4508
Type of sigmas: double, size=4508
Number of Miller indices: 4508
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24877
Completeness in resolution range: 0.602432
Completeness with d_max=infinity: 0.595587
Fraction of original data: 1/2.45 = 40.9%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSElrm,SIGFSElrm,DSElrm,SIGDSElrm
Observation type: xray.reconstructed_amplitude
Type of data: double, size=22797
Type of sigmas: double, size=22797
Number of Miller indices: 22797
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 760
Resolution range: 28.2923 2.76136
Completeness in resolution range: 0.961007
Completeness with d_max=infinity: 0.960116
Bijvoet pairs: 10902
Lone Bijvoet mates: 233
Anomalous signal: 0.1019

Removing systematic absences:
Number of reflections: 22797

Removing zero or negative observations:
Number of reflections: 22797

************************
Anomalous signal: 0.1019
************************

Applying resolution limits: 15 3.26136
Number of reflections: 13953

Applying sigma cutoff: 1
Number of reflections: 13953

Computing anomalous differences
Number of reflections: 6676

Applying difference sigma cutoff: 0.5
Number of reflections: 5996

Applying rms outlier cutoff: 4
Number of reflections: 5993

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=5993
Type of sigmas: double, size=5993
Number of Miller indices: 5993
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.26151
Completeness in resolution range: 0.8114
Completeness with d_max=infinity: 0.802061
Fraction of original data: 1/1.9 = 52.6%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SElrm,SIGF(+)SElrm,F(-)SElrm,SIGF(-)SElrm
Observation type: xray.amplitude
Type of data: double, size=22797
Type of sigmas: double, size=22797
Number of Miller indices: 22797
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 760
Resolution range: 28.2923 2.76136
Completeness in resolution range: 0.961007
Completeness with d_max=infinity: 0.960116
Bijvoet pairs: 10902
Lone Bijvoet mates: 233
Anomalous signal: 0.0987

Removing systematic absences:
Number of reflections: 22797

Removing zero or negative observations:
Number of reflections: 22797

************************
Anomalous signal: 0.0987
************************

Applying resolution limits: 15 3.26136
Number of reflections: 13953

Applying sigma cutoff: 1
Number of reflections: 13953

Computing anomalous differences
Number of reflections: 6676

Applying difference sigma cutoff: 0.5
Number of reflections: 5023

Applying rms outlier cutoff: 4
Number of reflections: 5020

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=5020
Type of sigmas: double, size=5020
Number of Miller indices: 5020
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.26151
Completeness in resolution range: 0.679664
Completeness with d_max=infinity: 0.671842
Fraction of original data: 1/2.27 = 44%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEpeak,SIGFSEpeak,DSEpeak,SIGDSEpeak
Observation type: xray.reconstructed_amplitude
Type of data: double, size=23010
Type of sigmas: double, size=23010
Number of Miller indices: 23010
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 766
Resolution range: 29.664 2.74731
Completeness in resolution range: 0.955763
Completeness with d_max=infinity: 0.955049
Bijvoet pairs: 11010
Lone Bijvoet mates: 224
Anomalous signal: 0.1237

Removing systematic absences:
Number of reflections: 23010

Removing zero or negative observations:
Number of reflections: 23010

************************
Anomalous signal: 0.1237
************************

Applying resolution limits: 15 3.24731
Number of reflections: 14110

Applying sigma cutoff: 1
Number of reflections: 14110

Computing anomalous differences
Number of reflections: 6755

Applying difference sigma cutoff: 0.5
Number of reflections: 6167

Applying rms outlier cutoff: 4
Number of reflections: 6165

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=6165
Type of sigmas: double, size=6165
Number of Miller indices: 6165
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24736
Completeness in resolution range: 0.823097
Completeness with d_max=infinity: 0.813754
Fraction of original data: 1/1.87 = 53.6%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak
Observation type: xray.amplitude
Type of data: double, size=23010
Type of sigmas: double, size=23010
Number of Miller indices: 23010
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 766
Resolution range: 29.664 2.74731
Completeness in resolution range: 0.955763
Completeness with d_max=infinity: 0.955049
Bijvoet pairs: 11010
Lone Bijvoet mates: 224
Anomalous signal: 0.1207

Removing systematic absences:
Number of reflections: 23010

Removing zero or negative observations:
Number of reflections: 23010

************************
Anomalous signal: 0.1207
************************

Applying resolution limits: 15 3.24731
Number of reflections: 14110

Applying sigma cutoff: 1
Number of reflections: 14110

Computing anomalous differences
Number of reflections: 6755

Applying difference sigma cutoff: 0.5
Number of reflections: 5250

Applying rms outlier cutoff: 4
Number of reflections: 5246

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24766
Completeness in resolution range: 0.700494
Completeness with d_max=infinity: 0.692541
Fraction of original data: 1/2.19 = 45.6%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:FSEhrm,SIGFSEhrm,DSEhrm,SIGDSEhrm
Observation type: xray.reconstructed_amplitude
Type of data: double, size=25745
Type of sigmas: double, size=25745
Number of Miller indices: 25745
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 823
Resolution range: 29.664 2.66232
Completeness in resolution range: 0.972611
Completeness with d_max=infinity: 0.97195
Bijvoet pairs: 12399
Lone Bijvoet mates: 124
Anomalous signal: 0.1061

Removing systematic absences:
Number of reflections: 25745

Removing zero or negative observations:
Number of reflections: 25745

************************
Anomalous signal: 0.1061
************************

Applying resolution limits: 15 3.16232
Number of reflections: 15328

Applying sigma cutoff: 1
Number of reflections: 15328

Computing anomalous differences
Number of reflections: 7337

Applying difference sigma cutoff: 0.5
Number of reflections: 6426

Applying rms outlier cutoff: 4
Number of reflections: 6417

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=6417
Type of sigmas: double, size=6417
Number of Miller indices: 6417
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.16242
Completeness in resolution range: 0.790368
Completeness with d_max=infinity: 0.782084
Fraction of original data: 1/2.01 = 49.9%

Input Miller array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEhrm,SIGF(+)SEhrm,F(-)SEhrm,SIGF(-)SEhrm
Observation type: xray.amplitude
Type of data: double, size=25745
Type of sigmas: double, size=25745
Number of Miller indices: 25745
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 823
Resolution range: 29.664 2.66232
Completeness in resolution range: 0.972611
Completeness with d_max=infinity: 0.97195
Bijvoet pairs: 12399
Lone Bijvoet mates: 124
Anomalous signal: 0.1004

Removing systematic absences:
Number of reflections: 25745

Removing zero or negative observations:
Number of reflections: 25745

************************
Anomalous signal: 0.1004
************************

Applying resolution limits: 15 3.16232
Number of reflections: 15328

Applying sigma cutoff: 1
Number of reflections: 15328

Computing anomalous differences
Number of reflections: 7337

Applying difference sigma cutoff: 0.5
Number of reflections: 4867

Applying rms outlier cutoff: 4
Number of reflections: 4865

Final anomalous difference array:
Miller array info: None
Observation type: None
Type of data: double, size=4865
Type of sigmas: double, size=4865
Number of Miller indices: 4865
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.827 3.16335
Completeness in resolution range: 0.599803
Completeness with d_max=infinity: 0.59322
Fraction of original data: 1/2.65 = 37.8%

Selecting anomalous differences derived from this input array:
Miller array info: /net/cci-filer1/vol1/share/structure-lib/gere/data/gere_MAD.mtz:F(+)SEpeak,SIGF(+)SEpeak,F(-)SEpeak,SIGF(-)SEpeak
Observation type: xray.amplitude
Type of data: double, size=23010
Type of sigmas: double, size=23010
Number of Miller indices: 23010
Anomalous flag: True
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 766
Resolution range: 29.664 2.74731
Completeness in resolution range: 0.955763
Completeness with d_max=infinity: 0.955049
Bijvoet pairs: 11010
Lone Bijvoet mates: 224
Anomalous signal: 0.1207

The corresponding anomalous differences again:
Miller array info: Strongest anomalous signal: 0.121
Observation type: None
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24766
Completeness in resolution range: 0.700494
Completeness with d_max=infinity: 0.692541

#---------------------------------------------------------------------------#
| Formula for calculating the number of molecules given a molecular weight. |
|---------------------------------------------------------------------------|
| n_mol = ((1.0-solvent_content)*v_cell)/(molecular_weight*n_sym*.783)      |
#---------------------------------------------------------------------------#
Number of molecules: 6
Number of sites: 12
Values used in calculation:
  Solvent content: 0.70
  Unit cell volume: 476839
  Molecular weight: 8000.00
  Number of symmetry operators: 4

Writing anomalous differences as SHELX HKLF file: gere_MAD_anom_diffs.hkl

Writing SHELXD ins file: gere_MAD_anom_diffs.ins

Starting the search procedure (fast mode):

Miller array info: Strongest anomalous signal: 0.121
Observation type: None
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)

Transformation to Niggli cell: x-y,2*x,z
Miller array info: Primitive Niggli setting
Observation type: None
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (61.679, 62.5082, 71.652, 96.2161, 90, 119.562)
Space group: Hall:  C 2y (x-y,2*x,z) (No. 5)

Substructure parameter: n_sites: 12
Substructure parameter: min_cross_distance: 3.5
Substructure parameter: min_distance_sym_equiv: 3.5
Substructure parameter: general_positions_only: True
Substructure parameter: min_distance: 3.5
hyss: using shelxd.q_value_estimation
Search parameter: n_high_extrapolation_scan_correlation_group: 0
Search parameter: min_low_correlation: 0.1
Search parameter: n_chunk: 1
Search parameter: real_space_squaring: None
Search parameter: high_low_correlation_factor: 2
Search parameter: peak_search_effective_resolution: None
Search parameter: site_recycling_min_use: 0
Search parameter: n_candidate_sites: 11
Search parameter: n_use_sites: 8
Search parameter: enable_early_termination: True
Search parameter: n_recycling_cycles: 10
Search parameter: occupancy_minimization: True
Search parameter: site_recycling_candidate_factor: 0.9
Search parameter: truncate_consensus_model: True
Search parameter: n_patterson_vectors: 33
Search parameter: max_relative_spread_top_correlations: 0.1
Search parameter: n_sites_final_factor: 1.3
Search parameter: min_top_n_matches: 8
Search parameter: e_min: 1.5
Search parameter: p1_n_recycling_cycles: 10
Search parameter: cos_sin_table: True
Search parameter: n_fragments: 3
Search parameter: i_chunk: 0
Search parameter: site_recycling_use_heights_as_occupancies: False
Search parameter: factor_top_n_matches: 0.666666666667
Search parameter: n_sites_final: 16
Search parameter: site_recycling_use_factor: 0.666666666667
Search parameter: n_top_models_to_compare: 3
Search parameter: minimize_consensus_model: True
Search parameter: compare_sites_if_correlation_is_over: 0.2
Patterson: harker_plane_min_distance: 1.75
Patterson: keep_map: False
Patterson: origin_peak_removal: False
Patterson: grid_resolution_factor: 0.333333333333
Patterson: number of reflections: 5246
Patterson: suppressing peaks near Harker planes.
Patterson: map gridding: (60, 60, 72)
Patterson: map min: -13.66 sigma
Patterson: map max: 91.68 sigma
Two-site translation: grid_resolution_factor: 0.333333333333
Two-site translation: number of reflections: 5246
Tangent refinement: use_fixed_only: True
Tangent refinement: reuse_results: True
Tangent refinement: n_cycles: 1
Tangent refinement: fraction_fixed_phases: 0.4
Tangent refinement: number of reflections: 595
Tangent refinement: n_fixed: 238
Tangent refinement: n_variable: 357
Tangent refinement: time triplet generation: 0.02 seconds
Tangent refinement: number of triplet phase relations:
Tangent refinement:    min:  40
Tangent refinement:    max:  226
Tangent refinement:    mean: 106.02
Tangent refinement: total number of triplets: 63084
Tangent refinement: use_fixed_only: True
Tangent refinement: reuse_results: True
Tangent refinement: n_cycles: 1
Tangent refinement: fraction_fixed_phases: 0.4
Tangent refinement: number of reflections: 1190
Tangent refinement: n_fixed: 476
Tangent refinement: n_variable: 714
Tangent refinement: time triplet generation: 0.03 seconds
Tangent refinement: number of triplet phase relations:
Tangent refinement:    min:  40
Tangent refinement:    max:  226
Tangent refinement:    mean: 106.02
Tangent refinement: total number of triplets: 126168

Entering search loop:

p = peaklist index in Patterson map
f = peaklist index in two-site translation function
cc = correlation coefficient after extrapolation scan
r = number of dual-space recycling cycles
cc = final correlation coefficient

p=000 f=000 cc=0.241 r=010 cc=0.411 [ best cc: 0.411 ]
p=000 f=001 cc=0.237 r=010 cc=0.398 [ best cc: 0.411 0.398 ]
Number of matching sites of top 2 structures: 13
p=000 f=002 cc=0.182 r=010 cc=0.405 [ best cc: 0.411 0.405 0.398 ]
Number of matching sites of top 2 structures: 13
Number of matching sites of top 3 structures: 11

Top 3 correlations:
p=000 f=000 cc=0.241 r=010 cc=0.411
p=000 f=002 cc=0.182 r=010 cc=0.405
p=000 f=001 cc=0.237 r=010 cc=0.398
Match summary:
  Operator:
       rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}}
    translation: {-3.56175e-36, -0.224884, 0.5}
  rms coordinate differences: 0.27
  Pairs: 11
    site001 site004 0.158
    site002 site002 0.182
    site003 site003 0.110
    site004 site005 0.199
    site005 site001 0.145
    site006 site011 0.145
    site007 site007 0.240
    site008 site009 0.345
    site009 site008 0.589
    site010 site006 0.192
    site011 site010 0.333
  Singles model 1: 2
    site013   site014
  Singles model 2: 5
    site012   site013   site014   site015   site016

Minimizing consensus model (11 sites).
Correlation coefficient for consensus model (11 sites): 0.400

Search finished.

time_log: label: n accumulation delta average
time_log: patterson_peaks: 1 0.21 0.21 0.21
time_log: two_site_search: 1 0.12 0.12 0.12
time_log: extrapolation_scan: 3 0.31 0.1 0.103
time_log: p1_recycling: 3 1.70 0.55 0.567
time_log: p1_recycling q_large_calc: 30 0.02 0 0.000667
time_log: p1_recycling tangent_refinement: 30 0.20 0.01 0.00667
time_log: p1_recycling squaring: 0 0.00 0 0
time_log: p1_recycling fft_map: 30 0.40 0.01 0.0133
time_log: p1_recycling peak_search: 30 0.61 0.02 0.0203
time_log: p1_recycling random_omit: 30 0.01 0 0.000333
time_log: p1_recycling recover_origin: 3 0.43 0.14 0.143
time_log: p1_recycling combine_duplicates: 3 0.03 0.01 0.01
time_log: p1_recycling total: 3 1.70 0.55 0.567
p1_recycling time unaccounted for: 0.00
time_log: compute_correlation: 3 0.05 0.02 0.0167
time_log: q_large_calc: 27 0.00 0 0
time_log: tangent_refinement: 27 0.09 0 0.00333
time_log: squaring: 0 0.00 0 0
time_log: fft_map: 30 0.43 0.01 0.0143
time_log: peak_search: 30 0.93 0.04 0.031
time_log: random_omit: 27 0.00 0 0
time_log: minimization: 4 1.43 0.66 0.357
time_log: euclidean_model_matching: 2 0.33 0.2 0.165
time_log: hyss total: 1 6.25 6.25 6.25
time unaccounted for: 0.65

Storing all substructures found: gere_MAD_hyss_models.pickle

Storing consensus model: gere_MAD_hyss_consensus_model.pickle

Writing consensus model as PDB file: gere_MAD_hyss_consensus_model.pdb

Writing consensus model as CNS SDB file: gere_MAD_hyss_consensus_model.sdb

Writing consensus model as SOLVE xyz records: gere_MAD_hyss_consensus_model.xyz
The fractional coordinates may also be useful in other programs.

If HySS was helpful please cite:
  Acta Cryst. 2003, D59, 1966-1973
  http://cci.lbl.gov/publications/download/ba5048_reprint.pdf
See also:
  http://www.phenix-online.org/download/documentation/cci_apps/hyss/
For help enter:
  phenix.hyss --help

Send bug reports to: bugs@phenix-online.org
For help write to: help@phenix-online.org

Total CPU time: 7.57 seconds
iotbx.pdb.insert_scale_records /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb
grep SCALE3
libtbx.assert_stdin SCALE3      0.000000  0.000000  0.066667        0.00000
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.insert_scale_records.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.pdb.superpose_centers_of_mass /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb /net/rosie/scratch1/rwgk/dist/regression/pdb/phe.pdb reference.atom_selection=name ca other.atom_selection=name c output.file=tmp.pdb output.atom_selection=name c* --space_group=p4 --unit_cell=20,20,21
grep Rotation
libtbx.assert_stdin Rotation in fractional space: x,y,z
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.superpose_centers_of_mass.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
iotbx.pdb.as_xray_structure --symmetry=gere_MAD_anom_diffs.ins /net/cci-filer1/vol1/share/structure-lib/gere/sites/12_se.pdb --pickle=12_se
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/pdb.as_xray_structure.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import pdb
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/pdb/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
file_name: /net/cci-filer1/vol1/share/structure-lib/gere/sites/12_se.pdb
Number of scatterers: 12
At special positions: 0
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)

Writing all xray structures to file: 12_se.pickle

cctbx.euclidean_model_matching 12_se.pickle gere_MAD_hyss_consensus_model.pickle
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:3: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  from libtbx import easy_pickle
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:4: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  from scitbx.python_utils import dicts
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/command_line/euclidean_model_matching.py:5: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import euclidean_model_matching as emma
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional
Reference model:
Number of scatterers: 12
At special positions: 0
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)

Number of scatterers: 11
At special positions: 0
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)

Match summary:
  Operator:
       rotation: {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}
    translation: {-2.91523e-36, -0.242927, 0}
  rms coordinate differences: 0.53
  Pairs: 11
    PEAK369 site002 0.235
    PEAK937 site005 0.586
    PEAK1076 site010 0.776
    PEAK1482 site003 0.142
    PEAK1617 site004 0.254
    PEAK2021 site001 0.361
    PEAK2156 site008 0.267
    PEAK2551 site009 0.987
    PEAK2686 site007 0.266
    PEAK2951 site006 0.333
    PEAK3086 site011 0.822
  Singles model 1: 1
    PEAK504
  Singles model 2: 0

match_list: [11/11]
matches: frequency
   11:   1 = 100.0%, 100.0%

iotbx.reflection_file_reader gere_MAD_anom_diffs.hkl=amplitudes --symmetry=gere_MAD_hyss_consensus_model.pdb --pickle=gere_MAD_anom_diffs.pickle
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/command_line/reflection_file_reader.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  from iotbx import reflection_file_reader
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/mtz/__init__.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  import cctbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
/net/rosie/scratch1/rwgk/dist/scitbx/scitbx/array_family/flex.py:2: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.optional

file_name: gere_MAD_anom_diffs.hkl=amplitudes
file_type: shelx_hklf

Miller array info: gere_MAD_anom_diffs.hkl:Fobs,SigFobs
Observation type: xray.amplitude
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.15, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 14.9539 3.24766
Completeness in resolution range: 0.700494
Completeness with d_max=infinity: 0.692541

Writing all Miller arrays to file: gere_MAD_anom_diffs.pickle

libtbx.show_dist_paths phenix
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
phenix.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/heavy_search/pc_multi.py gere_MAD_anom_diffs.pickle gere_MAD_hyss_consensus_model.pickle
/net/rosie/scratch1/rwgk/dist/phenix/phenix/heavy_search/pc_multi.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import xray
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/xray/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/boost_adaptbx/boost/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
Miller array info: gere_MAD_anom_diffs.hkl:Fobs,SigFobs
Observation type: xray.amplitude
Type of data: double, size=5246
Type of sigmas: double, size=5246
Number of Miller indices: 5246
Anomalous flag: False
Unit cell: (108.742, 61.679, 71.652, 90, 97.15, 90)
Space group: C 1 2 1 (No. 5)

Number of scatterers: 11
At special positions: 0
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)

gere_MAD_hyss_consensus_model.pickle: correlation after site refinement: 0.393
gere_MAD_hyss_consensus_model.pickle: correlation after occupancy refinement: 0.394
gere_MAD_hyss_consensus_model.pickle: correlation after site+occupancy refinement: 0.394

u+s,u,s: 1.59 1.53 0.06
endif
rm -rf tst_pdb2xplor
mkdir tst_pdb2xplor
cd tst_pdb2xplor
cp /net/rosie/scratch1/rwgk/dist/regression/misc/1CL7I.pdb .
libtbx.show_dist_paths phenix
/net/rosie/scratch1/rwgk/dist/libtbx/libtbx/command_line/show_dist_paths.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  import libtbx.load_env
phenix.python /net/rosie/scratch1/rwgk/dist/phenix/phenix/pdb_tools/pdb2xplor.py .
/net/rosie/scratch1/rwgk/dist/phenix/phenix/__init__.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/libtbx': missing __init__.py
  try: import libtbx.forward_compatibility
/net/rosie/scratch1/rwgk/dist/phenix/phenix/foundation/Structure.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/phenix/phenix/foundation/Structure.py:7: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx/math': missing __init__.py
  import math
/net/rosie/scratch1/rwgk/dist/phenix/phenix/pdb_tools/pdb2xplor.py:10: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/iotbx': missing __init__.py
  import iotbx.xplor.map
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/ext.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/boost': missing __init__.py
  import boost.python
/net/rosie/scratch1/rwgk/dist/iotbx/iotbx/xplor/map.py:32: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/cctbx': missing __init__.py
  from cctbx import miller
/net/rosie/scratch1/rwgk/dist/cctbx/cctbx/array_family/flex.py:1: ImportWarning: Not importing directory '/net/rosie/scratch1/rwgk/dist/scitbx': missing __init__.py
  import scitbx.array_family.flex
________________________________________________________________________________
1CL7I.pdb
Class : PDBClass
     606 atoms
       0 bonds and 0 conect records
       0 angles
       0 diherals
       0 impropers
       0 residues
Minimum and maximum B-factors:   2.00  51.89
Minimum and maximum occupancies:   1.00   1.00
Scatterers: {'C': 381, 'S': 4, 'O': 121, 'N': 100}
[36.895000000000003, 39.993000000000002, 44.993000000000002]
Map gridding: (40, 45, 50)
Number of scatterers: 606
At special positions: 0
Unit cell: (36.895, 39.993, 44.993, 90, 90, 90)
Space group: P 1 (No. 1)
PDB # 0 in 0.152448177338 seconds
if ( ! -f 1CL7I.xplor ) then
cd ..
set time_end=`libtbx.seconds_since_the_epoch`
libtbx.seconds_since_the_epoch
echo print 'Total time tests: %.2f seconds' % (1151291364.82-1151290469.09)
python
Total time tests: 895.73 seconds