date
Mon Feb  2 23:56:55 PST 2009
cat /etc/fedora-release
Fedora Core release 3 (Heidelberg)
gcc -v | & tail -1
gcc version 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)
$BUILD_PYTHON_EXE -V
Python 2.3.4
libtbx.show_date_and_time -v
Date 2009-02-02 Time 23:56:55 PST -0800 (1233647815.21 s) Seconds since the Epoch 1233647815.21
libtbx.show_host_and_user
HOST = longnose.lbl.gov
HOSTTYPE = i386-linux
VENDOR = intel
USER = rwgk
PID = 2827
boost_adaptbx.show_platform_info
__FILE__ = /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/meta_ext.cpp
__DATE__ = Feb  2 2009
__TIME__ = 23:54:59
__i386__
__linux
__GNUC__ = 3
__GNUC_MINOR__ = 4
__GNUC_PATCHLEVEL__ = 2
boost::python::cxxabi_cxa_demangle_is_broken(): true
__GXX_WEAK__ = 1
__VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
PY_VERSION = 2.3.4
PYTHON_API_VERSION = 1012
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 4
sizeof(std::size_t) = 4
sizeof(void*) = 4
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 12
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
sizeof(PY_UNICODE_TYPE) = 4
gnu libc version: 2.3.3
number of processors: 4
sys.byteorder: little
import thread: OK
boost_adaptbx.int_overflow
Now adding int values 2147483647 + 1 ...
Result: -2147483648
Now adding long values 2147483647 + 1 ...
Result: -2147483648
if ( $status == 0 ) then
if ( $SKIP_TESTS != 0 ) then

libtbx.python $LIBTBX_DIST/run_tests.py
libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/test_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/utils.py
### HOST = longnose.lbl.gov
### HOSTTYPE = i386-linux
### VENDOR = intel
### USER = rwgk
### PID = 2838
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/pbs_utils.py
*** MY_PBS_ARRAY_SIZE = None
*** MY_PBS_ARRAYID_OFFSET = None
*** PBS_ARRAYID = None
*** OMPI_MCA_ns_nds_num_procs = None
*** OMPI_MCA_ns_nds_vpid = None
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/sge_utils.py
*** JOB_ID = None
*** SGE_ARCH = None
*** SGE_TASK_FIRST = None
*** SGE_TASK_LAST = None
*** SGE_TASK_ID = None
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/introspection.py
number of processors: 4
Virtual memory size: 7,061,504
Resident set size:   3,538,944
Stack size:          1,658,880
Virtual memory size: 7,061,504   approx. max: 11,063,296
Resident set size:   3,547,136   approx. max:  7,548,928
Stack size:          1,658,880   approx. max:  1,658,880
Memory total:  2,122,080,256
Memory free:     259,272,704
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/thread_utils.py
multiprocessing requires Python >= 2.6 - skipping these tests.
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/easy_run.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_math_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/assert_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/str_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/table_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_dlite.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst_tokenizer.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/phil/tst.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_object_oriented_patterns.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/libtbx/tst_itertbx.py
OK

libtbx.python $BOOST_ADAPTBX_DIST/run_tests.py
libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py
show_stack(1): /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py(7) run
show_stack(2): /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_libc_backtrace.py(13) ?
libc backtrace (20 frames, most recent call last):
  /usr/bin/python [0x8048501]
  /lib/tls/libc.so.6(__libc_start_main+0xe3) [0xac4e33]
  /usr/bin/python(main+0x2a) [0x80485b2]
  /usr/lib/libpython2.3.so.1.0(Py_Main+0x578) [0xc9c68e]
  /usr/lib/libpython2.3.so.1.0(PyRun_AnyFileExFlags+0x6e) [0xc97994]
  /usr/lib/libpython2.3.so.1.0(PyRun_SimpleFileExFlags+0x185) [0xc96942]
  /usr/lib/libpython2.3.so.1.0 [0xc95817]
  /usr/lib/libpython2.3.so.1.0(PyEval_EvalCode+0x63) [0xc7c362]
  /usr/lib/libpython2.3.so.1.0(PyEval_EvalCodeEx+0x679) [0xc7c09e]
  /usr/lib/libpython2.3.so.1.0 [0xc7b97b]
  /usr/lib/libpython2.3.so.1.0 [0xc79b7f]
  /usr/lib/libpython2.3.so.1.0(PyObject_Call+0x33) [0xc24607]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so [0xf6eceb7f]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(bool boost::python::handle_exception<boost::python::objects::(anonymous namespace)::bind_return>(boost::python::objects::(anonymous namespace)::bind_return)+0x5d) [0xf6ecfa51]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x41) [0xf6ed6b71]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::function0<void>::operator()() const+0x9a) [0xf6ed7642]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&)+0x25) [0xf6ecf9dd]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0x150) [0xf6eccc80]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so(boost::python::objects::caller_py_function_impl<boost::python::detail::caller<bool (*)(int), boost::python::default_call_policies, boost::mpl::vector2<bool, int> > >::operator()(_object*, _object*)+0x89) [0xf6f04755]
  /net/longnose/scratch1/rwgk/auto_build/build/lib/boost_python_meta_ext.so((anonymous namespace)::boost_adptbx_libc_backtrace(int)+0x54) [0xf6efe0ec]
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_rational.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_rational_truediv.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_optional.py
exercise_wstring: <Boost.Python.function object at 0x8f4b8f0>
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_std_pair.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/boost_adaptbx/tst_tuple.py
OK

libtbx.python $OMPTBX_DIST/tst.py
omptbx.have_stubs_h
omtbx.omp_version: None
OK
libtbx.python $SCITBX_DIST/run_tests.py
/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_1
Total OK: 511

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_2
Total OK: 268

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_3
Total OK: 164

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_4
Total OK: 1420

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_af_5
Total OK: 23

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_vec3
Total OK: 67

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_unsigned_float_arithmetic
OK

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat3
Total OK: 82

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_sym_mat3
Total OK: 71

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_mat_ref
Total OK: 60

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/array_family/tst_accessors
Total OK: 1729

/net/longnose/scratch1/rwgk/auto_build/build/scitbx/serialization/tst_base_256
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/error/tst_error.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_map.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_set.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/stl/tst_vector.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/regression_test.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_flex.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_smart_selection.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_shared.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_integer_offsets_vs_pointers.py
data_size = 1000 n_repeats = 30000
  use_pointers = False
    use_iterators = 0 time = 0.11 s overhead = 0.00 s (d[p[i]] 0)
    use_iterators = 1 time = 0.11 s overhead = 0.00 s (d[*p++] 0)
  use_pointers = True
    use_iterators = 0 time = 0.11 s overhead = 0.00 s (*dp[i]  0)
    use_iterators = 1 time = 0.14 s overhead = 0.00 s (**dpi++ 0)
    use_iterators = 2 time = 0.12 s overhead = 0.00 s (**dpp++ 0)
data_size = 10000 n_repeats = 3000
  use_pointers = False
    use_iterators = 0 time = 0.12 s overhead = 0.00 s (d[p[i]] 1.8651e-11)
    use_iterators = 1 time = 0.12 s overhead = 0.00 s (d[*p++] 1.8651e-11)
  use_pointers = True
    use_iterators = 0 time = 0.12 s overhead = 0.00 s (*dp[i]  1.8651e-11)
    use_iterators = 1 time = 0.17 s overhead = 0.00 s (**dpi++ 1.8651e-11)
    use_iterators = 2 time = 0.12 s overhead = 0.00 s (**dpp++ 1.8651e-11)
data_size = 100000 n_repeats = 300
  use_pointers = False
    use_iterators = 0 time = 1.76 s overhead = 0.00 s (d[p[i]] 2.13122e-11)
    use_iterators = 1 time = 1.76 s overhead = 0.00 s (d[*p++] 2.13122e-11)
  use_pointers = True
    use_iterators = 0 time = 1.74 s overhead = 0.00 s (*dp[i]  2.13122e-11)
    use_iterators = 1 time = 1.75 s overhead = 0.00 s (**dpi++ 2.13122e-11)
    use_iterators = 2 time = 1.74 s overhead = 0.00 s (**dpp++ 2.13122e-11)
data_size = 1000000 n_repeats = 30
  use_pointers = False
    use_iterators = 0 time = 3.64 s overhead = 0.01 s (d[p[i]] 2.132e-10)
    use_iterators = 1 time = 3.63 s overhead = 0.01 s (d[*p++] 2.132e-10)
  use_pointers = True
    use_iterators = 0 time = 3.60 s overhead = 0.01 s (*dp[i]  2.132e-10)
    use_iterators = 1 time = 3.57 s overhead = 0.01 s (**dpi++ 2.132e-10)
    use_iterators = 2 time = 3.58 s overhead = 0.01 s (**dpp++ 2.132e-10)
data_size = 10000000 n_repeats = 3
  use_pointers = False
    use_iterators = 0 time = 4.45 s overhead = 0.13 s (d[p[i]] -2.15565e-10)
    use_iterators = 1 time = 4.45 s overhead = 0.13 s (d[*p++] -2.15565e-10)
  use_pointers = True
    use_iterators = 0 time = 4.48 s overhead = 0.13 s (*dp[i]  -2.15565e-10)
    use_iterators = 1 time = 4.49 s overhead = 0.13 s (**dpi++ -2.15565e-10)
    use_iterators = 2 time = 4.52 s overhead = 0.13 s (**dpp++ -2.15565e-10)
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/array_family/boost_python/tst_cost_of_m_handle_in_af_shared.py
Loop over af::shared<double>:
data_size=1000, n_repeats=30000
size+begin inside  loop: 0.42 s
     begin outside loop: 0.37 s
size+begin outside loop: 0.08 s

data_size=10000, n_repeats=3000
size+begin inside  loop: 0.42 s
     begin outside loop: 0.37 s
size+begin outside loop: 0.08 s

data_size=100000, n_repeats=300
size+begin inside  loop: 0.45 s
     begin outside loop: 0.40 s
size+begin outside loop: 0.26 s

data_size=1000000, n_repeats=30
size+begin inside  loop: 0.45 s
     begin outside loop: 0.39 s
size+begin outside loop: 0.26 s

data_size=10000000, n_repeats=3
size+begin inside  loop: 0.60 s
     begin outside loop: 0.41 s
size+begin outside loop: 0.26 s

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/matrix.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils/tst_random_transform.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/python_utils/tst_graph.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_math.py
time_eigensystem_real_symmetric: 5.311 micro seconds
Testing compatibility of cmath_lgamma and slatec_dlngam... OK
unimodular range 0: count=0, time=0.00 s
unimodular range 1: count=3480, time=0.00 s
unimodular range 2: count=67704, time=0.01 s
unimodular range 3: count=640824, time=0.20 s
unimodular range 4: count=2597208, time=1.42 s
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_r3_rotation.py
times unit quaternion <-> matrix
     py: 0.60 0.46 s
    c++: 0.25 0.26 s
  ratio: 2.43 1.72
u+s,u,s: 27.30 27.24 0.06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_resample.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_line_search.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_gaussian.py
u+s,u,s: 62.26 62.06 0.20

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_quadrature.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/boost_python/tst_halton.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_euler_angles.py
u+s,u,s: 6.05 5.99 0.06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/tst_superpose.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/sieve_of_eratosthenes.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/besselk.py
0.01 1.81901 1.81896284761 0.00259220079084
0.05 1.27752 1.27753829116 0.00143177079474
0.1 0.987739 0.986282193922 0.147488970054
0.5 -0.0404925 -0.0405939006888 0.250418444942
5.0 -5.5961 -5.59611201899 0.000214774434398
50 -51.7321 -51.65017 0.158373621021

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/math/scale_curves.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/minpack/tst.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgs/boost_python/tst_lbfgs.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/lbfgsb/boost_python/tst_lbfgsb.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/fftpack/boost_python/tst_fftpack.py
usr+sys time: 5.88 seconds
wall clock time: 5.88 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/flex_grid.py
grid = grid over N-dim box (but there is not array with data!)

origin = N-dim indices of lower-left corner of box
 focus = N-dim indices of upper-right corner of box as we want to use it
  last = N-dim indices of upper-right corner of box as actually allocated
   all = actual number or grid points to be allocated in each dimension

Motivation for focus/last distinction:
  padding required by real-to-complex FFT algorithms

origin: (0, 0, 0)
 focus: (3, 4, 6)
  last: (3, 4, 6)
   all: (3, 4, 6)

origin: (0, 0, 0)
 focus: (3, 4, 5)
  last: (3, 4, 6)
   all: (3, 4, 6)

origin: (-2, -3, -4)
 focus: (3, 4, 6)
  last: (3, 4, 6)
   all: (5, 7, 10)

origin: (-2, -3, -4)
 focus: (3, 4, 5)
  last: (3, 4, 6)
   all: (5, 7, 10)

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/flex_array_loops.py
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/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/principal_axes_of_inertia.py
(7.7966923076923074, 1.3650769230769233, 8.3576923076923073)
(38.140037692307693, 97.025267538461534, 79.022219692307701, -19.808558307692309, 35.142585230769235, 7.6620366923076908)
[104.22746487361263, 97.266425913775308, 12.69363413568899]
[-0.43905397167468402, 0.82221243371028996, -0.36221309171382515, 0.30372167962370772, 0.5152398514117883, 0.80142437999084604, 0.84556770946106941, 0.241856588434883, -0.47594184450140542]

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbfgs_recipe.py
refinery
compute_functional_and_gradients
callback_after_step
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/lbfgs_linear_least_squares_fit.py
fit.slope: -3.14104556668
fit.y_intercept: 1.78306795976
 x_obs  y_obs y_calc  diff
  1.00  -1.33  -1.36   0.02
  2.00  -4.47  -4.50   0.03
  3.00  -7.67  -7.64  -0.03
  4.00 -10.82 -10.78  -0.04
  5.00 -13.94 -13.92  -0.02
  6.00 -17.05 -17.06   0.02
  7.00 -20.20 -20.20   0.00
  8.00 -23.35 -23.35  -0.00
  9.00 -26.51 -26.49  -0.02
 10.00 -29.59 -29.63   0.04

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/chebyshev_lsq_example.py
Trying to determine the best number of terms 
 via cross validation techniques

Fitting with 12 terms

Least Squares residual: 1.988586
  R2-value            : 0.005655

Maximum deviation between fitted and error free data:
    0.180
Mean deviation between fitted and error free data:
    0.035

Maximum deviation between fitted and observed data:
    0.259
Mean deviation between fitted and observed data:
    0.121

Showing 10 points
   x    y_obs y_ideal y_fit
 0.010  1.282  1.195  1.252
 0.099  1.936  2.061  2.015
 0.188  0.832  0.814  0.817
 0.277  0.634  0.448  0.495
 0.366  2.046  2.025  2.037
 0.455  2.386  2.322  2.265
 0.545  1.221  0.980  1.024
 0.634  1.128  1.301  1.317
 0.723  2.798  2.931  2.892
 0.812  2.506  2.646  2.623
Preparing output for loggraph in a file called
   chebyshev.loggraph

Coefficients from weighted lsq
[4.5241402338890762, -2.0680091197226163, 0.12850863418067884, 0.19943100844005027, -0.090172144930261947]
Coefficients from non-weighted lsq
[3.4207285988126821, -0.97279683238298753, -1.3518557377924003, 1.6668999570374963, -1.4294103076327269]

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/immoptibox_ports.py
u+s,u,s: 38.15 38.07 0.08

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/examples/rigid_body_refinement_core.py
an ea: [0.0, 0.0, 0.0]
fd ea: [2.9856131013692537e-15, 8.4825039313388431e-16, 3.9566375143884119e-15]
an lt: [-0.0, -0.0, -0.0]
fd lt: [0.0, 0.0, 0.0]

an ea: [1.4293798315070272, -4.7699199336056015, -3.2848275925325994]
fd ea: [1.4293798322739804, -4.769919932368083, -3.2848275930419391]
an lt: [-2.6395370381698946, 3.8546779254822816, -3.7648774634679576]
fd lt: [-2.6395370360532411, 3.8546779257409014, -3.7648774640075544]

an ea: [-4.3864544713398521, 2.184889943611112, 5.0802158076235786]
fd ea: [-4.386454465432621, 2.1848899418586143, 5.0802158071405756]
an lt: [-4.6881328246835459, -10.874759921610867, -1.9393316543209451]
fd lt: [-4.6881328277237344, -10.874759922785415, -1.939331655265164]

an ea: [-5.0974589936941621, 2.0225151159319288, 4.4791032612277393]
fd ea: [-5.0974589882457622, 2.0225151171615607, 4.4791032607349734]
an lt: [-2.8154365578392593, -5.1570857812151694, -17.014046644874664]
fd lt: [-2.8154365576682494, -5.1570857788618696, -17.014046648000658]

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidity.py
double banana 3D dof (method=integer): 7
double banana 3D dof (method=float): 7

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_rigidity.py
repeat_log = {0: 85}
u+s,u,s: 3.73 3.71 0.02

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/rigidity_matrix_symbolic.py
u+s,u,s: 4.12 4.10 0.02

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/graph/tst_tardy_tree.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/essence/tst_basic.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/essence/tst_molecules.py
OK
usr+sys time: 11.04 seconds
wall clock time: 11.03 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/free_motion_reference_impl.py
e_kin tot ang lin: 0.0406605941304 0.0123105941304 0.02835
            e_pot: 0.64030878777
            e_tot: 0.680969381901
ang acc 3D: (0.44994052436717469, -0.22736369685250066, -0.68597630003289267)
lin acc 3D: (0.2108121283092794, 0.30448143672384792, -0.78243114289474458)

e_kin tot ang lin: 0.0433343867202 0.012335145794 0.0309992409262
            e_pot: 0.637520443168
            e_tot: 0.680854829888
ang acc 3D: (0.44915232838243152, -0.2233952828755118, -0.68836460903992402)
lin acc 3D: (0.20633054106767029, 0.30220128126092538, -0.78277910770482562)

e_kin tot ang lin: 0.0462449163781 0.0123908412125 0.0338540751655
            e_pot: 0.63449664984
            e_tot: 0.680741566218
ang acc 3D: (0.4482905223840879, -0.21934640631607011, -0.69061975198037251)
lin acc 3D: (0.20168867739512958, 0.29980890029936302, -0.78300792706075406)

e_kin tot ang lin: 0.0493898546021 0.0124776322264 0.0369122223756
            e_pot: 0.631239827538
            e_tot: 0.680629682141
ang acc 3D: (0.44735466644443667, -0.21521902126722914, -0.69274095848332595)
lin acc 3D: (0.19688964121862268, 0.29730414639378616, -0.78311556045599717)

e_kin tot ang lin: 0.0527666878789 0.0125954480796 0.0401712397993
            e_pot: 0.627752580076
            e_tot: 0.680519267955
ang acc 3D: (0.4463443200247767, -0.21101512397560779, -0.69472747655310196)
lin acc 3D: (0.19193669414908759, 0.29468687861617315, -0.78309994846029196)

e_kin tot ang lin: 0.0563727196994 0.0127441954807 0.0436285242187
            e_pot: 0.624037693245
            e_tot: 0.680410412944
ang acc 3D: (0.44525904268397543, -0.2067367517215091, -0.69657857317890515)
lin acc 3D: (0.18683325327725137, 0.29195696483157874, -0.78295901594034689)

e_kin tot ang lin: 0.0602050727137 0.0129237586762 0.0472813140375
            e_pot: 0.620098132599
            e_tot: 0.680303205313
ang acc 3D: (0.44409839480429714, -0.20238598167333133, -0.6982935349568492)
lin acc 3D: (0.18158288880693388, 0.2891142841060344, -0.7826906753299725)

e_kin tot ang lin: 0.0642606910252 0.0131339995361 0.0511266914891
            e_pot: 0.615937041095
            e_tot: 0.68019773212
ang acc 3D: (0.4428619383337592, -0.19796492971649071, -0.69987166872353157)
lin acc 3D: (0.17618932152521946, 0.28615872924108982, -0.78229282994446914)

e_kin tot ang lin: 0.0685363426208 0.013374757653 0.0551615849678
            e_pot: 0.611557736598
            e_tot: 0.680094079218
ang acc 3D: (0.4415492375442347, -0.19347574925710581, -0.70131230220025587)
lin acc 3D: (0.17065642010895676, 0.2830902094290727, -0.78176337733399448)

e_kin tot ang lin: 0.0730286219358 0.0136458504521 0.0593827714837
            e_pot: 0.606963709255
            e_tot: 0.679992331191
ang acc 3D: (0.44015985980451133, -0.18892063000069204, -0.70261478464703297)
lin acc 3D: (0.16498819826718966, 0.27990865302275331, -0.78110021267068175)

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_featherstone.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_free_motion.py
u+s,u,s: 1.29 1.23 0.06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_free_motion_hard.py
OK
usr+sys time: 5.41 seconds
wall clock time: 5.41 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_joint_lib.py
OK
usr+sys time: 4.17 seconds
wall clock time: 4.17 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_singular.py
OK
usr+sys time: 15.15 seconds
wall clock time: 15.14 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_spherical_refinement.py
OK
usr+sys time: 2.38 seconds
wall clock time: 2.37 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/rigid_body/proto/tst_molecules.py
OK
usr+sys time: 10.54 seconds
wall clock time: 10.54 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests/tst_sparse.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/sparse/tests/tst_lu_factorization.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/scitbx/iso_surface/tst_iso_surface.py
u+s,u,s: 34.91 34.84 0.07

( cd tst_featherstone_tmpdir ; "$TST_FEATHERSTONE_PYTHON" tst_featherstone.py )
libtbx.test_utils not available: approx_equal() disabled
OK
libtbx.python $SCITBX_DIST/rigid_body/essence/make_bundles.py
( cd scitbx_rigid_body_essence ; "$TST_FEATHERSTONE_PYTHON" tst_basic.py )
libtbx.test_utils not available: approx_equal() disabled
OK
libtbx.python $FFTW3TBX_DIST/tst_ext.py
Skipping fftw3tbx tests: Python extension not available.
usr+sys time: 0.75 seconds
wall clock time: 0.75 seconds
libtbx.python $CCTBX_DIST/run_tests.py --Quick
libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_aniso_restraints.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/math/boost_python/tst_math.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_python/tst_f_model.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/array_family/boost_python/tst_flex.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_python/tst_uctbx.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/uctbx/boost_python/tst_crystal_orientation.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_python/tst_sgtbx.py
u+s,u,s: 8.82 8.64 0.18

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/boost_python/tst_N_fold_rot.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/crystal/tst_ext.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/adptbx/boost_python/tst_adptbx.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/miller/boost_python/tst_miller.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_chemical_elements.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_xray_scattering.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_henke.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_icsd_radii.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_neutron.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_sasaki.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_tiny_pse.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/eltbx/boost_python/tst_wavelengths.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/xray/boost_python/tst_xray.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/boost_python/tst_maptbx.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/dmtbx/boost_python/tst_dmtbx.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/translation_search/boost_python/tst_translation_search.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_restraints/tst_ext.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/geometry_restraints/tst_proxy_registry.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/adp_restraints/tst_ext.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_math_module.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_krivy_gruber.py --Quick
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx.py
u+s,u,s: 7.62 7.53 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_itvb_2001_table_a1427_hall_symbols.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_space_group_type_tidy_cb_op_t.py
P 4 (No. 75)
P 31 1 2 (No. 151)
  cb_op=x-y,-y,-z -> P 31 1 2 (a,b,c+1/6)
  cb_op=-y,x-y,z -> P 31 1 2 (a,b,c+1/6)
  cb_op=-y,-x,-z -> P 31 1 2 (a,b,c+1/3)
  cb_op=y,x,-z -> P 31 1 2 (a,b,c+1/3)
  cb_op=-x+y,-x,z -> P 31 1 2 (a,b,c+1/3)
  cb_op=x-y,x,z -> P 31 1 2 (a,b,c+1/3)
  cb_op=-x+y,y,-z -> P 31 1 2 (a,b,c+1/6)
  cb_op=y,-x+y,z -> P 31 1 2 (a,b,c+1/6)
u+s,u,s: 6.71 6.65 0.06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_denominators.py P31
P 31
u+s,u,s: 0.53 0.46 0.07
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_subgroups.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_lattice_symmetry.py
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: 27.59 27.53 0.06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_constraints.py P3
P 3
u+s,u,s: 0.92 0.84 0.08

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_adp_constraints_cartesian.py
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
I 4/m c m (a+b-1/6,-a+b,c+1/4)
u+s,u,s: 1.06 0.96 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_site_constraints.py
u+s,u,s: 9.17 9.05 0.12

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_reflection_statistics.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sgtbx_harker.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_twin_target.py
u+s,u,s: 117.19 117.07 0.12

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/symbol_confidence.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/bravais_types.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_lookup_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal.py I41/acd
I 41/a c d :2
u+s,u,s: 1.14 1.04 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_direct_space_asu.py I41/acd
I 41/a c d :2
u+s,u,s: 8.40 8.27 0.13

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_pair_asu_table.py
u+s,u,s: 5.48 5.37 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal_asu_clusters.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_coordination_sequences.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_crystal_close_packing.py R-3mr
time groel_sampling: 3.13 seconds
R -3 m :R
u+s,u,s: 5.43 5.33 0.10
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray.py I41/acd
I 41/a c d :2
u+s,u,s: 17.08 16.97 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_structure_factors_multithread.py
omptbx.have_stubs_h
Skipping raw multithreaded structure factor computation tests
usr+sys time: 1.35 seconds
wall clock time: 1.35 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller.py P31
P 31
u+s,u,s: 11.45 10.86 0.59
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_reciprocal_space_asu.py P312
P 3 1 2
u+s,u,s: 0.94 0.86 0.08

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_triplet_generator.py P41
P 41
u+s,u,s: 1.05 0.96 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_emma.py P31
P 31
u+s,u,s: 3.28 3.18 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_find_centre_of_inversion.py P31
P 31
u+s,u,s: 1.13 1.04 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_expand_to_p1.py P31
P 31
u+s,u,s: 1.03 0.93 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_change_basis.py P31
P 31
u+s,u,s: 1.24 1.14 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_wilson_plot.py P31
P 31
u+s,u,s: 1.41 1.31 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_target_functors.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_derivatives.py P31
P 31
u+s,u,s: 9.05 8.91 0.14

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_fast_gradients.py P31
P 31
from_scatterers_direct:  4 calls, 0.12 s
from_scatterers_fft:    15 calls, 0.68 s
gradients_direct:       23 calls, 1.04 s
gradients_fft:           2 calls, 0.21 s
usr+sys time: 4.95 seconds
wall clock time: 4.95 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_minimization.py --F P31
Refinement against F
P 31
u+s,u,s: 30.69 30.48 0.21

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_xray_minimization.py --F_sq P31
Refinement against F^2
P 31
u+s,u,s: 13.00 12.87 0.13

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/maptbx/tst_real_space_refinement.py
u+s,u,s: 10.32 10.21 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_maptbx_structure_factors.py P31
P 31
u+s,u,s: 1.22 1.11 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_merge_equivalents.py P31
P 31
u+s,u,s: 1.10 0.99 0.11
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_grouped_data.py P31
P 31
u+s,u,s: 0.96 0.87 0.09
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_miller_fft_map.py P31
P 31
u+s,u,s: 2.14 2.02 0.12

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_sampled_model_density.py P31
P 31
usr+sys time: 5.55 seconds
wall clock time: 5.55 seconds

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_fast_nv1995.py F222
F 2 2 2
u+s,u,s: 1.52 1.43 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints_lbfgs.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_geometry_restraints_2.py
u+s,u,s: 4.09 3.93 0.16

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/make_cns_input.py P31
P 31
u+s,u,s: 1.03 0.94 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/tst_cns_epsilon.py P31
CNS not available.

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/tst_cns_hl.py P31
CNS not available.

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/development/run_shelx.py P31
SHELX not available.

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_pointgroup_tools.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/sub_lattice_tools.py
u+s,u,s: 1.14 1.06 0.08

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rational_matrices_point_groups.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/cosets.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_find_best_cell.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/regression/tst_normalised_amplitudes.py
OK

libtbx.python $CCTBX_DIST/run_examples.py --Quick
/net/longnose/scratch1/rwgk/auto_build/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/longnose/scratch1/rwgk/auto_build/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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/getting_started.py
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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/space_group_matrices.py P31
Space group: P 31 (No. 144)
  [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0]
  [0.0, -1.0, 0.0, 1.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.33333333333333331]
  [-1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.66666666666666663]

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/space_subgroups.py
Usage: cctbx.python space_subgroups.py max_index space_group_symbol
  Example: cctbx.python space_subgroups.py 2 P41212

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/trigonal_r_vs_tetragonal_i.py
This is the "tetragonal I" setting humans like:
Unit cell: (10, 10, 13, 90, 90, 90)
Space group: I 4 (No. 79)

Exact same symmetry, but using a basis system that is not very
accessible to humans:
Change of basis: y+z,x+z,x+y
Unit cell: (9.60469, 9.60469, 9.60469, 117.258, 117.258, 94.8191)
Space group: I 4 (y+z,x+z,x+y) (No. 79)

This is the "trigonal R" setting most humans like best:
Unit cell: (10, 10, 13, 90, 90, 120)
Space group: R 3 :H (No. 146)

Same symmetry, sometimes preferred:
Change of basis: x+z,-x+y+z,-y+z
Unit cell: (7.2188, 7.2188, 7.2188, 87.6782, 87.6782, 87.6782)
Space group: R 3 :R (No. 146)

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/quartz_structure.py
Number of scatterers: 2
At special positions: 2
Unit cell: (5.01, 5.01, 5.47, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
Si   Si     3 ( 0.5000  0.5000  0.3333) 1.00 0.2000 [ - ]
O    O      6 ( 0.1970 -0.1970  0.8333) 1.00 0.0000 [ - ]
Si:   0.5000   0.5000   0.3333
  point group type: 222
  special position operator: 1/2,1/2,1/3
O:   0.1970  -0.1970   0.8333
  point group type: 2
  special position operator: 1/2*x-1/2*y,-1/2*x+1/2*y,5/6
Miller array info: None
Observation type: None
Type of data: complex_double, size=7
Type of sigmas: None
Number of Miller indices: 7
Anomalous flag: False
Unit cell: (5.01, 5.01, 5.47, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
(1, 0, 0) (-11.346254184-1.26748373152e-15j)
(1, 0, 1) (-15.047826184-26.0635994942j)
(1, 0, 2) (1.61727835827-2.80120828651j)
(1, 1, 0) (-12.7983511271-5.60868616295e-16j)
(1, 1, 1) (5.52967787492-9.57768302885j)
(2, 0, 0) (-2.43055830372+0j)
(2, 0, 1) (4.96775720735+8.6044078828j)
(1, 0, 0) 4.33878727296
(1, 0, 1) 3.39927502294
(1, 0, 2) 2.31368408207
(1, 1, 0) 2.505
(1, 1, 1) 2.27753582331
(2, 0, 0) 2.16939363648
(2, 0, 1) 2.01658808355
(1, 0, 0) (-11.346254184-1.26748373152e-15j)
(1, 0, 1) (-15.047826184-26.0635994942j)
(1, 1, 0) (-12.7983511271-5.60868616295e-16j)

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/analyze_adp.py
Input Ucif: (0.17000000000000001, 0.17000000000000001, 0.19, 0.089999999999999997, 0, 0)
Warning: ADP tensor is incompatible with site symmetry.
Averaged Ucif: (0.16666666666666669, 0.16666666666666669, 0.19, 0.083333333333333343, 0.0, 0.0)
Eigenvectors and values:
  v=(0.00000 -0.00000 1.00000)  lambda=0.1900
  v=(0.85089 -0.52534 -0.00000)  lambda=0.1667
  v=(0.52534 0.85089 0.00000)  lambda=0.1667

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/g_exp_i_partial_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_exp_i_alpha_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_g_exp_i_alpha_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_2.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_3.py P31
P 31
u+s,u,s: 23.34 23.24 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_structure_factor_derivatives_4.py --tag=internal
P 1
strudat tag: EDI
u+s,u,s: 16.58 16.49 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/site_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/u_star_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/sites_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/structure_factor_calculus/sites_least_squares_derivatives.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/all_axes.py P31
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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/tst_phase_o_phrenia.py P2
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, Ustar as 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: 1.01 0.90 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/map_skewness.py
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, 2.66
fudge factor, phase difference, map skewness: 0.10,  8.75, 2.526
fudge factor, phase difference, map skewness: 0.20, 18.34, 2.182
fudge factor, phase difference, map skewness: 0.30, 26.87, 1.666
fudge factor, phase difference, map skewness: 0.40, 35.17, 1.292
fudge factor, phase difference, map skewness: 0.50, 44.04, 0.6092
fudge factor, phase difference, map skewness: 0.60, 55.57, 0.3374
fudge factor, phase difference, map skewness: 0.70, 62.39, 0.07028
fudge factor, phase difference, map skewness: 0.80, 73.69, -0.01595
fudge factor, phase difference, map skewness: 0.90, 83.53, -0.1369
fudge factor, phase difference, map skewness: 1.00, 88.73, -0.09588

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, 2.458
fudge factor, phase difference, map skewness: 0.10, 11.28, 2.225
fudge factor, phase difference, map skewness: 0.20, 16.92, 1.997
fudge factor, phase difference, map skewness: 0.30, 26.12, 1.589
fudge factor, phase difference, map skewness: 0.40, 33.60, 1.012
fudge factor, phase difference, map skewness: 0.50, 46.53, 0.4876
fudge factor, phase difference, map skewness: 0.60, 52.76, 0.3445
fudge factor, phase difference, map skewness: 0.70, 66.09, 0.08883
fudge factor, phase difference, map skewness: 0.80, 69.27, 0.07266
fudge factor, phase difference, map skewness: 0.90, 81.16, -0.03102
fudge factor, phase difference, map skewness: 1.00, 95.74, -0.04073

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, 2.627
fudge factor, phase difference, map skewness: 0.10,  9.12, 2.241
fudge factor, phase difference, map skewness: 0.20, 19.56, 1.753
fudge factor, phase difference, map skewness: 0.30, 24.31, 1.39
fudge factor, phase difference, map skewness: 0.40, 35.46, 0.8147
fudge factor, phase difference, map skewness: 0.50, 49.14, 0.3868
fudge factor, phase difference, map skewness: 0.60, 52.92, 0.3007
fudge factor, phase difference, map skewness: 0.70, 65.63, -0.003636
fudge factor, phase difference, map skewness: 0.80, 74.38, 0.09175
fudge factor, phase difference, map skewness: 0.90, 80.40, -0.003963
fudge factor, phase difference, map skewness: 1.00, 92.69, -0.1287

Number of scatterers: 20
At special positions: 1
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, 2.594
fudge factor, phase difference, map skewness: 0.10,  8.98, 2.35
fudge factor, phase difference, map skewness: 0.20, 16.21, 2.052
fudge factor, phase difference, map skewness: 0.30, 24.57, 1.612
fudge factor, phase difference, map skewness: 0.40, 33.27, 1.139
fudge factor, phase difference, map skewness: 0.50, 45.66, 0.6064
fudge factor, phase difference, map skewness: 0.60, 55.72, 0.3186
fudge factor, phase difference, map skewness: 0.70, 64.08, -0.004039
fudge factor, phase difference, map skewness: 0.80, 73.95, -0.1258
fudge factor, phase difference, map skewness: 0.90, 81.00, -0.002928
fudge factor, phase difference, map skewness: 1.00, 93.48, 0.1017

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, 2.878
fudge factor, phase difference, map skewness: 0.10,  6.38, 2.705
fudge factor, phase difference, map skewness: 0.20, 18.32, 2.016
fudge factor, phase difference, map skewness: 0.30, 24.99, 1.543
fudge factor, phase difference, map skewness: 0.40, 26.12, 1.504
fudge factor, phase difference, map skewness: 0.50, 45.60, 0.7481
fudge factor, phase difference, map skewness: 0.60, 59.30, 0.1682
fudge factor, phase difference, map skewness: 0.70, 64.27, 0.1207
fudge factor, phase difference, map skewness: 0.80, 76.39, -0.02815
fudge factor, phase difference, map skewness: 0.90, 80.10, 0.07912
fudge factor, phase difference, map skewness: 1.00, 88.55, -0.1605

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/site_symmetry_table.py
0,0,0
1/2,1/2,1/2
x,y,z
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/site_symmetry_constraints.py
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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/adp_symmetry_constraints.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/unit_cell_refinement.py
( 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:   0.00289855 gradient norm:     0.873261
functional:  0.000926904 gradient norm:     0.164675
LBFGS step
functional:  0.000721103 gradient norm:      0.10673
LBFGS step
functional:  0.000496383 gradient norm:    0.0156637
LBFGS step
functional:  0.000436098 gradient norm:    0.0187088
LBFGS step
functional:  0.000405012 gradient norm:    0.0141628
LBFGS step
functional:  0.000437224 gradient norm:    0.0606773
functional:   0.00040312 gradient norm:    0.0132962
LBFGS step
functional:  0.000400413 gradient norm:   0.00486465
LBFGS step
functional:  0.000400027 gradient norm:   0.00909807
LBFGS step
functional:  0.000399624 gradient norm:   0.00699388
LBFGS step
functional:  0.000398287 gradient norm:   0.00462518
LBFGS step
functional:  0.000395684 gradient norm:   0.00493147
LBFGS step
functional:  0.000391549 gradient norm:   0.00839497
LBFGS step
functional:  0.000397073 gradient norm:    0.0313132
functional:  0.000389325 gradient norm:   0.00955155
LBFGS step
functional:  0.000387577 gradient norm:    0.0299186
LBFGS step
functional:  0.000384514 gradient norm:   0.00250453
LBFGS step
functional:  0.000384214 gradient norm:   0.00179241
LBFGS step
functional:  0.000384067 gradient norm:   0.00168088
LBFGS step
functional:  0.000383912 gradient norm:   0.00139478
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: 0.41 0.36 0.05

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/miller_common_sets.py
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) 0.190996543311
asu a: (1, 2, 3) 0.839368200477
asu a: (2, 3, 4) 0.641108620077
asu a: (3, 4, 5) 0.657120549745
asu a: (4, 5, 6) 0.347894088342

asu b: (5, 6, 7) 0.133592229858
asu b: (0, 1, 2) 0.125840088064
asu b: (3, 4, 5) 0.380366656966
asu b: (1, 2, 3) 0.692508912218
asu b: (4, 5, 6) 0.816294136961

common a: (0, 1, 2) 0.190996543311
common a: (3, 4, 5) 0.657120549745
common a: (1, 2, 3) 0.839368200477
common a: (4, 5, 6) 0.347894088342

common b: (0, 1, 2) 0.125840088064
common b: (3, 4, 5) 0.380366656966
common b: (1, 2, 3) 0.692508912218
common b: (4, 5, 6) 0.816294136961

lone a: (2, 3, 4) 0.641108620077

lone b: (5, 6, 7) 0.133592229858

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/miller_transform.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/change_hand_p31.py

This example shows that a change of hand ("flipping coordinates") involves
changing the space group if the space group is enantimorphic.
Note that the interatomic distances do not change if the space group
symmetry is transformed correctly, but do change if the original space
group symmetry is simply retained.

==================
Original structure
==================
Number of scatterers: 3
At special positions: 0
Unit cell: (5, 5, 6, 90, 90, 120)
Space group: P 31 (No. 144)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
Se1  Se     3 ( 0.7624  0.5887  0.3937) 1.00 0.0000 [ - ]
Se2  Se     3 ( 0.2813  0.9896  0.9449) 1.00 0.0000 [ - ]
Se3  Se     3 ( 0.4853  0.8980  0.4707) 1.00 0.0000 [ - ]
Interatomic distances:
Se1  pair count:   3       <<  0.7624,  0.5887,  0.3937>>
  Se2:   1.5428             (  0.7083,  0.7187,  0.6116)
  Se3:   2.2165             (  0.4127,  0.5147,  0.1374)
  Se2:   2.4626             (  1.0104,  0.2917,  0.2782)
Se2  pair count:   3       <<  0.2813,  0.9896,  0.9449>>
  Se1:   1.5428             (  0.4113,  1.1737,  0.7270)
  Se3:   1.9393             (  0.1020,  0.5873,  0.8040)
  Se1:   2.4626             (  0.8263,  1.2376,  1.0604)
Se3  pair count:   2       <<  0.4853,  0.8980,  0.4707>>
  Se2:   1.9393             (  0.7083,  0.7187,  0.6116)
  Se1:   2.2165             (  0.4113,  1.1737,  0.7270)

=====================================================
Other hand with sites flipped and space group changed
=====================================================
Number of scatterers: 3
At special positions: 0
Unit cell: (5, 5, 6, 90, 90, 120)
Space group: P 32 (No. 145)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
Se1  Se     3 (-0.7624 -0.5887 -0.3937) 1.00 0.0000 [ - ]
Se2  Se     3 (-0.2813 -0.9896 -0.9449) 1.00 0.0000 [ - ]
Se3  Se     3 (-0.4853 -0.8980 -0.4707) 1.00 0.0000 [ - ]
Interatomic distances:
Se1  pair count:   3       << -0.7624, -0.5887, -0.3937>>
  Se2:   1.5428             ( -0.7083, -0.7187, -0.6116)
  Se3:   2.2165             ( -0.4127, -0.5147, -0.1374)
  Se2:   2.4626             ( -1.0104, -0.2917, -0.2782)
Se2  pair count:   3       << -0.2813, -0.9896, -0.9449>>
  Se1:   1.5428             ( -0.4113, -1.1737, -0.7270)
  Se3:   1.9393             ( -0.1020, -0.5873, -0.8040)
  Se1:   2.4626             ( -0.8263, -1.2376, -1.0604)
Se3  pair count:   2       << -0.4853, -0.8980, -0.4707>>
  Se2:   1.9393             ( -0.7083, -0.7187, -0.6116)
  Se1:   2.2165             ( -0.4113, -1.1737, -0.7270)

==================================
Other hand with sites flipped only
==================================
Number of scatterers: 3
At special positions: 0
Unit cell: (5, 5, 6, 90, 90, 120)
Space group: P 31 (No. 144)
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
Se1  Se     3 (-0.7624 -0.5887 -0.3937) 1.00 0.0000 [ - ]
Se2  Se     3 (-0.2813 -0.9896 -0.9449) 1.00 0.0000 [ - ]
Se3  Se     3 (-0.4853 -0.8980 -0.4707) 1.00 0.0000 [ - ]
Interatomic distances:
Se1  pair count:   2       << -0.7624, -0.5887, -0.3937>>
  Se2:   1.0731             ( -0.7083, -0.7187, -0.2782)
  Se3:   2.2936             ( -1.1020, -0.5873, -0.1374)
Se2  pair count:   2       << -0.2813, -0.9896, -0.9449>>
  Se1:   1.0731             ( -0.4113, -1.1737, -1.0604)
  Se3:   2.0929             ( -0.1020, -0.5873, -1.1374)
Se3  pair count:   2       << -0.4853, -0.8980, -0.4707>>
  Se2:   2.0929             ( -0.7083, -0.7187, -0.2782)
  Se1:   2.2936             ( -0.8263, -1.2376, -0.7270)

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/steve_collins.py
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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o3_primitive_cell.py
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, Ustar as 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, Ustar as 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, Ustar as 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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/cr2o3_consistency_checks.py
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, Ustar as 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, Ustar as 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, Ustar as 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             (  0.7500,  0.4442,  0.0558)
  O1:    1.9654             (  0.0558,  0.7500,  0.4442)
  O1:    1.9654             (  0.4442,  0.0558,  0.7500)
  O1:    2.0157             (  0.5558, -0.0558,  0.2500)
  O1:    2.0157             (  0.2500,  0.5558, -0.0558)
  O1:    2.0157             ( -0.0558,  0.2500,  0.5558)
Cr1  pair count:   6       <<  0.1524,  0.1524,  0.1524>>
  O1:    1.9654             ( -0.2500,  0.4442,  0.0558)
  O1:    1.9654             (  0.0558, -0.2500,  0.4442)
  O1:    1.9654             (  0.4442,  0.0558, -0.2500)
  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             ( -0.7500, -0.4442, -0.0558)
  O1:    1.9654             ( -0.0558, -0.7500, -0.4442)
  O1:    1.9654             ( -0.4442, -0.0558, -0.7500)
  O1:    2.0157             ( -0.5558,  0.0558, -0.2500)
  O1:    2.0157             ( -0.2500, -0.5558,  0.0558)
  O1:    2.0157             (  0.0558, -0.2500, -0.5558)
Cr1  pair count:   6       << -0.1524, -0.1524, -0.1524>>
  O1:    1.9654             (  0.2500, -0.4442, -0.0558)
  O1:    1.9654             ( -0.0558,  0.2500, -0.4442)
  O1:    1.9654             ( -0.4442, -0.0558,  0.2500)
  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             (  0.8476, -0.1524, -0.1524)
  Cr1:   1.9654             (  0.6524, -0.3476,  0.6524)
  Cr1:   2.0157             (  0.3476,  0.3476,  0.3476)
  Cr1:   2.0157             (  0.1524,  0.1524,  0.1524)
O1   pair count:   4       <<  0.2500,  0.5558, -0.0558>>
  Cr1:   1.9654             ( -0.1524,  0.8476, -0.1524)
  Cr1:   1.9654             (  0.6524,  0.6524, -0.3476)
  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             (  0.1524,  0.1524,  0.1524)
  Cr1:   2.0157             (  0.3476,  0.3476,  0.3476)
O1   pair count:   4       << -0.5558,  0.0558, -0.2500>>
  Cr1:   1.9654             ( -0.8476,  0.1524,  0.1524)
  Cr1:   1.9654             ( -0.6524,  0.3476, -0.6524)
  Cr1:   2.0157             ( -0.3476, -0.3476, -0.3476)
  Cr1:   2.0157             ( -0.1524, -0.1524, -0.1524)
O1   pair count:   4       << -0.2500, -0.5558,  0.0558>>
  Cr1:   1.9654             (  0.1524, -0.8476,  0.1524)
  Cr1:   1.9654             ( -0.6524, -0.6524,  0.3476)
  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             ( -0.1524, -0.1524, -0.1524)
  Cr1:   2.0157             ( -0.3476, -0.3476, -0.3476)

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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/reduced_cell_two_folds.py
(-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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/lebedev_2005_perturbation.py
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/longnose/scratch1/rwgk/auto_build/sources/cctbx/examples/le_page_1982_vs_lebedev_2005.py
OK

libtbx.python $CCTBX_DIST/regression/tst_structure_factors_multithread.py --verbose
omptbx.have_stubs_h
OpenMP
# CPU   run-time   speed-up
1       3.55       x 1.00
2       3.55       x 1.00
Skipping raw multithreaded structure factor computation tests
usr+sys time: 11.14 seconds
wall clock time: 11.15 seconds
libtbx.python $CCTBX_DIST/web/replay.py $BUILD_SRC/phenix_regression/cctbx/web/[a-z]* | grep -i error
  cctbx Error: Brick is not available for the given space group representation.
libtbx.python $RSTBX_DIST/run_tests.py
OK
libtbx.python $IOTBX_DIST/run_tests.py --Quick
/net/longnose/scratch1/rwgk/auto_build/build/iotbx/boost_spirit/tst_parsers
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_wildcard.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_simple_parser.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phil.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/ranges.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_crystal_symmetry_from_any.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/kriber/tst_strudat.py
u+s,u,s: 12.02 11.92 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cif/tst_xray_structure.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_lex_parse_build.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/shelx/tst_hklf.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/hybrid_36.py exercise
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_hierarchy.py
iotbx.pdb.hierarchy.atom.sizeof_data(): 168
u+s,u,s: 5.15 4.96 0.19

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_ext.py
time hy36recode_width_4_all: 0.50 s (0.205 micro s per encode-decode cycle)
u+s,u,s: 2.68 2.49 0.19

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_selection.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_rna_dna_atom_names.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_atom_name_interpretation.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_extract_rfactors_resolutions_sigma.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/pdb/tst_pdb.py
u+s,u,s: 9.50 9.28 0.22

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/examples/pdb_truncate_to_ala/tst.py
total number of:
  models:      1
  chains:      2
  alt. conf.:  4
  residues:    3
  atoms:      23
  anisou:      0
number of atom element+charge types: 3
histogram of atom element+charge frequency:
  " C  " 16
  " O  "  5
  " N  "  2
residue name classes:
  "common_amino_acid" 2
  "other"             1
number of chain ids: 2
histogram of chain id frequency:
  " " 1
  "A" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 2
  "B" 2
residue alt. conf. situations:
  pure main conf.:     1
  pure alt. conf.:     1
  proper alt. conf.:   1
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 3
histogram of residue name frequency:
  "EOH" 1    other
  "ILE" 1
  "SER" 1
total number of:
  models:      1
  chains:      2
  alt. conf.:  4
  residues:    3
  atoms:      23
  anisou:      0
number of atom element+charge types: 3
histogram of atom element+charge frequency:
  " C  " 16
  " O  "  5
  " N  "  2
residue name classes:
  "common_amino_acid" 2
  "other"             1
number of chain ids: 2
histogram of chain id frequency:
  " " 1
  "A" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 2
  "B" 2
residue alt. conf. situations:
  pure main conf.:     1
  pure alt. conf.:     1
  proper alt. conf.:   1
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 3
histogram of residue name frequency:
  "EOH" 1    other
  "ILE" 1
  "SER" 1
resid: "   6 "
  altloc: "", resname: "SER"
      N  
      CA 
      C  
      O  
      CB 
      OG 
resid: "   7 "
  altloc: "", resname: "ILE"
      N  
      CA 
      C  
      O  
      CG2
  altloc: "A", resname: "ILE"
      CB 
      CG1
      CD1
  altloc: "B", resname: "ILE"
      CB 
      CG1
      CD1
resid: "  66 "
  altloc: "A", resname: "EOH"
      C1 
      C2 
      O  
  altloc: "B", resname: "EOH"
      C1 
      C2 
      O  
total number of:
  models:      1
  chains:      2
  alt. conf.:  4
  residues:    3
  atoms:      23
  anisou:      0
number of atom element+charge types: 3
histogram of atom element+charge frequency:
  " C  " 16
  " O  "  5
  " N  "  2
residue name classes:
  "common_amino_acid" 2
  "other"             1
number of chain ids: 2
histogram of chain id frequency:
  " " 1
  "A" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 2
  "B" 2
residue alt. conf. situations:
  pure main conf.:     1
  pure alt. conf.:     1
  proper alt. conf.:   1
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 3
histogram of residue name frequency:
  "EOH" 1    other
  "ILE" 1
  "SER" 1
total number of:
  models:      1
  chains:      2
  alt. conf.:  4
  residues:    3
  atoms:      23
  anisou:      0
number of atom element+charge types: 3
histogram of atom element+charge frequency:
  " C  " 16
  " O  "  5
  " N  "  2
residue name classes:
  "common_amino_acid" 2
  "other"             1
number of chain ids: 2
histogram of chain id frequency:
  " " 1
  "A" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 2
  "B" 2
residue alt. conf. situations:
  pure main conf.:     1
  pure alt. conf.:     1
  proper alt. conf.:   1
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 3
histogram of residue name frequency:
  "EOH" 1    other
  "ILE" 1
  "SER" 1
total number of:
  models:      1
  chains:      2
  alt. conf.:  4
  residues:    3
  atoms:      23
  anisou:      0
number of atom element+charge types: 3
histogram of atom element+charge frequency:
  " C  " 16
  " O  "  5
  " N  "  2
residue name classes:
  "common_amino_acid" 2
  "other"             1
number of chain ids: 2
histogram of chain id frequency:
  " " 1
  "A" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 2
  "B" 2
residue alt. conf. situations:
  pure main conf.:     1
  pure alt. conf.:     1
  proper alt. conf.:   1
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 3
histogram of residue name frequency:
  "EOH" 1    other
  "ILE" 1
  "SER" 1
Number of amino acid residues: 2
Number of other residues: 1
Number of atoms removed: 6
Writing file: v4_truncated_to_ala_crambin_pieces.pdb

total number of:
  models:      1
  chains:      1
  alt. conf.:  2
  residues:    3 (1 with mixed residue names)
  atoms:      31
  anisou:      0
number of atom element+charge types: 4
histogram of atom element+charge frequency:
  " C  " 18
  " O  "  7
  " N  "  4
  " S  "  2
residue name classes:
  "common_amino_acid" 3
  "other"             1
number of chain ids: 1
histogram of chain id frequency:
  "B" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 1
  "B" 1
residue alt. conf. situations:
  pure main conf.:     2
  pure alt. conf.:     1
  proper alt. conf.:   0
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 4
histogram of residue name frequency:
  "ALA" 1
  "CSD" 1    other
  "CYS" 1
  "TYR" 1
total number of:
  models:      1
  chains:      1
  alt. conf.:  2
  residues:    3 (1 with mixed residue names)
  atoms:      31
  anisou:      0
number of atom element+charge types: 4
histogram of atom element+charge frequency:
  " C  " 18
  " O  "  7
  " N  "  4
  " S  "  2
residue name classes:
  "common_amino_acid" 3
  "other"             1
number of chain ids: 1
histogram of chain id frequency:
  "B" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 1
  "B" 1
residue alt. conf. situations:
  pure main conf.:     2
  pure alt. conf.:     1
  proper alt. conf.:   0
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 4
histogram of residue name frequency:
  "ALA" 1
  "CSD" 1    other
  "CYS" 1
  "TYR" 1
resid: " 110 "
  altloc: "", resname: "ALA"
      N  
      CA 
      C  
      O  
      CB 
resid: " 111 "
  altloc: "A", resname: "CSD"
      N  
      CA 
      CB 
      SG 
      C  
      O  
      OD1
      OD2
  altloc: "B", resname: "CYS"
      N  
      CA 
      C  
      O  
      CB 
      SG 
resid: " 112 "
  altloc: "", resname: "TYR"
      N  
      CA 
      C  
      O  
      CB 
      CG 
      CD1
      CD2
      CE1
      CE2
      CZ 
      OH 
total number of:
  models:      1
  chains:      1
  alt. conf.:  2
  residues:    3 (1 with mixed residue names)
  atoms:      31
  anisou:      0
number of atom element+charge types: 4
histogram of atom element+charge frequency:
  " C  " 18
  " O  "  7
  " N  "  4
  " S  "  2
residue name classes:
  "common_amino_acid" 3
  "other"             1
number of chain ids: 1
histogram of chain id frequency:
  "B" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 1
  "B" 1
residue alt. conf. situations:
  pure main conf.:     2
  pure alt. conf.:     1
  proper alt. conf.:   0
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 4
histogram of residue name frequency:
  "ALA" 1
  "CSD" 1    other
  "CYS" 1
  "TYR" 1
total number of:
  models:      1
  chains:      1
  alt. conf.:  2
  residues:    3 (1 with mixed residue names)
  atoms:      31
  anisou:      0
number of atom element+charge types: 4
histogram of atom element+charge frequency:
  " C  " 18
  " O  "  7
  " N  "  4
  " S  "  2
residue name classes:
  "common_amino_acid" 3
  "other"             1
number of chain ids: 1
histogram of chain id frequency:
  "B" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 1
  "B" 1
residue alt. conf. situations:
  pure main conf.:     2
  pure alt. conf.:     1
  proper alt. conf.:   0
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 4
histogram of residue name frequency:
  "ALA" 1
  "CSD" 1    other
  "CYS" 1
  "TYR" 1
total number of:
  models:      1
  chains:      1
  alt. conf.:  2
  residues:    3 (1 with mixed residue names)
  atoms:      31
  anisou:      0
number of atom element+charge types: 4
histogram of atom element+charge frequency:
  " C  " 18
  " O  "  7
  " N  "  4
  " S  "  2
residue name classes:
  "common_amino_acid" 3
  "other"             1
number of chain ids: 1
histogram of chain id frequency:
  "B" 1
number of alt. conf. ids: 2
histogram of alt. conf. id frequency:
  "A" 1
  "B" 1
residue alt. conf. situations:
  pure main conf.:     2
  pure alt. conf.:     1
  proper alt. conf.:   0
  improper alt. conf.: 0
chains with mix of proper and improper alt. conf.: 0
number of residue names: 4
histogram of residue name frequency:
  "ALA" 1
  "CSD" 1    other
  "CYS" 1
  "TYR" 1
Number of amino acid residues: 3
Number of other residues: 0
Number of atoms removed: 11
Writing file: v4_truncated_to_ala_resname_mix.pdb

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cns/space_group_symbols.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/cns/tst_cns.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/tst_merge.py P31
P 31
u+s,u,s: 1.25 1.14 0.11

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/scalepack/no_merge_original_index.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/ccp4_map/tst.py
u+s,u,s: 0.67 0.57 0.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst_ext.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/extract_from_symop_lib.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/mtz/tst.py P31
P 31
u+s,u,s: 1.80 1.68 0.12

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/examples/tst_mtz_free_flipper.py
Reading file: /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/reflection_files/l.mtz
Number of 0: 13469
Number of 1: 1065
Writing file: free_flipped_l.mtz
Reading file: free_flipped_l.mtz
Number of 0: 1065
Number of 1: 13469
Writing file: free_flipped_free_flipped_l.mtz
Reading file: /net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/reflection_files/l.mtz
Input number of free reflections: 1065
Input number of work reflections: 13469
Number of reflections converted from free to work: 533
Output number of free reflections: 532
Output number of work reflections: 14002
Writing file: less_free_l.mtz
u+s,u,s: 12.97 12.84 0.13

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_reflection_file_utils.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst_adsc.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/detectors/tst_debug_write.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/xplor/tst_xplormap.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_phases.py P31
Writing tmp.pdb
Writing: tmp.phs
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/regression/tst_lattice_symmetry.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/regression/tst_reflection_statistics.py Fdd2 P31m
F d d 2
P 3 1 m
u+s,u,s: 11.79 11.61 0.18
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_data_plots.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/iotbx/tst_csv_utils.py
OK

libtbx.python $PYCIFRW_DIST/example_quartz.py
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, Ustar as 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) 16.3662770268
(1, 0, 1) 36.7226624914
(1, 0, 2) 6.96161334665
(1, 1, 0) 14.716747416
(1, 1, 1) 0.539734721891
(2, 0, 0) 14.6748185743
(2, 0, 1) 12.9746389785
OK
libtbx.python $CLIPPER_ADAPTBX_DIST/clipper/tst_sigmaa.py
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
I 4/m c m (a+b-1/6,-a+b,c+1/4)
u+s,u,s: 3.78 3.63 0.15
libtbx.python $SMTBX_DIST/run_tests.py --Quick
libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tests/tst_ab_initio_ext.py
u+s,u,s: 4.55 4.46 0.09

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/ab_initio/tests/tst_charge_flipping.py
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
u+s,u,s: 139.35 138.23 1.12
16 test cases:
	16 successes
	16 phase transitions
	16 Euclidean matches with correct structure in P1
	16 found shifts
	16 Euclidean matches with correct structure in original spacegroup

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/smtbx/refinement/constraints/tests/tst_constraints.py
OK

libtbx.python $MMTBX_DIST/run_tests.py --Quick
libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/chemical_components/tst.py

________________________________________________________________________________
HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH 

Atom names
['O', 'H1', 'H2']

Alternate atom names
['O', '1H', '2H']

Hydrogen names
['H1', 'H2']

Alternate hydrogen names
['1H', '2H']

Wrapped hydrogen names
['H1', 'H2']

Bond pairs
[['O', 'H1'], ['O', 'H2']]

Alternate name bond pairs
[['O', '1H'], ['O', '2H']]

________________________________________________________________________________
ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP ATP 

Atom names
['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', 'HOG2', 'HOG3', 'HOB2', 'HOA2', "H5'1", "H5'2", "H4'", "H3'", "HO3'", "H2'", "HO2'", "H1'", 'H8', 'HN61', 'HN62', 'H2']

Alternate atom names
['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', 'O5*', 'C5*', 'C4*', 'O4*', 'C3*', 'O3*', 'C2*', 'O2*', 'C1*', 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', '2HOG', '3HOG', '2HOB', '2HOA', '1H5*', '2H5*', 'H4*', 'H3*', '*HO3', 'H2*', '*HO2', 'H1*', 'H8', '1HN6', '2HN6', 'H2']

Hydrogen names
['HOG2', 'HOG3', 'HOB2', 'HOA2', "H5'1", "H5'2", "H4'", "H3'", "HO3'", "H2'", "HO2'", "H1'", 'H8', 'HN61', 'HN62', 'H2']

Alternate hydrogen names
['2HOG', '3HOG', '2HOB', '2HOA', '1H5*', '2H5*', 'H4*', 'H3*', '*HO3', 'H2*', '*HO2', 'H1*', 'H8', '1HN6', '2HN6', 'H2']

Wrapped hydrogen names
['2HOG', '3HOG', '2HOB', '2HOA', "1H5'", "2H5'", "H4'", "H3'", "'HO3", "H2'", "'HO2", "H1'", 'H8', '1HN6', '2HN6', 'H2']

Bond pairs
[['PG', 'O1G'], ['PG', 'O2G'], ['PG', 'O3G'], ['PG', 'O3B'], ['O2G', 'HOG2'], ['O3G', 'HOG3'], ['PB', 'O1B'], ['PB', 'O2B'], ['PB', 'O3B'], ['PB', 'O3A'], ['O2B', 'HOB2'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', "O5'"], ['O2A', 'HOA2'], ["O5'", "C5'"], ["C5'", "C4'"], ["C5'", "H5'1"], ["C5'", "H5'2"], ["C4'", "O4'"], ["C4'", "C3'"], ["C4'", "H4'"], ["O4'", "C1'"], ["C3'", "O3'"], ["C3'", "C2'"], ["C3'", "H3'"], ["O3'", "HO3'"], ["C2'", "O2'"], ["C2'", "C1'"], ["C2'", "H2'"], ["O2'", "HO2'"], ["C1'", 'N9'], ["C1'", "H1'"], ['N9', 'C8'], ['N9', 'C4'], ['C8', 'N7'], ['C8', 'H8'], ['N7', 'C5'], ['C5', 'C6'], ['C5', 'C4'], ['C6', 'N6'], ['C6', 'N1'], ['N6', 'HN61'], ['N6', 'HN62'], ['N1', 'C2'], ['C2', 'N3'], ['C2', 'H2'], ['N3', 'C4']]

Alternate name bond pairs
[['PG', 'O1G'], ['PG', 'O2G'], ['PG', 'O3G'], ['PG', 'O3B'], ['O2G', '2HOG'], ['O3G', '3HOG'], ['PB', 'O1B'], ['PB', 'O2B'], ['PB', 'O3B'], ['PB', 'O3A'], ['O2B', '2HOB'], ['PA', 'O1A'], ['PA', 'O2A'], ['PA', 'O3A'], ['PA', 'O5*'], ['O2A', '2HOA'], ['O5*', 'C5*'], ['C5*', 'C4*'], ['C5*', '1H5*'], ['C5*', '2H5*'], ['C4*', 'O4*'], ['C4*', 'C3*'], ['C4*', 'H4*'], ['O4*', 'C1*'], ['C3*', 'O3*'], ['C3*', 'C2*'], ['C3*', 'H3*'], ['O3*', '*HO3'], ['C2*', 'O2*'], ['C2*', 'C1*'], ['C2*', 'H2*'], ['O2*', '*HO2'], ['C1*', 'N9'], ['C1*', 'H1*'], ['N9', 'C8'], ['N9', 'C4'], ['C8', 'N7'], ['C8', 'H8'], ['N7', 'C5'], ['C5', 'C6'], ['C5', 'C4'], ['C6', 'N6'], ['C6', 'N1'], ['N6', '1HN6'], ['N6', '2HN6'], ['N1', 'C2'], ['C2', 'N3'], ['C2', 'H2'], ['N3', 'C4']]

________________________________________________________________________________
hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem hem 

Atom names
['FE', 'CHA', 'CHB', 'CHC', 'CHD', 'NA', 'C1A', 'C2A', 'C3A', 'C4A', 'CMA', 'CAA', 'CBA', 'CGA', 'O1A', 'O2A', 'NB', 'C1B', 'C2B', 'C3B', 'C4B', 'CMB', 'CAB', 'CBB', 'NC', 'C1C', 'C2C', 'C3C', 'C4C', 'CMC', 'CAC', 'CBC', 'ND', 'C1D', 'C2D', 'C3D', 'C4D', 'CMD', 'CAD', 'CBD', 'CGD', 'O1D', 'O2D', 'HHA', 'HHB', 'HHC', 'HHD', 'HMA1', 'HMA2', 'HMA3', 'HAA1', 'HAA2', 'HBA1', 'HBA2', 'H2A', 'HMB1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HMC3', 'HAC', 'HBC1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'HBD2', 'H2D']

Alternate atom names
['FE', 'CHA', 'CHB', 'CHC', 'CHD', 'N A', 'C1A', 'C2A', 'C3A', 'C4A', 'CMA', 'CAA', 'CBA', 'CGA', 'O1A', 'O2A', 'N B', 'C1B', 'C2B', 'C3B', 'C4B', 'CMB', 'CAB', 'CBB', 'N C', 'C1C', 'C2C', 'C3C', 'C4C', 'CMC', 'CAC', 'CBC', 'N D', 'C1D', 'C2D', 'C3D', 'C4D', 'CMD', 'CAD', 'CBD', 'CGD', 'O1D', 'O2D', 'HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D']

Hydrogen names
['HHA', 'HHB', 'HHC', 'HHD', 'HMA1', 'HMA2', 'HMA3', 'HAA1', 'HAA2', 'HBA1', 'HBA2', 'H2A', 'HMB1', 'HMB2', 'HMB3', 'HAB', 'HBB1', 'HBB2', 'HMC1', 'HMC2', 'HMC3', 'HAC', 'HBC1', 'HBC2', 'HMD1', 'HMD2', 'HMD3', 'HAD1', 'HAD2', 'HBD1', 'HBD2', 'H2D']

Alternate hydrogen names
['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D']

Wrapped hydrogen names
['HHA', 'HHB', 'HHC', 'HHD', '1HMA', '2HMA', '3HMA', '1HAA', '2HAA', '1HBA', '2HBA', 'H2A', '1HMB', '2HMB', '3HMB', 'HAB', '1HBB', '2HBB', '1HMC', '2HMC', '3HMC', 'HAC', '1HBC', '2HBC', '1HMD', '2HMD', '3HMD', '1HAD', '2HAD', '1HBD', '2HBD', 'H2D']

Bond pairs
[['FE', 'NA'], ['FE', 'NB'], ['FE', 'NC'], ['FE', 'ND'], ['CHA', 'C1A'], ['CHA', 'C4D'], ['CHA', 'HHA'], ['CHB', 'C4A'], ['CHB', 'C1B'], ['CHB', 'HHB'], ['CHC', 'C4B'], ['CHC', 'C1C'], ['CHC', 'HHC'], ['CHD', 'C4C'], ['CHD', 'C1D'], ['CHD', 'HHD'], ['NA', 'C1A'], ['NA', 'C4A'], ['C1A', 'C2A'], ['C2A', 'C3A'], ['C2A', 'CAA'], ['C3A', 'C4A'], ['C3A', 'CMA'], ['CMA', 'HMA1'], ['CMA', 'HMA2'], ['CMA', 'HMA3'], ['CAA', 'CBA'], ['CAA', 'HAA1'], ['CAA', 'HAA2'], ['CBA', 'CGA'], ['CBA', 'HBA1'], ['CBA', 'HBA2'], ['CGA', 'O1A'], ['CGA', 'O2A'], ['O2A', 'H2A'], ['NB', 'C1B'], ['NB', 'C4B'], ['C1B', 'C2B'], ['C2B', 'C3B'], ['C2B', 'CMB'], ['C3B', 'C4B'], ['C3B', 'CAB'], ['CMB', 'HMB1'], ['CMB', 'HMB2'], ['CMB', 'HMB3'], ['CAB', 'CBB'], ['CAB', 'HAB'], ['CBB', 'HBB1'], ['CBB', 'HBB2'], ['NC', 'C1C'], ['NC', 'C4C'], ['C1C', 'C2C'], ['C2C', 'C3C'], ['C2C', 'CMC'], ['C3C', 'C4C'], ['C3C', 'CAC'], ['CMC', 'HMC1'], ['CMC', 'HMC2'], ['CMC', 'HMC3'], ['CAC', 'CBC'], ['CAC', 'HAC'], ['CBC', 'HBC1'], ['CBC', 'HBC2'], ['ND', 'C1D'], ['ND', 'C4D'], ['C1D', 'C2D'], ['C2D', 'C3D'], ['C2D', 'CMD'], ['C3D', 'C4D'], ['C3D', 'CAD'], ['CMD', 'HMD1'], ['CMD', 'HMD2'], ['CMD', 'HMD3'], ['CAD', 'CBD'], ['CAD', 'HAD1'], ['CAD', 'HAD2'], ['CBD', 'CGD'], ['CBD', 'HBD1'], ['CBD', 'HBD2'], ['CGD', 'O1D'], ['CGD', 'O2D'], ['O2D', 'H2D']]

Alternate name bond pairs
[['FE', 'N A'], ['FE', 'N B'], ['FE', 'N C'], ['FE', 'N D'], ['CHA', 'C1A'], ['CHA', 'C4D'], ['CHA', 'HHA'], ['CHB', 'C4A'], ['CHB', 'C1B'], ['CHB', 'HHB'], ['CHC', 'C4B'], ['CHC', 'C1C'], ['CHC', 'HHC'], ['CHD', 'C4C'], ['CHD', 'C1D'], ['CHD', 'HHD'], ['N A', 'C1A'], ['N A', 'C4A'], ['C1A', 'C2A'], ['C2A', 'C3A'], ['C2A', 'CAA'], ['C3A', 'C4A'], ['C3A', 'CMA'], ['CMA', '1HMA'], ['CMA', '2HMA'], ['CMA', '3HMA'], ['CAA', 'CBA'], ['CAA', '1HAA'], ['CAA', '2HAA'], ['CBA', 'CGA'], ['CBA', '1HBA'], ['CBA', '2HBA'], ['CGA', 'O1A'], ['CGA', 'O2A'], ['O2A', 'H2A'], ['N B', 'C1B'], ['N B', 'C4B'], ['C1B', 'C2B'], ['C2B', 'C3B'], ['C2B', 'CMB'], ['C3B', 'C4B'], ['C3B', 'CAB'], ['CMB', '1HMB'], ['CMB', '2HMB'], ['CMB', '3HMB'], ['CAB', 'CBB'], ['CAB', 'HAB'], ['CBB', '1HBB'], ['CBB', '2HBB'], ['N C', 'C1C'], ['N C', 'C4C'], ['C1C', 'C2C'], ['C2C', 'C3C'], ['C2C', 'CMC'], ['C3C', 'C4C'], ['C3C', 'CAC'], ['CMC', '1HMC'], ['CMC', '2HMC'], ['CMC', '3HMC'], ['CAC', 'CBC'], ['CAC', 'HAC'], ['CBC', '1HBC'], ['CBC', '2HBC'], ['N D', 'C1D'], ['N D', 'C4D'], ['C1D', 'C2D'], ['C2D', 'C3D'], ['C2D', 'CMD'], ['C3D', 'C4D'], ['C3D', 'CAD'], ['CMD', '1HMD'], ['CMD', '2HMD'], ['CMD', '3HMD'], ['CAD', 'CBD'], ['CAD', '1HAD'], ['CAD', '2HAD'], ['CBD', 'CGD'], ['CBD', '1HBD'], ['CBD', '2HBD'], ['CGD', 'O1D'], ['CGD', 'O2D'], ['O2D', 'H2D']]
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_add_h_to_water.py
Number of H added: 9
X-H deviation from ideal before regularization (bond): mean= 0.013 max= 0.020
X-H deviation from ideal after  regularization (bond): mean= 0.000 max= 0.000
u+s,u,s: 16.30 15.99 0.31

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/rotamer/rotamer_eval.py
Processing data files in "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/rotarama_data":
  rota500-cys.data -> rota500-cys.pickle: already up to date.
  rota500-asp.data -> rota500-asp.pickle: already up to date.
  rota500-ser.data -> rota500-ser.pickle: already up to date.
  rota500-gln.data -> rota500-gln.pickle: already up to date.
  rota500-ile.data -> rota500-ile.pickle: already up to date.
  rota500-pro.data -> rota500-pro.pickle: already up to date.
  rota500-lys.data -> rota500-lys.pickle: already up to date.
  rota500-thr.data -> rota500-thr.pickle: already up to date.
  rota500-phetyr.data -> rota500-phetyr.pickle: already up to date.
  rota500-asn.data -> rota500-asn.pickle: already up to date.
  rota500-met.data -> rota500-met.pickle: already up to date.
  rota500-his.data -> rota500-his.pickle: already up to date.
  rota500-leu.data -> rota500-leu.pickle: already up to date.
  rota500-arg.data -> rota500-arg.pickle: already up to date.
  rota500-trp.data -> rota500-trp.pickle: already up to date.
  rota500-glu.data -> rota500-glu.pickle: already up to date.
  rota500-phetyr.data -> rota500-phetyr.pickle: already up to date.
  rota500-val.data -> rota500-val.pickle: already up to date.
Processing data files in "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/rotarama_data":
  rama500-prepro.data -> rama500-prepro.pickle: already up to date.
  rama500-pro.data -> rama500-pro.pickle: already up to date.
  rama500-gly-sym.data -> rama500-gly-sym.pickle: already up to date.
  rama500-general.data -> rama500-general.pickle: already up to date.
u+s,u,s: 2.10 1.92 0.18
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/wwpdb/tst_standard_geometry_cif.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_pdbtools.py
OK
usr+sys time: 33.52 seconds
wall clock time: 2 minutes 53.30 seconds (173.30 seconds total)

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/real_space/tst.py
OK: real_space:  u+s,u,s: 166.41 162.06 4.35

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ias/tst_ias.py
>>> Adding IAS..........
Total number of covalent bonds =  40
IAS considered: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS selected: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS scattering dictionary:
Number of scattering types: 1
  Type Number    sf(0)   Gaussians
   D10     4      0.05       1
  sf(0) = scattering factor at diffraction angle 0.
HETATM    1 D10  IAS     1       2.370   3.660  -0.690  1.00  0.83          D1
HETATM    2 D10  IAS     2       2.614   3.609  -1.283  1.00  0.83          D1
HETATM    3 D10  IAS     3       1.345   4.997   2.883  1.00  0.91          D1
HETATM    4 D10  IAS     4       1.076   4.418   2.809  1.00  0.91          D1
Scattering dictionary for combined xray_structure:
Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   O       6      8.00       6
   N       3      7.00       6
   C      13      6.00       6
   H      19      1.00       6
   D10     4      0.05       1
  sf(0) = scattering factor at diffraction angle 0.
>>> Adding IAS..........
Total number of covalent bonds =  40
IAS considered: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS selected: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS scattering dictionary:
Number of scattering types: 1
  Type Number    sf(0)   Gaussians
   D9      1     -0.30       1
  sf(0) = scattering factor at diffraction angle 0.
HETATM    1 D9   IAS     1       1.075   0.334  -2.554  1.00  0.95          D9
Scattering dictionary for combined xray_structure:
Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   O       6      8.00       6
   N       3      7.00       6
   C      13      6.00       6
   H      19      1.00       6
   D9      1     -0.30       1
  sf(0) = scattering factor at diffraction angle 0.
>>> Adding IAS..........
Total number of covalent bonds =  40
IAS considered: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS selected: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS scattering dictionary:
Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   D5      6      0.20       1
   D4      5      0.14       1
   D8      4      0.11       1
   D6      5      0.08       1
   D7      1      0.07       1
  sf(0) = scattering factor at diffraction angle 0.
HETATM    1 D7   IAS     1       1.630  -1.554  -1.815  1.00  1.27          D7
HETATM    2 D5   IAS     2       1.733  -0.685  -2.660  1.00  1.03          D5
HETATM    3 D5   IAS     3       0.997  -0.542  -1.713  1.00  1.03          D5
HETATM    4 D5   IAS     4       1.817   0.185  -3.486  1.00  1.03          D5
HETATM    5 D5   IAS     5       0.343   0.464  -1.605  1.00  1.03          D5
HETATM    6 D5   IAS     6       1.158   1.204  -3.380  1.00  0.95          D5
HETATM    7 D5   IAS     7       0.420   1.340  -2.446  1.00  0.95          D5
HETATM    8 D4   IAS     8       0.477   2.272  -3.299  1.00  0.91          D4
HETATM    9 D4   IAS     9       0.677   3.542  -3.289  1.00  0.91          D4
HETATM   10 D6   IAS    10       1.816   4.161  -3.359  1.00  0.91          D6
HETATM   11 D4   IAS    11       1.192   4.075  -2.265  1.00  0.83          D4
HETATM   12 D8   IAS    12       1.752   3.869  -1.311  1.00  0.99          D8
HETATM   13 D6   IAS    13       0.749   4.146  -1.136  1.00  0.83          D6
HETATM   14 D8   IAS    14       1.042   4.890   2.030  1.00  0.99          D8
HETATM   15 D4   IAS    15       0.584   4.487   1.090  1.00  0.91          D4
HETATM   16 D6   IAS    16       1.092   5.584   1.239  1.00  0.95          D6
HETATM   17 D6   IAS    17       0.217   4.137  -0.109  1.00  0.91          D6
HETATM   18 D8   IAS    18       1.410   8.867   2.122  1.00  0.99          D8
HETATM   19 D8   IAS    19       0.653   8.303   2.249  1.00  1.03          D8
HETATM   20 D6   IAS    20       1.592   6.648   1.254  1.00  1.07          D6
HETATM   21 D4   IAS    21       1.576   7.806   1.851  1.00  0.99          D4
Scattering dictionary for combined xray_structure:
Number of scattering types: 9
  Type Number    sf(0)   Gaussians
   O       6      8.00       6
   N       3      7.00       6
   C      13      6.00       6
   H      19      1.00       6
   D5      6      0.20       1
   D4      5      0.14       1
   D8      4      0.11       1
   D6      5      0.08       1
   D7      1      0.07       1
  sf(0) = scattering factor at diffraction angle 0.
>>> Adding IAS..........
Total number of covalent bonds =  40
IAS considered: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS selected: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS scattering dictionary:
Number of scattering types: 3
  Type Number    sf(0)   Gaussians
   D1     11      0.22       1
   D2      5      0.16       1
   D3      3      0.09       1
  sf(0) = scattering factor at diffraction angle 0.
HETATM    1 D3   IAS     1       2.387  -2.396  -1.821  1.00  1.34          D3
HETATM    2 D1   IAS     2       2.576  -0.898  -3.654  1.00  1.19          D1
HETATM    3 D1   IAS     3       0.253  -0.476  -0.641  1.00  1.19          D1
HETATM    4 D1   IAS     4       1.974   1.097  -4.424  1.00  1.19          D1
HETATM    5 D1   IAS     5      -0.384   1.541  -1.402  1.00  1.19          D1
HETATM    6 D1   IAS     6       0.333   2.962  -4.401  1.00  1.10          D1
HETATM    7 D1   IAS     7      -0.539   3.079  -3.350  1.00  1.10          D1
HETATM    8 D1   IAS     8       0.677   4.846  -3.199  1.00  0.99          D1
HETATM    9 D2   IAS     9       2.896   4.727  -3.371  1.00  1.10          D2
HETATM   10 D2   IAS    10       2.849   3.558  -3.510  1.00  1.10          D2
HETATM   11 D2   IAS    11       2.394   4.228  -4.408  1.00  1.10          D2
HETATM   12 D1   IAS    12       0.619   3.240   0.828  1.00  1.10          D1
HETATM   13 D1   IAS    13      -0.568   3.906   0.916  1.00  1.10          D1
HETATM   14 D2   IAS    14      -0.470   4.416  -1.090  1.00  1.06          D2
HETATM   15 D2   IAS    15       1.099   6.286   0.217  1.00  1.15          D2
HETATM   16 D1   IAS    16       2.366   6.934   2.309  1.00  1.27          D1
HETATM   17 D1   IAS    17       2.565   7.521   1.061  1.00  1.27          D1
HETATM   18 D3   IAS    18       0.918   1.686   3.084  1.00  1.46          D3
HETATM   19 D3   IAS    19       0.782   2.788   3.272  1.00  1.46          D3
Scattering dictionary for combined xray_structure:
Number of scattering types: 7
  Type Number    sf(0)   Gaussians
   O       6      8.00       6
   N       3      7.00       6
   C      13      6.00       6
   H      19      1.00       6
   D1     11      0.22       1
   D2      5      0.16       1
   D3      3      0.09       1
  sf(0) = scattering factor at diffraction angle 0.
>>> Adding IAS..........
Total number of covalent bonds =  40
IAS considered: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS selected: 
Number of IAS built:
   total:              45
   bond (X-X):         21
   bond (X-H):         19
   ring centers:       1
   lone pairs:         4
IAS scattering dictionary:
Number of scattering types: 10
  Type Number    sf(0)   Gaussians
   D1     11      0.22       1
   D5      6      0.20       1
   D2      5      0.16       1
   D4      5      0.14       1
   D8      4      0.11       1
   D3      3      0.09       1
   D6      5      0.08       1
   D7      1      0.07       1
   D10     4      0.05       1
   D9      1     -0.30       1
  sf(0) = scattering factor at diffraction angle 0.
HETATM    1 D7   IAS     1       1.630  -1.554  -1.815  1.00  1.27          D7
HETATM    2 D3   IAS     2       2.387  -2.396  -1.821  1.00  1.34          D3
HETATM    3 D5   IAS     3       1.733  -0.685  -2.660  1.00  1.03          D5
HETATM    4 D5   IAS     4       0.997  -0.542  -1.713  1.00  1.03          D5
HETATM    5 D5   IAS     5       1.817   0.185  -3.486  1.00  1.03          D5
HETATM    6 D1   IAS     6       2.576  -0.898  -3.654  1.00  1.19          D1
HETATM    7 D5   IAS     7       0.343   0.464  -1.605  1.00  1.03          D5
HETATM    8 D1   IAS     8       0.253  -0.476  -0.641  1.00  1.19          D1
HETATM    9 D5   IAS     9       1.158   1.204  -3.380  1.00  0.95          D5
HETATM   10 D1   IAS    10       1.974   1.097  -4.424  1.00  1.19          D1
HETATM   11 D5   IAS    11       0.420   1.340  -2.446  1.00  0.95          D5
HETATM   12 D1   IAS    12      -0.384   1.541  -1.402  1.00  1.19          D1
HETATM   13 D4   IAS    13       0.477   2.272  -3.299  1.00  0.91          D4
HETATM   14 D4   IAS    14       0.677   3.542  -3.289  1.00  0.91          D4
HETATM   15 D1   IAS    15       0.333   2.962  -4.401  1.00  1.10          D1
HETATM   16 D1   IAS    16      -0.539   3.079  -3.350  1.00  1.10          D1
HETATM   17 D6   IAS    17       1.816   4.161  -3.359  1.00  0.91          D6
HETATM   18 D1   IAS    18       0.677   4.846  -3.199  1.00  0.99          D1
HETATM   19 D4   IAS    19       1.192   4.075  -2.265  1.00  0.83          D4
HETATM   20 D2   IAS    20       2.896   4.727  -3.371  1.00  1.10          D2
HETATM   21 D2   IAS    21       2.849   3.558  -3.510  1.00  1.10          D2
HETATM   22 D2   IAS    22       2.394   4.228  -4.408  1.00  1.10          D2
HETATM   23 D8   IAS    23       1.752   3.869  -1.311  1.00  0.99          D8
HETATM   24 D6   IAS    24       0.749   4.146  -1.136  1.00  0.83          D6
HETATM   25 D8   IAS    25       1.042   4.890   2.030  1.00  0.99          D8
HETATM   26 D4   IAS    26       0.584   4.487   1.090  1.00  0.91          D4
HETATM   27 D6   IAS    27       1.092   5.584   1.239  1.00  0.95          D6
HETATM   28 D6   IAS    28       0.217   4.137  -0.109  1.00  0.91          D6
HETATM   29 D1   IAS    29       0.619   3.240   0.828  1.00  1.10          D1
HETATM   30 D1   IAS    30      -0.568   3.906   0.916  1.00  1.10          D1
HETATM   31 D2   IAS    31      -0.470   4.416  -1.090  1.00  1.06          D2
HETATM   32 D8   IAS    32       1.410   8.867   2.122  1.00  0.99          D8
HETATM   33 D8   IAS    33       0.653   8.303   2.249  1.00  1.03          D8
HETATM   34 D6   IAS    34       1.592   6.648   1.254  1.00  1.07          D6
HETATM   35 D2   IAS    35       1.099   6.286   0.217  1.00  1.15          D2
HETATM   36 D4   IAS    36       1.576   7.806   1.851  1.00  0.99          D4
HETATM   37 D1   IAS    37       2.366   6.934   2.309  1.00  1.27          D1
HETATM   38 D1   IAS    38       2.565   7.521   1.061  1.00  1.27          D1
HETATM   39 D3   IAS    39       0.918   1.686   3.084  1.00  1.46          D3
HETATM   40 D3   IAS    40       0.782   2.788   3.272  1.00  1.46          D3
HETATM   41 D9   IAS    41       1.075   0.334  -2.554  1.00  0.95          D9
HETATM   42 D10  IAS    42       2.370   3.660  -0.690  1.00  0.83          D1
HETATM   43 D10  IAS    43       2.614   3.609  -1.283  1.00  0.83          D1
HETATM   44 D10  IAS    44       1.345   4.997   2.883  1.00  0.91          D1
HETATM   45 D10  IAS    45       1.076   4.418   2.809  1.00  0.91          D1
Scattering dictionary for combined xray_structure:
Number of scattering types: 14
  Type Number    sf(0)   Gaussians
   O       6      8.00       6
   N       3      7.00       6
   C      13      6.00       6
   H      19      1.00       6
   D1     11      0.22       1
   D5      6      0.20       1
   D2      5      0.16       1
   D4      5      0.14       1
   D8      4      0.11       1
   D3      3      0.09       1
   D6      5      0.08       1
   D7      1      0.07       1
   D10     4      0.05       1
   D9      1     -0.30       1
  sf(0) = scattering factor at diffraction angle 0.
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_anomalous_scatterer_groups.py P3
P 3
u+s,u,s: 2.73 2.57 0.16

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_rigid_body.py
test 1:  xyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   3.01 (80 reflections)
  WARNING: Final number of reflections for first resolution zone is greater
           than the number of available reflections (100 > 80).
  INFO: Number of resolution zones reset to 1.

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.6176   r_free= 0.1832   ksol= 0.00   Bsol= 0.00   scale= 0.703    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00   -0.50  -0.70  -0.90   1.24 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00   -0.50  -0.70  -0.90   1.24 |
|-----------------------------------------------------------------------------|

test 2:  xyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   3.01 (80 reflections)
  WARNING: Final number of reflections for first resolution zone is greater
           than the number of available reflections (100 > 80).
  INFO: Number of resolution zones reset to 1.

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

test 3:  xyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   2.00 (256 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   11.14 -  2.75         100    ls_wunit_k1
      2   11.14 -  2.75         101    ls_wunit_k1
      3   11.14 -  2.69         110    ls_wunit_k1
      4   11.14 -  2.42         149    ls_wunit_k1
      5   11.14 -  2.00         256    ls_wunit_k1
    zone number of reflections = 100 + 0.609375 * (zone-1)**4

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.1885   r_free= 0.1410   ksol= 0.00   Bsol= 0.00   scale= 0.974    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.69 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.42 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.945   -1.104    3.76    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

test 4:  xyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       41.94 -   2.00 (7315 reflections)
  Resolution for rigid body refinement:  41.94 -   2.00 (7315 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   41.94 -  9.06         100    ls_wunit_k1
      2   41.94 -  8.29         128    ls_wunit_k1
      3   41.94 -  4.92         551    ls_wunit_k1
      4   41.94 -  2.95        2383    ls_wunit_k1
      5   41.94 -  2.00        7315    ls_wunit_k1
    zone number of reflections = 100 + 28.1836 * (zone-1)**4

|-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------|
|                                                                             |
| r_work= 0.5468   r_free= 0.5461   ksol= 0.00   Bsol= 0.00   scale= 0.848    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 9.06 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0177   r_free= 0.0163   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.060   -1.913   -1.190    3.78   -0.48  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 8.29 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0110   r_free= 0.0124   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.002   -1.985   -1.172    3.77   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 4.92 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0025   r_free= 0.0026   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.036   -1.943   -1.099    3.75   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.95 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0006   r_free= 0.0007   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.039   -1.940   -1.105    3.76   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.039   -1.940   -1.102    3.76   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.039   -1.940   -1.102    3.76   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

test 5:  xyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 2
    Resulting number of reflections: 200
    Requested low-resolution limit: None
    Final number of reflections: 200
  Data resolution:                       41.94 -   2.00 (7315 reflections)
  Resolution for rigid body refinement:  41.94 -   2.00 (7315 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   41.94 -  7.02         200    ls_wunit_k1
      2   41.94 -  6.73         228    ls_wunit_k1
      3   41.94 -  4.65         645    ls_wunit_k1
      4   41.94 -  2.92        2451    ls_wunit_k1
      5   41.94 -  2.00        7315    ls_wunit_k1
    zone number of reflections = 200 + 27.793 * (zone-1)**4

|-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------|
|                                                                             |
| r_work= 0.5519   r_free= 0.4926   ksol= 0.00   Bsol= 0.00   scale= 0.833    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
| group    2:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 7.02 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0078   r_free= 0.0103   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.012   -1.953   -1.160    3.76   -0.50  -1.00  -1.50   1.87 |
| group    2:   -1.095   -1.936   -3.061    3.77   -1.50  -0.50  -0.99   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 6.73 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0062   r_free= 0.0068   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.027   -1.943   -1.144    3.76   -0.50  -1.00  -1.49   1.87 |
| group    2:   -1.088   -1.950   -3.045    3.76   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 4.65 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0047   r_free= 0.0047   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.034   -1.949   -1.082    3.75   -0.50  -1.00  -1.51   1.88 |
| group    2:   -1.093   -1.949   -3.043    3.76   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.92 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0012   r_free= 0.0012   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.038   -1.940   -1.108    3.76   -0.50  -1.00  -1.50   1.87 |
| group    2:   -1.103   -1.946   -3.043    3.76   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0003   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.039   -1.941   -1.105    3.76   -0.50  -1.00  -1.50   1.87 |
| group    2:   -1.105   -1.944   -3.036    3.76   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------|
|                                                                             |
| r_work= 0.0003   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -3.039   -1.941   -1.105    3.76   -0.50  -1.00  -1.50   1.87 |
| group    2:   -1.105   -1.944   -3.036    3.76   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

test 1:  zyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   3.01 (80 reflections)
  WARNING: Final number of reflections for first resolution zone is greater
           than the number of available reflections (100 > 80).
  INFO: Number of resolution zones reset to 1.

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.6176   r_free= 0.1832   ksol= 0.00   Bsol= 0.00   scale= 0.703    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00   -0.50  -0.70  -0.90   1.24 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00   -0.50  -0.70  -0.90   1.24 |
|-----------------------------------------------------------------------------|

test 2:  zyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   3.01 (80 reflections)
  WARNING: Final number of reflections for first resolution zone is greater
           than the number of available reflections (100 > 80).
  INFO: Number of resolution zones reset to 1.

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 3.01 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

test 3:  zyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       11.14 -   2.00 (256 reflections)
  Resolution for rigid body refinement:  11.14 -   2.00 (256 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   11.14 -  2.75         100    ls_wunit_k1
      2   11.14 -  2.75         101    ls_wunit_k1
      3   11.14 -  2.69         110    ls_wunit_k1
      4   11.14 -  2.42         149    ls_wunit_k1
      5   11.14 -  2.00         256    ls_wunit_k1
    zone number of reflections = 100 + 0.609375 * (zone-1)**4

|-Start-(resolution: 2.00 - 11.14 A; n_refl. = 259)---------------------------|
|                                                                             |
| r_work= 0.2132   r_free= 0.1989   ksol= 0.00   Bsol= 0.00   scale= 0.966    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.75 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.69 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.42 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 11.14 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 11.14 A; n_refl. = 259)-----------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 11.14 A; n_refl. = 259)------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.035   -2.000   -4.001    4.47    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

test 4:  zyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 1
    Resulting number of reflections: 100
    Requested low-resolution limit: None
    Final number of reflections: 100
  Data resolution:                       41.94 -   2.00 (7315 reflections)
  Resolution for rigid body refinement:  41.94 -   2.00 (7315 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   41.94 -  9.06         100    ls_wunit_k1
      2   41.94 -  8.29         128    ls_wunit_k1
      3   41.94 -  4.92         551    ls_wunit_k1
      4   41.94 -  2.95        2383    ls_wunit_k1
      5   41.94 -  2.00        7315    ls_wunit_k1
    zone number of reflections = 100 + 28.1836 * (zone-1)**4

|-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------|
|                                                                             |
| r_work= 0.5392   r_free= 0.4766   ksol= 0.00   Bsol= 0.00   scale= 0.850    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 9.06 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0206   r_free= 0.0190   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.052   -1.973   -4.107    4.56   -0.48  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 8.29 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0116   r_free= 0.0129   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.001   -2.051   -4.074    4.56   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 4.92 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0027   r_free= 0.0028   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.034   -2.004   -3.996    4.47   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.95 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0006   r_free= 0.0006   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.038   -2.000   -4.002    4.47   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.037   -2.000   -4.000    4.47   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.037   -2.000   -4.000    4.47   -0.50  -1.00  -1.50   1.87 |
|-----------------------------------------------------------------------------|

test 5:  zyz
Rigid body refinement:
  Requested number of resolution zones: 5
  Calculation for first resolution zone:
    Requested number of reflections per body: 100
    Requested factor per body: 1.0
    Number of bodies: 2
    Resulting number of reflections: 200
    Requested low-resolution limit: None
    Final number of reflections: 200
  Data resolution:                       41.94 -   2.00 (7315 reflections)
  Resolution for rigid body refinement:  41.94 -   2.00 (7315 reflections)
  Resolution cutoffs for multiple zones: 
                          number of
    zone     resolution  reflections  target
      1   41.94 -  7.02         200    ls_wunit_k1
      2   41.94 -  6.73         228    ls_wunit_k1
      3   41.94 -  4.65         645    ls_wunit_k1
      4   41.94 -  2.92        2451    ls_wunit_k1
      5   41.94 -  2.00        7315    ls_wunit_k1
    zone number of reflections = 200 + 27.793 * (zone-1)**4

|-Start-(resolution: 2.00 - 41.94 A; n_refl. = 7389)--------------------------|
|                                                                             |
| r_work= 0.5539   r_free= 0.4628   ksol= 0.00   Bsol= 0.00   scale= 0.830    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
| group    2:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 7.02 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0085   r_free= 0.0108   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.008   -2.008   -4.060    4.53   -0.50  -1.00  -1.49   1.87 |
| group    2:   -0.096   -1.988   -4.019    4.48   -1.50  -0.50  -0.99   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 6.73 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0066   r_free= 0.0075   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.023   -2.004   -4.047    4.52   -0.50  -1.00  -1.49   1.87 |
| group    2:   -0.087   -2.006   -4.014    4.49   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 4.65 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0043   r_free= 0.0043   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.033   -2.009   -3.980    4.46   -0.50  -1.00  -1.51   1.88 |
| group    2:   -0.093   -2.003   -4.009    4.48   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.92 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0012   r_free= 0.0012   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.037   -1.999   -4.004    4.48   -0.50  -1.00  -1.50   1.87 |
| group    2:   -0.103   -1.999   -4.009    4.48   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

 ----------Refinement at resolution: 41.94 - 2.00 target=ls_wunit_k1---------- 

|-Rigid body refinement-(resolution: 2.00 - 41.94 A; n_refl. = 7389)----------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.037   -2.000   -4.001    4.47   -0.50  -1.00  -1.50   1.87 |
| group    2:   -0.105   -1.997   -4.002    4.47   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 2.00 - 41.94 A; n_refl. = 7389)-----------------|
|                                                                             |
| r_work= 0.0002   r_free= 0.0003   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -0.037   -2.000   -4.001    4.47   -0.50  -1.00  -1.50   1.87 |
| group    2:   -0.105   -1.997   -4.002    4.47   -1.50  -0.50  -1.00   1.87 |
|-----------------------------------------------------------------------------|

finite_differences_test: 
u+s,u,s: 215.47 212.37 3.10

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/refinement/tst_refinement_flags.py
u+s,u,s: 2.31 2.16 0.15

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_model.py
|-Geometry statistics---------------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.041:    40 |   0.004 -   3.586:    52 |  2.642 -  2.868:       15 |
| 0.041 - 0.082:     0 |   3.586 -   7.169:     0 |  2.868 -  3.094:       15 |
| 0.082 - 0.123:     0 |   7.169 -  10.751:     0 |  3.094 -  3.319:       21 |
| 0.123 - 0.165:     0 |  10.751 -  14.334:     0 |  3.319 -  3.545:       33 |
| 0.165 - 0.206:     0 |  14.334 -  17.916:     0 |  3.545 -  3.770:       50 |
| 0.206 - 0.247:     0 |  17.916 -  21.499:     1 |  3.770 -  3.996:       71 |
| 0.247 - 0.288:     0 |  21.499 -  25.081:     0 |  3.996 -  4.222:       59 |
| 0.288 - 0.329:     0 |  25.081 -  28.663:     0 |  4.222 -  4.447:       78 |
| 0.329 - 0.370:     0 |  28.663 -  32.246:     0 |  4.447 -  4.673:       91 |
| 0.370 - 0.412:     1 |  32.246 -  35.828:     1 |  4.673 -  4.899:      108 |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |       41 |   0.064    0.412  0.000 |      10.330 |              |
|     angle |       54 |   5.564   35.828  0.004 |       3.441 |              |
| chirality |        4 |   0.002    0.003  0.001 |       0.000 |        1.228 |
| planarity |        7 |   0.052    0.138  0.000 |      27.185 |              |
|  dihedral |       11 |  22.383   69.790  0.067 |       0.667 |              |
| nonbonded |       41 |   4.176    4.899  2.642 |       0.028 |              |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.041:    40 |   0.004 -   3.586:    52 |  2.642 -  2.868:       15 |
| 0.041 - 0.082:     0 |   3.586 -   7.169:     0 |  2.868 -  3.094:       15 |
| 0.082 - 0.123:     0 |   7.169 -  10.751:     0 |  3.094 -  3.319:       21 |
| 0.123 - 0.165:     0 |  10.751 -  14.334:     0 |  3.319 -  3.545:       33 |
| 0.165 - 0.206:     0 |  14.334 -  17.916:     0 |  3.545 -  3.770:       50 |
| 0.206 - 0.247:     0 |  17.916 -  21.499:     1 |  3.770 -  3.996:       71 |
| 0.247 - 0.288:     0 |  21.499 -  25.081:     0 |  3.996 -  4.222:       59 |
| 0.288 - 0.329:     0 |  25.081 -  28.663:     0 |  4.222 -  4.447:       78 |
| 0.329 - 0.370:     0 |  28.663 -  32.246:     0 |  4.447 -  4.673:       91 |
| 0.370 - 0.412:     1 |  32.246 -  35.828:     1 |  4.673 -  4.899:      108 |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |       41 |   0.064    0.412  0.000 |      10.330 |              |
|     angle |       54 |   5.564   35.828  0.004 |       3.441 |              |
| chirality |        4 |   0.002    0.003  0.001 |       0.000 |        1.228 |
| planarity |        7 |   0.052    0.138  0.000 |      27.185 |              |
|  dihedral |       11 |  22.383   69.790  0.067 |       0.667 |              |
| nonbonded |       41 |   4.176    4.899  2.642 |       0.028 |              |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.041:    40 |   0.004 -   3.586:    52 |  1.157 -  1.532:        1 |
| 0.041 - 0.082:     0 |   3.586 -   7.169:     0 |  1.532 -  1.906:        0 |
| 0.082 - 0.123:     0 |   7.169 -  10.751:     0 |  1.906 -  2.280:        0 |
| 0.123 - 0.165:     0 |  10.751 -  14.334:     0 |  2.280 -  2.654:        3 |
| 0.165 - 0.206:     0 |  14.334 -  17.916:     0 |  2.654 -  3.028:       29 |
| 0.206 - 0.247:     0 |  17.916 -  21.499:     1 |  3.028 -  3.402:       59 |
| 0.247 - 0.288:     0 |  21.499 -  25.081:     0 |  3.402 -  3.776:       86 |
| 0.288 - 0.329:     0 |  25.081 -  28.663:     0 |  3.776 -  4.150:      125 |
| 0.329 - 0.370:     0 |  28.663 -  32.246:     0 |  4.150 -  4.524:      158 |
| 0.370 - 0.412:     1 |  32.246 -  35.828:     1 |  4.524 -  4.899:      197 |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |       41 |   0.064    0.412  0.000 |      10.330 |              |
|     angle |       54 |   5.564   35.828  0.004 |       3.441 |              |
| chirality |        4 |   0.002    0.003  0.001 |       0.000 |        1.329 |
| planarity |        7 |   0.052    0.138  0.000 |      27.185 |              |
|  dihedral |       11 |  22.383   69.790  0.067 |       0.667 |              |
| nonbonded |       41 |   4.147    4.899  1.157 |       5.430 |              |
|-----------------------------------------------------------------------------|

|-Geometry statistics---------------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.041:    40 |   0.004 -   3.586:    52 |  2.642 -  2.868:       15 |
| 0.041 - 0.082:     0 |   3.586 -   7.169:     0 |  2.868 -  3.094:       15 |
| 0.082 - 0.123:     0 |   7.169 -  10.751:     0 |  3.094 -  3.319:       21 |
| 0.123 - 0.165:     0 |  10.751 -  14.334:     0 |  3.319 -  3.545:       33 |
| 0.165 - 0.206:     0 |  14.334 -  17.916:     0 |  3.545 -  3.770:       50 |
| 0.206 - 0.247:     0 |  17.916 -  21.499:     1 |  3.770 -  3.996:       71 |
| 0.247 - 0.288:     0 |  21.499 -  25.081:     0 |  3.996 -  4.222:       59 |
| 0.288 - 0.329:     0 |  25.081 -  28.663:     0 |  4.222 -  4.447:       78 |
| 0.329 - 0.370:     0 |  28.663 -  32.246:     0 |  4.447 -  4.673:       91 |
| 0.370 - 0.412:     1 |  32.246 -  35.828:     1 |  4.673 -  4.899:      108 |
|-----------------------------------------------------------------------------|
|-Geometry statistics---------------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |       41 |   0.064    0.412  0.000 |      10.330 |              |
|     angle |       54 |   5.564   35.828  0.004 |       3.441 |              |
| chirality |        4 |   0.002    0.003  0.001 |       0.000 |        1.228 |
| planarity |        7 |   0.052    0.138  0.000 |      27.185 |              |
|  dihedral |       11 |  22.383   69.790  0.067 |       0.667 |              |
| nonbonded |       41 |   4.176    4.899  2.642 |       0.028 |              |
|-----------------------------------------------------------------------------|
|-ADP statistics-------------------------------------------------------|
| Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max |
| type    |iso    aniso | min     max     mean   | min   max    mean   |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all     : 40     0      0.85    1.88    1.20     None  None   None   |
| all(noH): 40     0      0.85    1.88    1.20     None  None   None   |
| Sol.    : 0      0      None    None    None     None  None   None   |
| Mac.    : 40     0      0.85    1.88    1.20     None  None   None   |
| Hyd.    : 0      0      None    None    None     None  None   None   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  |
|    Distribution of isotropic (or equivalent) ADP for non-H atoms:    |
| Bin#      value range     #atoms | Bin#      value range     #atoms  |
|   0:     0.850 -   0.953:    9   |   5:     1.365 -   1.468:    4    |
|   1:     0.953 -   1.056:    6   |   6:     1.468 -   1.571:    4    |
|   2:     1.056 -   1.159:    8   |   7:     1.571 -   1.674:    2    |
|   3:     1.159 -   1.262:    3   |   8:     1.674 -   1.777:    0    |
|   4:     1.262 -   1.365:    2   |   9:     1.777 -   1.880:    2    |
|                            =>continue=>                              |
|----------------------------------------------------------------------|

|-ADP statistics-------------------------------------------------------|
| Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max |
| type    |iso    aniso | min     max     mean   | min   max    mean   |
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - |
| all     : 40     0      0.85    1.88    1.20     None  None   None   |
| all(noH): 40     0      0.85    1.88    1.20     None  None   None   |
| Sol.    : 0      0      None    None    None     None  None   None   |
| Mac.    : 40     0      0.85    1.88    1.20     None  None   None   |
| Hyd.    : 0      0      None    None    None     None  None   None   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  |
|    Distribution of isotropic (or equivalent) ADP for non-H atoms:    |
| Bin#      value range     #atoms | Bin#      value range     #atoms  |
|   0:     0.850 -   0.953:    9   |   5:     1.365 -   1.468:    4    |
|   1:     0.953 -   1.056:    6   |   6:     1.468 -   1.571:    4    |
|   2:     1.056 -   1.159:    8   |   7:     1.571 -   1.674:    2    |
|   3:     1.159 -   1.262:    3   |   8:     1.674 -   1.777:    0    |
|   4:     1.262 -   1.365:    2   |   9:     1.777 -   1.880:    2    |
|                            =>continue=>                              |
|----------------------------------------------------------------------|
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 46
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
          Modifications used: {'NH3': 1}
    Chain: "S"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 20
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 0.09, per 1000 atoms: 1.96

  Number of scatterers: 46
  At special positions: 0
  Unit cell: (15.343, 15.541, 15.674, 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      10      8.00
     N       4      7.00
     C       6      6.00
     H      26      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:
        0.54 -     0.77: 2
        0.77 -     1.01: 11
        1.01 -     1.24: 8
        1.24 -     1.48: 11
        1.48 -     1.72: 4
  Bond restraints sorted by residual:
                 atom i - atom j                ideal  model  delta   weight residual
  pdb=" O   HOH S   7 " - pdb=" H1  HOH S   7 " 0.980  1.476 -0.496 2.50e+03 6.14e+02
  pdb=" CG  ARG A   1 " - pdb=" HG3 ARG A   1 " 0.970  0.537  0.433 2.50e+03 4.70e+02
  pdb=" O   HOH S   9 " - pdb=" H2  HOH S   9 " 0.980  1.323 -0.343 2.50e+03 2.95e+02
  pdb=" CA  ARG A   1 " - pdb=" HA  ARG A   1 " 0.980  1.263 -0.283 2.50e+03 2.00e+02
  pdb=" O   HOH S   1 " - pdb=" H1  HOH S   1 " 0.980  1.262 -0.282 2.50e+03 1.99e+02
  ... (remaining 31 not shown)
  Histogram of nonbonded interaction distances:
        0.71 -     1.55: 14
        1.55 -     2.38: 25
        2.38 -     3.22: 86
        3.22 -     4.05: 56
        4.05 -     4.89: 108
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HH12 ARG A   1 " - pdb=" H1  HOH S   4 "  0.712 2.400
  pdb="HH11 ARG A   1 " - pdb=" H2  HOH S   4 "  0.791 2.400
  pdb=" H1  HOH S   1 " - pdb=" H1  HOH S   9 "  0.840 2.400
  pdb=" O   HOH S   5 " - pdb=" H1  HOH S   8 "  0.902 2.720
  pdb=" H2  HOH S   1 " - pdb=" H2  HOH S   9 "  0.914 2.400
  ... (remaining 284 not shown)
  Histogram of dihedral angle deviations from ideal:
        3.91 -     6.53: 3
        6.53 -     9.16: 1
        9.16 -    11.79: 1
       11.79 -    14.42: 1
       14.42 -    17.04: 1
  Dihedral angle restraints sorted by residual:
  pdb=" CD  ARG A   1 "
  pdb=" NE  ARG A   1 "
  pdb=" CZ  ARG A   1 "
  pdb=" NH2 ARG A   1 "
      ideal   model   delta periodicty    weight residual
       0.00  170.11    9.89     2       1.00e-02 9.78e-01
  pdb=" NE  ARG A   1 "
  pdb=" CZ  ARG A   1 "
  pdb=" NH1 ARG A   1 "
  pdb="HH12 ARG A   1 "
      ideal   model   delta periodicty    weight residual
       0.00   17.04  -17.04     2       2.50e-03 7.26e-01
  pdb=" NE  ARG A   1 "
  pdb=" CZ  ARG A   1 "
  pdb=" NH2 ARG A   1 "
  pdb="HH22 ARG A   1 "
      ideal   model   delta periodicty    weight residual
       0.00  167.09   12.91     2       2.50e-03 4.16e-01
  ... (remaining 4 not shown)
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 1191
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 1191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 1191
          Unusual residues: {'AU ': 1}
          Inner-chain residues flagged as termini: ['pdbres="CYS   127 "']
          Classifications: {'undetermined': 1, 'water': 208, 'peptide': 127}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, None: 209, 'TRANS': 124}
  Time building chain proxies: 2.44, per 1000 atoms: 2.05

  Number of scatterers: 1191
  At special positions: 0
  Unit cell: (28.174, 52.857, 68.929, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Au      1     78.96
     S      10     16.00
     O     391      8.00
     N     188      7.00
     C     601      6.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS     6 " - pdb=" SG  CYS   127 " distance=1.99
    Simple disulfide: pdb=" SG  CYS    30 " - pdb=" SG  CYS   115 " distance=1.98
    Simple disulfide: pdb=" SG  CYS    64 " - pdb=" SG  CYS    80 " distance=1.98
    Simple disulfide: pdb=" SG  CYS    76 " - pdb=" SG  CYS    94 " distance=1.98
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.19 -     1.35: 352
        1.35 -     1.51: 579
        1.51 -     1.67: 59
        1.67 -     1.83: 12
        1.83 -     1.99: 4
  Bond restraints sorted by residual:
                 atom i - atom j                ideal  model  delta   weight residual
  pdb=" CA  TYR    53 " - pdb=" C   TYR    53 " 1.525  1.451  0.074 2.27e+03 1.25e+01
  pdb=" CA  TRP    63 " - pdb=" C   TRP    63 " 1.525  1.451  0.074 2.27e+03 1.23e+01
  pdb=" CB  CYS    76 " - pdb=" SG  CYS    76 " 1.808  1.697  0.111 9.18e+02 1.14e+01
  pdb=" CG  MET    12 " - pdb=" SD  MET    12 " 1.803  1.719  0.084 1.60e+03 1.12e+01
  pdb=" CB  TRP   123 " - pdb=" CG  TRP   123 " 1.498  1.401  0.097 1.04e+03 9.71e+00
  ... (remaining 1001 not shown)
  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 565
        2.72 -     3.26: 1653
        3.26 -     3.81: 3296
        3.81 -     4.35: 4089
        4.35 -     4.90: 5786
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw sym.op. j
  pdb=" O   THR    43 " - pdb=" O   HOH   164 "  2.172 3.040
  pdb=" NH2 ARG    61 " - pdb=" O   GLY   102 "  2.237 3.120 x-1/2,-y-1/2,-z+1
  pdb=" O   HOH    81 " - pdb=" O   HOH    91 "  2.251 3.040
  pdb=" O   HOH   191 " - pdb=" O   HOH   195 "  2.271 3.040
  pdb=" O   HOH    21 " - pdb=" O   HOH   139 "  2.273 3.040
  ... (remaining 15384 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.04 -    16.72: 305
       16.72 -    33.40: 32
       33.40 -    50.08: 7
       50.08 -    66.75: 6
       66.75 -    83.43: 3
  Dihedral angle restraints sorted by residual:
  pdb=" CA  TRP    62 "
  pdb=" C   TRP    62 "
  pdb=" N   TRP    63 "
  pdb=" CA  TRP    63 "
      ideal   model   delta periodicty    weight residual
     180.00 -155.81  -24.19     1       4.00e-02 2.34e+01
  pdb=" CA  PHE     3 "
  pdb=" C   PHE     3 "
  pdb=" N   GLY     4 "
  pdb=" CA  GLY     4 "
      ideal   model   delta periodicty    weight residual
     180.00  160.44   19.56     1       4.00e-02 1.53e+01
  pdb=" CA  ASN   113 "
  pdb=" C   ASN   113 "
  pdb=" N   ARG   114 "
  pdb=" CA  ARG   114 "
      ideal   model   delta periodicty    weight residual
     180.00 -161.24  -18.76     1       4.00e-02 1.41e+01
  ... (remaining 350 not shown)
u+s,u,s: 10.57 10.38 0.19

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_fmodel.py
P 1
P 4
C 1 2/c 1
u+s,u,s: 196.44 193.26 3.18

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_utils.py
u+s,u,s: 20.86 20.62 0.24

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_alignment.py
testError (__main__.test_blosum62) ... ok
testSelected (__main__.test_blosum62) ... ok
testSymmetric (__main__.test_blosum62) ... ok

----------------------------------------------------------------------
Ran 3 tests in 0.002s

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_fmodel_fd.py P31
P 31
   ls_wexp_kunit
   lsm_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_k1_fixed
   ls_wunit_kunit
   lsm_k2
   lsm_k1
   lsm_k1_fixed
   mlhl
   ls_wunit_k1ask3_fixed
   ml
   ls_wff_k1_fixed
   ls_wff_kunit
   ls_wexp_k2
   ls_wff_k1ask3_fixed
   lsm_k1ask3_fixed
   ls_wexp_k1
   ls_wexp_kunit
   lsm_kunit
   ls_wff_k1
   ls_wff_k2
   ls_wunit_k1
   ls_wunit_k2
   ls_wunit_k1_fixed
   ls_wunit_kunit
   lsm_k2
   lsm_k1
   lsm_k1_fixed
   ls_wunit_k1ask3_fixed
   ml
   ls_wff_k1_fixed
   ls_wff_kunit
   ls_wexp_k2
   ls_wff_k1ask3_fixed
   lsm_k1ask3_fixed
   ls_wexp_k1
u+s,u,s: 14.50 14.23 0.27

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restraints.py
u+s,u,s: 3.31 3.16 0.15

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/tst_restraints.py
u+s,u,s: 3.28 3.12 0.16

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/ncs/ncs.py exercise
Reading NCS information from:  TEST.NCS
 based on  TEST.NCS

GROUP 1
Summary of NCS group with 2 operators:
ID of chain/residue where these apply: [['A', 'B'], [[[1, 26]], [[101, 126]]]]
RMSD (A) from chain A:  0.2  0.1
Number of residues matching chain A:[12.0, 15.0]
Source of NCS info: TEST.NCS
NCS domains represented by: TEST.NCS
Correlation of NCS: 0.92

OPERATOR 1
CENTER:   30.2920   -2.8923   16.6160

ROTA 1:    1.0000    0.0000    0.0000
ROTA 2:    0.0000    1.0000    0.0000
ROTA 3:    0.0000    0.0000    1.0000
TRANS:     0.0000    0.0000    0.0000

OPERATOR 2
CENTER:   39.8735    3.8824   16.7239

ROTA 1:   -0.9971    0.0424   -0.0635
ROTA 2:   -0.0297   -0.9816   -0.1889
ROTA 3:   -0.0703   -0.1864    0.9800
TRANS:    70.9461    5.2622    3.7549

GROUP 2
Summary of NCS group with 2 operators:
ID of chain/residue where these apply: [['A', 'B'], [[[1, 25]], [[101, 124]]]]
RMSD (A) from chain A:  0.6  0.5
Number of residues matching chain A:[13.0, 11.0]
Source of NCS info: TEST.NCS
NCS domains represented by: TEST.NCS
Correlation of NCS: 0.95

OPERATOR 1
CENTER:   31.2920   -2.8923   16.6160

ROTA 1:    1.0000    0.0000    0.0000
ROTA 2:    0.0000    1.0000    0.0000
ROTA 3:    0.0000    0.0000    1.0000
TRANS:     0.0000    0.0000    0.0001

OPERATOR 2
CENTER:   38.8735    3.8824   16.7239

ROTA 1:   -0.9970    0.0424   -0.0635
ROTA 2:   -0.0297   -0.9816   -0.1889
ROTA 3:   -0.0703   -0.1864    0.9800
TRANS:    70.9461    5.2622    3.7549

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_adp_restraints.py
u+s,u,s: 3.11 2.94 0.17

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_scaling.py
very_quick_erf*15000000 optimized=False: 14.20 s
very_quick_erf*15000000 optimized=True: 1.36 s
quick_ei0*5000000 optimized=False: 1.85 s
quick_ei0*5000000 optimized=True: 0.83 s
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/tst_outlier.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/absence_likelihood.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/scaling/thorough_outlier_test.py P21
P 1 21 1
u+s,u,s: 30.83 30.40 0.43

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/twinning/probabalistic_detwinning.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_rna_sugar_pucker_analysis.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_cif_types.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_motif.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_selection.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_tyr_from_gly_and_bnz.py
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.67

  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        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
    "ATOM    145  CB  GLY     1 .*.     C  "
  Time building chain proxies: 0.04, per 1000 atoms: 3.33

geo_tyr
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.03 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
  pdb=" CD1 TYR     1 " - pdb=" CE1 TYR     1 " 1.382  1.394 -0.012 1.11e+03 1.67e-01
  pdb=" CD2 TYR     1 " - pdb=" CE2 TYR     1 " 1.382  1.393 -0.011 1.11e+03 1.31e-01
  pdb=" CE2 TYR     1 " - pdb=" CZ  TYR     1 " 1.378  1.386 -0.008 1.74e+03 1.09e-01
  pdb=" N   TYR     1 " - pdb=" CA  TYR     1 " 1.458  1.453  0.005 2.77e+03 6.34e-02
  pdb=" CG  TYR     1 " - pdb=" 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 -     3.19: 4
        3.19 -     3.60: 7
        3.60 -     4.02: 7
        4.02 -     4.44: 5
        4.44 -     4.85: 7
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb=" CD2 TYR     1 " - pdb=" CE1 TYR     1 "  2.772 2.912
  pdb=" CD1 TYR     1 " - pdb=" CE2 TYR     1 "  2.773 2.912
  pdb=" CG  TYR     1 " - pdb=" CZ  TYR     1 "  2.797 2.784
  pdb=" C   TYR     1 " - pdb=" CG  TYR     1 "  2.865 2.792
  pdb=" O   TYR     1 " - pdb=" CG  TYR     1 "  3.226 3.260
  ... (remaining 25 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:
  pdb=" N   TYR     1 "
  pdb=" CA  TYR     1 "
  pdb=" CB  TYR     1 "
  pdb=" CG  TYR     1 "
      ideal   model   delta periodicty    weight residual
     180.00  170.12    9.88     3       4.44e-03 4.34e-01
  pdb=" CA  TYR     1 "
  pdb=" CB  TYR     1 "
  pdb=" CG  TYR     1 "
  pdb=" CD1 TYR     1 "
      ideal   model   delta periodicty    weight residual
      90.00   78.11   11.89     2       2.50e-03 3.53e-01
  target: 3.72568
    bond_residual_sum (n=12): 0.630997
    nonbonded_residual_sum (n=30): 0.155571
    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: 0.02 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
  pdb=" CA  GLY     1 " - pdb=" C   GLY     1 " 1.516  1.527 -0.011 3.09e+03 3.98e-01
  pdb=" CD1 BNZ     2 " - pdb=" CE1 BNZ     2 " 1.382  1.394 -0.012 1.11e+03 1.67e-01
  pdb=" CD2 BNZ     2 " - pdb=" CE2 BNZ     2 " 1.382  1.393 -0.011 1.11e+03 1.31e-01
  pdb=" CE2 BNZ     2 " - pdb=" CZ  BNZ     2 " 1.378  1.386 -0.008 1.74e+03 1.09e-01
  pdb=" CG  BNZ     2 " - pdb=" 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
  pdb=" CA  GLY     1 " - pdb=" CB  GLY     1 "  1.529 1.000
  pdb=" N   GLY     1 " - pdb=" CB  GLY     1 "  2.455 1.000
  pdb=" C   GLY     1 " - pdb=" CB  GLY     1 "  2.498 1.000
  pdb=" CA  GLY     1 " - pdb=" CG  BNZ     2 "  2.534 3.660
  pdb=" CD2 BNZ     2 " - pdb=" CE1 BNZ     2 "  2.772 2.912
  ... (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:
  pdb=" N   GLY     1 "
  pdb=" CA  GLY     1 "
  pdb=" CB  GLY     1 "
  pdb=" CG  BNZ     2 "
      ideal   model   delta periodicty    weight residual
     180.00  170.12    9.88     3       4.44e-03 4.34e-01
  pdb=" CA  GLY     1 "
  pdb=" CB  GLY     1 "
  pdb=" CG  BNZ     2 "
  pdb=" CD1 BNZ     2 "
      ideal   model   delta periodicty    weight residual
      90.00   78.11   11.89     2       2.50e-03 3.53e-01
  target: 32.4767
    bond_residual_sum (n=11): 0.970446
    nonbonded_residual_sum (n=33): 29.2511
    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/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_pdb_interpretation.py
u+s,u,s: 7.64 7.47 0.17

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_rna_dna_interpretation.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/monomer_library/tst_protein_interpretation.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/regression/tst_altloc_chain_break.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/hydrogens/build_hydrogens.py
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/arg.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.05, per 1000 atoms: 4.17

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 24
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.05, per 1000 atoms: 2.08
  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: 0.02 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
  pdb=" CA  ARG     1 " - pdb="HA   ARG     1 " 0.980  1.062 -0.082 2.50e+03 1.69e+01
  pdb=" NE  ARG     1 " - pdb=" CZ  ARG     1 " 1.329  1.367 -0.038 5.10e+03 7.42e+00
  pdb=" CA  ARG     1 " - pdb=" N   ARG     1 " 1.458  1.507 -0.049 2.77e+03 6.52e+00
  pdb=" NE  ARG     1 " - pdb="HE   ARG     1 " 0.970  1.010 -0.040 2.50e+03 4.09e+00
  pdb=" CB  ARG     1 " - pdb=" 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 -     2.70: 28
        2.70 -     3.25: 34
        3.25 -     3.80: 33
        3.80 -     4.34: 28
        4.34 -     4.89: 30
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HD2  ARG     1 " - pdb="HH12 ARG     1 "  2.158 2.400
  pdb="HE   ARG     1 " - pdb="HH21 ARG     1 "  2.266 2.400
  pdb="HD1  ARG     1 " - pdb="HG2  ARG     1 "  2.275 1.920
  pdb="HE   ARG     1 " - pdb="HD1  ARG     1 "  2.285 1.920
  pdb="HH22 ARG     1 " - pdb="HH11 ARG     1 "  2.294 2.400
  ... (remaining 148 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:
  pdb=" OXT ARG     1 "
  pdb=" C   ARG     1 "
  pdb=" CA  ARG     1 "
  pdb=" N   ARG     1 "
      ideal   model   delta periodicty    weight residual
     160.00  132.82   27.18     2       1.11e-03 8.21e-01
  pdb=" CB  ARG     1 "
  pdb=" CG  ARG     1 "
  pdb=" CD  ARG     1 "
  pdb=" NE  ARG     1 "
      ideal   model   delta periodicty    weight residual
     180.00   71.06  -11.06     3       4.44e-03 5.44e-01
  pdb=" CG  ARG     1 "
  pdb=" CB  ARG     1 "
  pdb=" CA  ARG     1 "
  pdb=" 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: 60.28
    bond_residual_sum (n=23): 43.5818
    nonbonded_residual_sum (n=153): 1.14145
    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: 60.28
  bond_residual_sum (n=23): 43.5818
  nonbonded_residual_sum (n=153): 1.14145
  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: 781.811

Energies after minimization:
target: 4.23207
  bond_residual_sum (n=23): 0.058584
  nonbonded_residual_sum (n=153): 3.00516
  angle_residual_sum (n=39): 0.93043
  dihedral_residual_sum (n=8): 0.22035
  chirality_residual_sum (n=1): 0.0173148
  planarity_residual_sum (n=2): 0.00022968
  norm of gradients: 9.08072e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/lys.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 10
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 4.00

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 25
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Duplicate atoms: {'LYS%COO,HB1': 3}
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of atoms with unknown scattering type symbols: 3
    "ATOM     22 HB2  LYS     1 .*.        "
    "ATOM     23 HB1  LYS     1 .*.        "
    "ATOM     24 HB2  LYS     1 .*.        "
  Number of atoms with unknown nonbonded energy type symbols: 3
    "ATOM     22 HB2  LYS     1 .*.        "
    "ATOM     23 HB1  LYS     1 .*.        "
    "ATOM     24 HB2  LYS     1 .*.        "
  Time building chain proxies: 0.04, per 1000 atoms: 1.60
  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: 0.02 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
  pdb=" CA  LYS     1 " - pdb=" N   LYS     1 " 1.458  1.506 -0.048 2.77e+03 6.37e+00
  pdb=" CA  LYS     1 " - pdb="HA   LYS     1 " 0.980  1.020 -0.040 2.50e+03 4.08e+00
  pdb=" CB  LYS     1 " - pdb=" CA  LYS     1 " 1.530  1.555 -0.025 2.50e+03 1.52e+00
  pdb=" C   LYS     1 " - pdb=" OXT LYS     1 " 1.231  1.250 -0.019 2.50e+03 8.82e-01
  pdb=" C   LYS     1 " - pdb=" 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 -     1.57: 8
        1.57 -     2.39: 26
        2.39 -     3.21: 65
        3.21 -     4.03: 44
        4.03 -     4.85: 42
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HB1  LYS     1 " - pdb="HB2  LYS     1 "  0.754 1.000
  pdb="HB2  LYS     1 " - pdb="HB1  LYS     1 "  0.795 1.000
  pdb=" CB  LYS     1 " - pdb="HB1  LYS     1 "  0.970 1.000
  pdb=" CB  LYS     1 " - pdb="HB2  LYS     1 "  0.970 1.000
  pdb=" CB  LYS     1 " - pdb="HB2  LYS     1 "  0.970 1.000
  ... (remaining 180 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:
  pdb=" CD  LYS     1 "
  pdb=" CE  LYS     1 "
  pdb=" NZ  LYS     1 "
  pdb="HZ3  LYS     1 "
      ideal   model   delta periodicty    weight residual
      60.00  141.07   38.93     3       1.11e-03 1.68e+00
  pdb=" OXT LYS     1 "
  pdb=" C   LYS     1 "
  pdb=" CA  LYS     1 "
  pdb=" N   LYS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.77   29.77     2       1.11e-03 9.85e-01
  pdb=" CA  LYS     1 "
  pdb=" CB  LYS     1 "
  pdb=" CG  LYS     1 "
  pdb=" 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: 668.898
    bond_residual_sum (n=21): 14.6924
    nonbonded_residual_sum (n=185): 10.7633
    angle_residual_sum (n=39): 638.229
    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: 668.898
  bond_residual_sum (n=21): 14.6924
  nonbonded_residual_sum (n=185): 10.7633
  angle_residual_sum (n=39): 638.229
  dihedral_residual_sum (n=6): 4.52202
  chirality_residual_sum (n=1): 0.690449
  planarity_residual_sum (n=1): 0.000506488
  norm of gradients: 1336.79

Energies after minimization:
target: 1.47913
  bond_residual_sum (n=21): 0.0112116
  nonbonded_residual_sum (n=182): 0.626626
  angle_residual_sum (n=39): 0.419968
  dihedral_residual_sum (n=6): 0.397743
  chirality_residual_sum (n=1): 0.0235834
  planarity_residual_sum (n=1): 7.35854e-15
  norm of gradients: 2.11422e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ala.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 6
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 5.00

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 10
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 2.00
  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
  pdb=" CA  ALA     1 " - pdb="HA   ALA     1 " 0.980  1.050 -0.070 2.50e+03 1.23e+01
  pdb=" CA  ALA     1 " - pdb=" N   ALA     1 " 1.458  1.503 -0.045 2.77e+03 5.55e+00
  pdb=" C   ALA     1 " - pdb=" OXT ALA     1 " 1.231  1.250 -0.019 2.50e+03 9.41e-01
  pdb=" C   ALA     1 " - pdb=" O   ALA     1 " 1.231  1.249 -0.018 2.50e+03 7.81e-01
  pdb=" C   ALA     1 " - pdb=" 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
  pdb="HA   ALA     1 " - pdb="HB3  ALA     1 "  2.298 1.920
  pdb=" OXT ALA     1 " - pdb="HA   ALA     1 "  2.457 2.176
  pdb="HA   ALA     1 " - pdb="HB1  ALA     1 "  2.473 1.920
  pdb=" N   ALA     1 " - pdb="HB1  ALA     1 "  2.586 2.240
  pdb=" C   ALA     1 " - pdb="HB2  ALA     1 "  2.615 2.360
  ... (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:
  pdb=" N   ALA     1 "
  pdb=" CB  ALA     1 "
  pdb=" CA  ALA     1 "
  pdb="HB3  ALA     1 "
      ideal   model   delta periodicty    weight residual
     -60.00  163.29   16.71     3       4.44e-03 1.24e+00
  pdb=" OXT ALA     1 "
  pdb=" C   ALA     1 "
  pdb=" CA  ALA     1 "
  pdb=" 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): 1.76642e-12
  chirality_residual_sum (n=1): 0.0188403
  planarity_residual_sum (n=1): 3.55183e-15
  norm of gradients: 9.04354e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/gly.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 5
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.01, per 1000 atoms: 2.00

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        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: 0.01 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
  pdb=" CA  GLY     1 " - pdb=" N   GLY     1 " 1.451  1.491 -0.040 3.91e+03 6.31e+00
  pdb=" C   GLY     1 " - pdb=" O   GLY     1 " 1.231  1.250 -0.019 2.50e+03 8.56e-01
  pdb=" OXT GLY     1 " - pdb=" C   GLY     1 " 1.231  1.249 -0.018 2.50e+03 7.95e-01
  pdb=" C   GLY     1 " - pdb=" CA  GLY     1 " 1.516  1.524 -0.008 3.09e+03 2.10e-01
  pdb=" CA  GLY     1 " - pdb="HA2  GLY     1 " 0.970  0.970  0.000 2.50e+03 4.41e-04
  pdb=" CA  GLY     1 " - pdb="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
  pdb=" OXT GLY     1 " - pdb="HA2  GLY     1 "  2.435 2.176
  pdb=" O   GLY     1 " - pdb="HA1  GLY     1 "  2.646 2.176
  pdb=" O   GLY     1 " - pdb=" N   GLY     1 "  2.924 2.496
  pdb=" OXT GLY     1 " - pdb="HA1  GLY     1 "  2.983 2.176
  pdb=" O   GLY     1 " - pdb="HA2  GLY     1 "  3.158 2.176
  pdb=" OXT GLY     1 " - pdb=" N   GLY     1 "  3.421 2.496
  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:
  pdb=" OXT GLY     1 "
  pdb=" C   GLY     1 "
  pdb=" CA  GLY     1 "
  pdb=" 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): 2.73974e-15
  nonbonded_residual_sum (n=6): 0
  angle_residual_sum (n=9): 0.13971
  dihedral_residual_sum (n=1): 1.01429e-14
  chirality_residual_sum (n=0): 0
  planarity_residual_sum (n=1): 5.24466e-16
  norm of gradients: 8.48013e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/his.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 3.64

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 18
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 2.22
  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: 0.01 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
  pdb=" CA  HIS     1 " - pdb=" N   HIS     1 " 1.458  1.505 -0.047 2.77e+03 6.20e+00
  pdb=" CA  HIS     1 " - pdb="HA   HIS     1 " 0.980  1.028 -0.048 2.50e+03 5.66e+00
  pdb=" CB  HIS     1 " - pdb=" CA  HIS     1 " 1.530  1.557 -0.027 2.50e+03 1.76e+00
  pdb=" C   HIS     1 " - pdb=" OXT HIS     1 " 1.231  1.250 -0.019 2.50e+03 9.07e-01
  pdb=" C   HIS     1 " - pdb=" 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 -     2.87: 14
        2.87 -     3.38: 21
        3.38 -     3.88: 22
        3.88 -     4.39: 12
        4.39 -     4.90: 18
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HE1  HIS     1 " - pdb="HD1  HIS     1 "  2.363 1.920
  pdb="HE2  HIS     1 " - pdb="HE1  HIS     1 "  2.364 1.920
  pdb="HE2  HIS     1 " - pdb="HD2  HIS     1 "  2.426 1.920
  pdb=" OXT HIS     1 " - pdb="HA   HIS     1 "  2.462 2.176
  pdb="HD1  HIS     1 " - pdb="HB1  HIS     1 "  2.486 2.400
  ... (remaining 82 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:
  pdb=" CG  HIS     1 "
  pdb=" CB  HIS     1 "
  pdb=" CA  HIS     1 "
  pdb=" N   HIS     1 "
      ideal   model   delta periodicty    weight residual
     180.00 -160.63  -19.37     3       4.44e-03 1.67e+00
  pdb=" CA  HIS     1 "
  pdb=" CB  HIS     1 "
  pdb=" CG  HIS     1 "
  pdb=" ND1 HIS     1 "
      ideal   model   delta periodicty    weight residual
      90.00  110.09  -20.09     2       2.50e-03 1.01e+00
  pdb=" OXT HIS     1 "
  pdb=" C   HIS     1 "
  pdb=" CA  HIS     1 "
  pdb=" N   HIS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  130.66   29.34     2       1.11e-03 9.57e-01
  target: 27.8229
    bond_residual_sum (n=18): 16.2986
    nonbonded_residual_sum (n=87): 7.16918e-05
    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: 27.8229
  bond_residual_sum (n=18): 16.2986
  nonbonded_residual_sum (n=87): 7.16918e-05
  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: 0.340824
  bond_residual_sum (n=18): 0.00284261
  nonbonded_residual_sum (n=87): 0.0382526
  angle_residual_sum (n=30): 0.253362
  dihedral_residual_sum (n=3): 0.0251822
  chirality_residual_sum (n=1): 0.0211128
  planarity_residual_sum (n=2): 7.20967e-05
  norm of gradients: 1.50079e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ile.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 9
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 4.44

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 20
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Duplicate atoms: {'ILE%COO,HG11': 1}
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Number of atoms with unknown scattering type symbols: 1
    "ATOM     14 HG12 ILE     1 .*.        "
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM     14 HG12 ILE     1 .*.        "
  Time building chain proxies: 0.04, per 1000 atoms: 2.00
  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: 0.02 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
  pdb=" CA  ILE     1 " - pdb="HA   ILE     1 " 0.980  1.117 -0.137 2.50e+03 4.71e+01
  pdb=" CB  ILE     1 " - pdb="HB   ILE     1 " 0.970  1.035 -0.065 2.50e+03 1.07e+01
  pdb=" CA  ILE     1 " - pdb=" N   ILE     1 " 1.458  1.506 -0.048 2.77e+03 6.33e+00
  pdb=" CB  ILE     1 " - pdb=" CA  ILE     1 " 1.540  1.588 -0.048 1.37e+03 3.18e+00
  pdb=" CB  ILE     1 " - pdb=" CG1 ILE     1 " 1.530  1.565 -0.035 2.50e+03 3.08e+00
  ... (remaining 13 not shown)
  Histogram of nonbonded interaction distances:
        0.57 -     1.41: 5
        1.41 -     2.26: 6
        2.26 -     3.11: 39
        3.11 -     3.96: 46
        3.96 -     4.80: 35
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb=" CD1 ILE     1 " - pdb="HG12 ILE     1 "  0.566 1.000
  pdb=" CG1 ILE     1 " - pdb="HG12 ILE     1 "  0.970 1.000
  pdb="HG12 ILE     1 " - pdb="HD11 ILE     1 "  1.196 1.000
  pdb="HG12 ILE     1 " - pdb="HD12 ILE     1 "  1.284 1.000
  pdb="HG12 ILE     1 " - pdb="HD13 ILE     1 "  1.320 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:
  pdb=" CB  ILE     1 "
  pdb=" CD1 ILE     1 "
  pdb=" CG1 ILE     1 "
  pdb="HD13 ILE     1 "
      ideal   model   delta periodicty    weight residual
     -60.00  104.34  -44.34     3       1.11e-03 2.18e+00
  pdb=" CA  ILE     1 "
  pdb=" CB  ILE     1 "
  pdb=" CG1 ILE     1 "
  pdb=" CD1 ILE     1 "
      ideal   model   delta periodicty    weight residual
     180.00   74.80  -14.80     3       4.44e-03 9.73e-01
  pdb=" N   ILE     1 "
  pdb=" CB  ILE     1 "
  pdb=" CA  ILE     1 "
  pdb=" 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: 95.5006
    bond_residual_sum (n=18): 73.456
    nonbonded_residual_sum (n=131): 1.23375
    angle_residual_sum (n=33): 16.1902
    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: 95.5006
  bond_residual_sum (n=18): 73.456
  nonbonded_residual_sum (n=131): 1.23375
  angle_residual_sum (n=33): 16.1902
  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: 1071.14

Energies after minimization:
target: 6.15839
  bond_residual_sum (n=18): 0.0539857
  nonbonded_residual_sum (n=131): 2.25277
  angle_residual_sum (n=33): 0.944518
  dihedral_residual_sum (n=5): 2.87315
  chirality_residual_sum (n=2): 0.0320489
  planarity_residual_sum (n=1): 0.00191259
  norm of gradients: 7.23681e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/leu.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 9
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 4.44

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 22
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Duplicate atoms: {'LEU%COO,HB1': 3}
          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
    "ATOM     18 HB2  LEU     1 .*.    C   "
    "ATOM     19 HB1  LEU     1 .*.    C   "
    "ATOM     20 HB2  LEU     1 .*.    C   "
  Time building chain proxies: 0.04, per 1000 atoms: 1.82
  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: 0.02 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
  pdb=" CG  LEU     1 " - pdb="HG   LEU     1 " 0.970  1.055 -0.085 2.50e+03 1.81e+01
  pdb=" CA  LEU     1 " - pdb="HA   LEU     1 " 0.980  1.032 -0.052 2.50e+03 6.72e+00
  pdb=" CA  LEU     1 " - pdb=" N   LEU     1 " 1.458  1.503 -0.045 2.77e+03 5.52e+00
  pdb=" CB  LEU     1 " - pdb=" CG  LEU     1 " 1.530  1.565 -0.035 2.50e+03 2.99e+00
  pdb=" CB  LEU     1 " - pdb=" 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
  pdb="HB1  LEU     1 " - pdb="HB2  LEU     1 "  0.021 1.000
  pdb="HB2  LEU     1 " - pdb="HB3  LEU     1 "  0.143 1.000
  pdb=" CG  LEU     1 " - pdb="HB1  LEU     1 "  0.630 1.000
  pdb=" CB  LEU     1 " - pdb="HB2  LEU     1 "  0.970 1.000
  pdb=" CB  LEU     1 " - pdb="HB2  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:
  pdb=" CA  LEU     1 "
  pdb=" CB  LEU     1 "
  pdb=" CG  LEU     1 "
  pdb=" CD2 LEU     1 "
      ideal   model   delta periodicty    weight residual
     180.00   82.11  -22.11     3       4.44e-03 2.17e+00
  pdb=" CB  LEU     1 "
  pdb=" CG  LEU     1 "
  pdb=" CD2 LEU     1 "
  pdb="HD23 LEU     1 "
      ideal   model   delta periodicty    weight residual
      60.00  149.28   30.72     3       1.11e-03 1.05e+00
  pdb=" OXT LEU     1 "
  pdb=" C   LEU     1 "
  pdb=" CA  LEU     1 "
  pdb=" 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: 82.4974
    bond_residual_sum (n=18): 38.445
    nonbonded_residual_sum (n=166): 24.1
    angle_residual_sum (n=33): 14.8442
    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: 82.4974
  bond_residual_sum (n=18): 38.445
  nonbonded_residual_sum (n=166): 24.1
  angle_residual_sum (n=33): 14.8442
  dihedral_residual_sum (n=5): 4.4702
  chirality_residual_sum (n=2): 0.637222
  planarity_residual_sum (n=1): 0.000879497
  norm of gradients: 805.49

Energies after minimization:
target: 4.15158
  bond_residual_sum (n=18): 0.0497747
  nonbonded_residual_sum (n=164): 1.89993
  angle_residual_sum (n=33): 1.12896
  dihedral_residual_sum (n=5): 1.0388
  chirality_residual_sum (n=2): 0.0341183
  planarity_residual_sum (n=1): 1.48221e-15
  norm of gradients: 2.22707e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/phe.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 12
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.05, per 1000 atoms: 4.17

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 20
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 2.00
  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
  pdb=" CA  PHE     1 " - pdb=" N   PHE     1 " 1.458  1.491 -0.033 2.77e+03 3.05e+00
  pdb=" CD2 PHE     1 " - pdb=" CE2 PHE     1 " 1.382  1.430 -0.048 1.11e+03 2.53e+00
  pdb=" CD1 PHE     1 " - pdb=" CE1 PHE     1 " 1.382  1.430 -0.048 1.11e+03 2.51e+00
  pdb=" CG  PHE     1 " - pdb=" CD1 PHE     1 " 1.384  1.414 -0.030 2.27e+03 2.04e+00
  pdb=" CA  PHE     1 " - pdb="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 -     2.84: 20
        2.84 -     3.35: 24
        3.35 -     3.85: 16
        3.85 -     4.35: 11
        4.35 -     4.85: 26
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HD2  PHE     1 " - pdb="HB2  PHE     1 "  2.341 2.400
  pdb="HZ   PHE     1 " - pdb="HE1  PHE     1 "  2.353 1.920
  pdb="HZ   PHE     1 " - pdb="HE2  PHE     1 "  2.353 1.920
  pdb="HE1  PHE     1 " - pdb="HD1  PHE     1 "  2.354 1.920
  pdb="HE2  PHE     1 " - pdb="HD2  PHE     1 "  2.354 1.920
  ... (remaining 92 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:
  pdb=" OXT PHE     1 "
  pdb=" C   PHE     1 "
  pdb=" CA  PHE     1 "
  pdb=" N   PHE     1 "
      ideal   model   delta periodicty    weight residual
     160.00  120.83   39.17     2       1.11e-03 1.70e+00
  pdb=" CA  PHE     1 "
  pdb=" CB  PHE     1 "
  pdb=" CG  PHE     1 "
  pdb=" CD1 PHE     1 "
      ideal   model   delta periodicty    weight residual
      90.00   70.30   19.70     2       2.50e-03 9.71e-01
  pdb=" CG  PHE     1 "
  pdb=" CB  PHE     1 "
  pdb=" CA  PHE     1 "
  pdb=" N   PHE     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -61.50    1.50     3       4.44e-03 9.94e-03
  target: 29.5196
    bond_residual_sum (n=20): 19.3992
    nonbonded_residual_sum (n=97): 0.509062
    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: 29.5196
  bond_residual_sum (n=20): 19.3992
  nonbonded_residual_sum (n=97): 0.509062
  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: 454.835

Energies after minimization:
target: 0.339579
  bond_residual_sum (n=20): 0.0117639
  nonbonded_residual_sum (n=97): 0.0368481
  angle_residual_sum (n=33): 0.268212
  dihedral_residual_sum (n=3): 0.00366822
  chirality_residual_sum (n=1): 0.0190864
  planarity_residual_sum (n=2): 5.70301e-14
  norm of gradients: 1.39329e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/tyr.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 13
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.05, per 1000 atoms: 3.85

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 21
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 1.90
  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
  pdb=" CA  TYR     1 " - pdb=" N   TYR     1 " 1.458  1.507 -0.049 2.77e+03 6.73e+00
  pdb=" CA  TYR     1 " - pdb="HA   TYR     1 " 0.980  1.021 -0.041 2.50e+03 4.14e+00
  pdb=" CD2 TYR     1 " - pdb=" CG  TYR     1 " 1.389  1.429 -0.040 2.27e+03 3.69e+00
  pdb=" CG  TYR     1 " - pdb=" CD1 TYR     1 " 1.389  1.429 -0.040 2.27e+03 3.65e+00
  pdb=" CZ  TYR     1 " - pdb=" 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 -     2.79: 18
        2.79 -     3.31: 23
        3.31 -     3.83: 22
        3.83 -     4.35: 12
        4.35 -     4.87: 28
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HE2  TYR     1 " - pdb="HH   TYR     1 "  2.274 2.400
  pdb="HE1  TYR     1 " - pdb="HD1  TYR     1 "  2.340 1.920
  pdb="HE2  TYR     1 " - pdb="HD2  TYR     1 "  2.341 1.920
  pdb=" CE2 TYR     1 " - pdb="HH   TYR     1 "  2.402 2.416
  pdb="HA   TYR     1 " - pdb="HB2  TYR     1 "  2.442 1.920
  ... (remaining 98 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:
  pdb=" CE1 TYR     1 "
  pdb=" OH  TYR     1 "
  pdb=" CZ  TYR     1 "
  pdb="HH   TYR     1 "
      ideal   model   delta periodicty    weight residual
     -60.00 -179.97  -60.03     2       1.11e-03 4.00e+00
  pdb=" OXT TYR     1 "
  pdb=" C   TYR     1 "
  pdb=" CA  TYR     1 "
  pdb=" N   TYR     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.67   29.67     2       1.11e-03 9.78e-01
  pdb=" CG  TYR     1 "
  pdb=" CB  TYR     1 "
  pdb=" CA  TYR     1 "
  pdb=" N   TYR     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -68.78    8.78     3       4.44e-03 3.42e-01
  pdb=" CA  TYR     1 "
  pdb=" CB  TYR     1 "
  pdb=" CG  TYR     1 "
  pdb=" CD1 TYR     1 "
      ideal   model   delta periodicty    weight residual
      90.00  -85.51   -4.49     2       2.50e-03 5.04e-02
  target: 40.7003
    bond_residual_sum (n=21): 28.8817
    nonbonded_residual_sum (n=103): 0.00538344
    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: 40.7003
  bond_residual_sum (n=21): 28.8817
  nonbonded_residual_sum (n=103): 0.00538344
  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: 573.508

Energies after minimization:
target: 0.330276
  bond_residual_sum (n=21): 0.00424817
  nonbonded_residual_sum (n=103): 0.031871
  angle_residual_sum (n=34): 0.272515
  dihedral_residual_sum (n=4): 0.00247102
  chirality_residual_sum (n=1): 0.0191155
  planarity_residual_sum (n=2): 5.49542e-05
  norm of gradients: 9.49242e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/trp.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 15
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.06, per 1000 atoms: 4.00

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 24
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.05, per 1000 atoms: 2.08
  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: 0.02 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
  pdb=" CA  TRP     1 " - pdb=" N   TRP     1 " 1.458  1.507 -0.049 2.77e+03 6.78e+00
  pdb=" CE3 TRP     1 " - pdb=" CD2 TRP     1 " 1.398  1.433 -0.035 3.91e+03 4.74e+00
  pdb=" CA  TRP     1 " - pdb="HA   TRP     1 " 0.980  1.020 -0.040 2.50e+03 4.09e+00
  pdb=" CZ2 TRP     1 " - pdb=" CH2 TRP     1 " 1.368  1.403 -0.035 2.77e+03 3.34e+00
  pdb=" CZ2 TRP     1 " - pdb=" 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 -     2.85: 20
        2.85 -     3.36: 33
        3.36 -     3.87: 26
        3.87 -     4.38: 22
        4.38 -     4.90: 35
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw
  pdb="HH2  TRP     1 " - pdb="HZ2  TRP     1 "  2.339 1.920
  pdb="HH2  TRP     1 " - pdb="HZ3  TRP     1 "  2.347 1.920
  pdb="HE3  TRP     1 " - pdb="HZ3  TRP     1 "  2.349 1.920
  pdb="HE1  TRP     1 " - pdb="HD1  TRP     1 "  2.411 1.920
  pdb="HA   TRP     1 " - pdb="HB2  TRP     1 "  2.445 1.920
  ... (remaining 131 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:
  pdb=" N   TRP     1 "
  pdb=" C   TRP     1 "
  pdb=" CA  TRP     1 "
  pdb=" OXT TRP     1 "
      ideal   model   delta periodicty    weight residual
    -160.00 -130.62  -29.38     2       1.11e-03 9.59e-01
  pdb=" CG  TRP     1 "
  pdb=" CB  TRP     1 "
  pdb=" CA  TRP     1 "
  pdb=" N   TRP     1 "
      ideal   model   delta periodicty    weight residual
     180.00  -69.24    9.24     3       4.44e-03 3.79e-01
  pdb=" CA  TRP     1 "
  pdb=" CB  TRP     1 "
  pdb=" CG  TRP     1 "
  pdb=" 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=136): 3.30721e-05
    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=136): 3.30721e-05
  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: 676.857

Energies after minimization:
target: 0.281772
  bond_residual_sum (n=25): 0.0065275
  nonbonded_residual_sum (n=136): 0.00317817
  angle_residual_sum (n=42): 0.252815
  dihedral_residual_sum (n=3): 6.65914e-07
  chirality_residual_sum (n=1): 0.0192505
  planarity_residual_sum (n=2): 6.86899e-16
  norm of gradients: 9.41684e-06
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/thr.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 8
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 3.75

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 13
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 2.31
  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: 0.01 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
  pdb=" CB  THR     1 " - pdb="HB   THR     1 " 0.970  1.029 -0.059 2.50e+03 8.81e+00
  pdb=" CA  THR     1 " - pdb=" N   THR     1 " 1.458  1.508 -0.050 2.77e+03 6.87e+00
  pdb=" CA  THR     1 " - pdb="HA   THR     1 " 0.980  1.031 -0.051 2.50e+03 6.60e+00
  pdb=" C   THR     1 " - pdb=" OXT THR     1 " 1.231  1.250 -0.019 2.50e+03 8.89e-01
  pdb=" C   THR     1 " - pdb=" 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
  pdb="HG21 THR     1 " - pdb="HB   THR     1 "  2.165 1.920
  pdb="HA   THR     1 " - pdb="HG22 THR     1 "  2.360 2.400
  pdb=" OG1 THR     1 " - pdb="HG23 THR     1 "  2.377 2.176
  pdb="HA   THR     1 " - pdb="HB   THR     1 "  2.451 1.920
  pdb=" O   THR     1 " - pdb="HA   THR     1 "  2.459 2.176
  ... (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:
  pdb=" CA  THR     1 "
  pdb=" CB  THR     1 "
  pdb=" CG2 THR     1 "
  pdb="HG23 THR     1 "
      ideal   model   delta periodicty    weight residual
      60.00  100.94  -40.94     3       1.11e-03 1.86e+00
  pdb=" OXT THR     1 "
  pdb=" C   THR     1 "
  pdb=" CA  THR     1 "
  pdb=" N   THR     1 "
      ideal   model   delta periodicty    weight residual
     160.00  -49.57   29.57     2       1.11e-03 9.72e-01
  pdb=" N   THR     1 "
  pdb=" CB  THR     1 "
  pdb=" CA  THR     1 "
  pdb=" CG2 THR     1 "
      ideal   model   delta periodicty    weight residual
    -180.00   68.60   -8.60     3       4.44e-03 3.28e-01
  target: 41.9254
    bond_residual_sum (n=12): 24.73
    nonbonded_residual_sum (n=44): 8.6912e-05
    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: 41.9254
  bond_residual_sum (n=12): 24.73
  nonbonded_residual_sum (n=44): 8.6912e-05
  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: 845.061

Energies after minimization:
target: 0.316755
  bond_residual_sum (n=12): 0.00186294
  nonbonded_residual_sum (n=44): 0.0106859
  angle_residual_sum (n=21): 0.279242
  dihedral_residual_sum (n=3): 0.00149716
  chirality_residual_sum (n=2): 0.0234672
  planarity_residual_sum (n=1): 6.68696e-17
  norm of gradients: 1.04277e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/val.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 8
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 5.00

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 16
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 2.50
  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: 0.01 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
  pdb=" CA  VAL     1 " - pdb="HA   VAL     1 " 0.980  1.091 -0.111 2.50e+03 3.07e+01
  pdb=" CA  VAL     1 " - pdb=" N   VAL     1 " 1.458  1.505 -0.047 2.77e+03 6.17e+00
  pdb=" CB  VAL     1 " - pdb="HB   VAL     1 " 0.980  1.026 -0.046 2.50e+03 5.22e+00
  pdb=" CB  VAL     1 " - pdb=" CA  VAL     1 " 1.540  1.581 -0.041 1.37e+03 2.30e+00
  pdb=" C   VAL     1 " - pdb=" 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
  pdb="HG23 VAL     1 " - pdb="HG13 VAL     1 "  2.050 2.400
  pdb="HG12 VAL     1 " - pdb="HB   VAL     1 "  2.164 1.920
  pdb="HG21 VAL     1 " - pdb="HB   VAL     1 "  2.186 1.920
  pdb="HG11 VAL     1 " - pdb="HA   VAL     1 "  2.372 2.400
  pdb=" CG2 VAL     1 " - pdb="HG13 VAL     1 "  2.458 2.512
  ... (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:
  pdb=" CA  VAL     1 "
  pdb=" CB  VAL     1 "
  pdb=" CG1 VAL     1 "
  pdb="HG13 VAL     1 "
      ideal   model   delta periodicty    weight residual
      60.00  123.81  -63.81     2       1.11e-03 4.52e+00
  pdb=" OXT VAL     1 "
  pdb=" C   VAL     1 "
  pdb=" CA  VAL     1 "
  pdb=" N   VAL     1 "
      ideal   model   delta periodicty    weight residual
     160.00  135.14   24.86     2       1.11e-03 6.87e-01
  pdb=" CA  VAL     1 "
  pdb=" CB  VAL     1 "
  pdb=" CG2 VAL     1 "
  pdb="HG23 VAL     1 "
      ideal   model   delta periodicty    weight residual
      60.00 -135.02   15.02     2       1.11e-03 2.51e-01
  pdb=" N   VAL     1 "
  pdb=" CB  VAL     1 "
  pdb=" CA  VAL     1 "
  pdb=" CG2 VAL     1 "
      ideal   model   delta periodicty    weight residual
    -180.00  -55.39   -4.61     3       4.44e-03 9.44e-02
  target: 64.3136
    bond_residual_sum (n=15): 47.3506
    nonbonded_residual_sum (n=74): 0.352835
    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: 64.3136
  bond_residual_sum (n=15): 47.3506
  nonbonded_residual_sum (n=74): 0.352835
  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: 882.162

Energies after minimization:
target: 0.463554
  bond_residual_sum (n=15): 0.00177692
  nonbonded_residual_sum (n=74): 0.184628
  angle_residual_sum (n=27): 0.241823
  dihedral_residual_sum (n=4): 0.0197403
  chirality_residual_sum (n=2): 0.0155556
  planarity_residual_sum (n=1): 2.97146e-05
  norm of gradients: 1.62062e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/cys.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 4.29

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.82
  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
  pdb=" CA  CYS     1 " - pdb="HA   CYS     1 " 0.980  1.072 -0.092 2.50e+03 2.12e+01
  pdb=" CA  CYS     1 " - pdb=" N   CYS     1 " 1.458  1.506 -0.048 2.77e+03 6.44e+00
  pdb=" CB  CYS     1 " - pdb=" CA  CYS     1 " 1.530  1.561 -0.031 2.50e+03 2.47e+00
  pdb=" C   CYS     1 " - pdb=" OXT CYS     1 " 1.231  1.250 -0.019 2.50e+03 9.05e-01
  pdb=" C   CYS     1 " - pdb=" 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
  pdb="HA   CYS     1 " - pdb="HB1  CYS     1 "  2.369 1.920
  pdb="HA   CYS     1 " - pdb="HB2  CYS     1 "  2.402 1.920
  pdb=" OXT CYS     1 " - pdb="HA   CYS     1 "  2.467 2.176
  pdb=" O   CYS     1 " - pdb="HG   CYS     1 "  2.593 2.720
  pdb=" C   CYS     1 " - pdb="HB2  CYS     1 "  2.721 2.360
  ... (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:
  pdb=" CA  CYS     1 "
  pdb=" CB  CYS     1 "
  pdb=" SG  CYS     1 "
  pdb="HG   CYS     1 "
      ideal   model   delta periodicty    weight residual
     180.00   -0.01  -59.99     3       4.44e-03 1.60e+01
  pdb=" OXT CYS     1 "
  pdb=" C   CYS     1 "
  pdb=" CA  CYS     1 "
  pdb=" N   CYS     1 "
      ideal   model   delta periodicty    weight residual
     160.00  133.17   26.83     2       1.11e-03 8.00e-01
  pdb=" N   CYS     1 "
  pdb=" CB  CYS     1 "
  pdb=" CA  CYS     1 "
  pdb=" SG  CYS     1 "
      ideal   model   delta periodicty    weight residual
    -180.00  -59.31   -0.69     3       4.44e-03 2.14e-03
  target: 59.9793
    bond_residual_sum (n=10): 32.5394
    nonbonded_residual_sum (n=29): 0.00698155
    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: 59.9793
  bond_residual_sum (n=10): 32.5394
  nonbonded_residual_sum (n=29): 0.00698155
  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: 705.658

Energies after minimization:
target: 0.29813
  bond_residual_sum (n=10): 0.00163257
  nonbonded_residual_sum (n=29): 5.90638e-05
  angle_residual_sum (n=16): 0.2772
  dihedral_residual_sum (n=3): 4.26806e-07
  chirality_residual_sum (n=1): 0.0192382
  planarity_residual_sum (n=1): 8.51102e-15
  norm of gradients: 1.28033e-05
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
/net/longnose/scratch1/rwgk/auto_build/sources/phenix_regression/hydrogens/ser.pdb
  Monomer Library directory:
    "/net/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 7
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.03, per 1000 atoms: 4.29

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/longnose/scratch1/rwgk/auto_build/sources/chem_data/mon_lib"
  Total number of atoms: 11
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: " "
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.02, per 1000 atoms: 1.82
  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
  pdb=" CA  SER     1 " - pdb=" N   SER     1 " 1.458  1.504 -0.046 2.77e+03 5.86e+00
  pdb=" CA  SER     1 " - pdb="HA   SER     1 " 0.980  1.027 -0.047 2.50e+03 5.50e+00
  pdb=" C   SER     1 " - pdb=" OXT SER     1 " 1.231  1.249 -0.018 2.50e+03 8.06e-01
  pdb=" C   SER     1 " - pdb=" O   SER     1 " 1.231  1.249 -0.018 2.50e+03 7.75e-01
  pdb=" CB  SER     1 " - pdb=" 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
  pdb="HA   SER     1 " - pdb="HB1  SER     1 "  2.352 1.920
  pdb=" CA  SER     1 " - pdb="HG   SER     1 "  2.363 2.520
  pdb="HA   SER     1 " - pdb="HB2  SER     1 "  2.400 1.920
  pdb=" O   SER     1 " - pdb="HG   SER     1 "  2.419 2.720
  pdb=" OXT SER     1 " - pdb="HA   SER     1 "  2.458 2.176
  ... (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:
  pdb=" N   SER     1 "
  pdb=" C   SER     1 "
  pdb=" CA  SER     1 "
  pdb=" OXT SER     1 "
      ideal   model   delta periodicty    weight residual
    -160.00 -131.41  -28.59     2       1.11e-03 9.08e-01
  pdb=" OG  SER     1 "
  pdb=" CB  SER     1 "
  pdb=" CA  SER     1 "
  pdb=" N   SER     1 "
      ideal   model   delta periodicty    weight residual
     180.00   57.04    2.96     3       4.44e-03 3.89e-02
  pdb=" CA  SER     1 "
  pdb=" OG  SER     1 "
  pdb=" CB  SER     1 "
  pdb="HG   SER     1 "
      ideal   model   delta periodicty    weight residual
    -180.00   -0.03    0.03     2       1.11e-03 1.32e-06
  target: 21.382
    bond_residual_sum (n=10): 13.8342
    nonbonded_residual_sum (n=29): 0.277467
    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: 21.382
  bond_residual_sum (n=10): 13.8342
  nonbonded_residual_sum (n=29): 0.277467
  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: 480.001

Energies after minimization:
target: 0.502005
  bond_residual_sum (n=10): 0.00103528
  nonbonded_residual_sum (n=29): 0.230399
  angle_residual_sum (n=16): 0.246422
  dihedral_residual_sum (n=3): 0.00957638
  chirality_residual_sum (n=1): 0.0145721
  planarity_residual_sum (n=1): 2.53367e-15
  norm of gradients: 6.3777e-06

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_maxlik.py
u+s,u,s: 35.14 34.99 0.15

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/masks/tst_masks.py
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
I 4/m c m (a+b-1/6,-a+b,c+1/4)
u+s,u,s: 18.09 16.84 1.25

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/max_lik/tst_max_lik.py
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
I 4/m c m (a+b-1/6,-a+b,c+1/4)
u+s,u,s: 31.30 30.68 0.62
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
I 4/m c m (a+b-1/6,-a+b,c+1/4)
u+s,u,s: 97.86 93.76 4.10
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/dynamics/tst_cartesian_dynamics.py
u+s,u,s: 6.36 6.19 0.17

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls.py
|-----------------------------------------------------------------------------|
|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: 1658.52 1631.91 26.61

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_get_t_scheme.py
P 1 (6.76703, 8.79714, 11.504, 83, 109, 129)

.............................. P 1
i=  10000 out of  100000
branch_0       =  2006
branch_1       =  7994
branch_1_1     =  2478
branch_1_2     =  5516
branch_1_2_1   =  246
branch_1_2_2   =  1996
branch_1_2_3   =  3274
branch_1_2_3_1 =  1466
branch_1_2_3_2 =  1808
.............................. P 1
i=  20000 out of  100000
branch_0       =  3938
branch_1       =  16062
branch_1_1     =  4979
branch_1_2     =  11083
branch_1_2_1   =  481
branch_1_2_2   =  3961
branch_1_2_3   =  6641
branch_1_2_3_1 =  3090
branch_1_2_3_2 =  3551
.............................. P 1
i=  30000 out of  100000
branch_0       =  5944
branch_1       =  24056
branch_1_1     =  7510
branch_1_2     =  16546
branch_1_2_1   =  705
branch_1_2_2   =  6021
branch_1_2_3   =  9820
branch_1_2_3_1 =  4570
branch_1_2_3_2 =  5250
.............................. P 1
i=  40000 out of  100000
branch_0       =  7884
branch_1       =  32116
branch_1_1     =  10037
branch_1_2     =  22079
branch_1_2_1   =  933
branch_1_2_2   =  8024
branch_1_2_3   =  13122
branch_1_2_3_1 =  6091
branch_1_2_3_2 =  7031
.............................. P 1
i=  50000 out of  100000
branch_0       =  9910
branch_1       =  40090
branch_1_1     =  12475
branch_1_2     =  27615
branch_1_2_1   =  1172
branch_1_2_2   =  10047
branch_1_2_3   =  16396
branch_1_2_3_1 =  7591
branch_1_2_3_2 =  8805
.............................. P 1
i=  60000 out of  100000
branch_0       =  11886
branch_1       =  48114
branch_1_1     =  14922
branch_1_2     =  33192
branch_1_2_1   =  1411
branch_1_2_2   =  12083
branch_1_2_3   =  19698
branch_1_2_3_1 =  8955
branch_1_2_3_2 =  10743
.............................. P 1
i=  70000 out of  100000
branch_0       =  13893
branch_1       =  56107
branch_1_1     =  17321
branch_1_2     =  38786
branch_1_2_1   =  1642
branch_1_2_2   =  14113
branch_1_2_3   =  23031
branch_1_2_3_1 =  10339
branch_1_2_3_2 =  12692
.............................. P 1
i=  80000 out of  100000
branch_0       =  15889
branch_1       =  64111
branch_1_1     =  19746
branch_1_2     =  44365
branch_1_2_1   =  1873
branch_1_2_2   =  16150
branch_1_2_3   =  26342
branch_1_2_3_1 =  11719
branch_1_2_3_2 =  14623
.............................. P 1
i=  90000 out of  100000
branch_0       =  17832
branch_1       =  72168
branch_1_1     =  22255
branch_1_2     =  49913
branch_1_2_1   =  2130
branch_1_2_2   =  18141
branch_1_2_3   =  29642
branch_1_2_3_1 =  13073
branch_1_2_3_2 =  16569
.............................. P 1
i=  100000 out of  100000
branch_0       =  19836
branch_1       =  80164
branch_1_1     =  24732
branch_1_2     =  55432
branch_1_2_1   =  2352
branch_1_2_2   =  20129
branch_1_2_3   =  32951
branch_1_2_3_1 =  14392
branch_1_2_3_2 =  18559
..............................
i=  10000 out of  100000
branch_0       =  9
branch_1       =  9991
branch_1_1     =  124
branch_1_2     =  9867
branch_1_2_1   =  7813
branch_1_2_2   =  0
branch_1_2_3   =  2054
branch_1_2_3_1 =  1265
branch_1_2_3_2 =  789
..............................
i=  20000 out of  100000
branch_0       =  12
branch_1       =  19988
branch_1_1     =  262
branch_1_2     =  19726
branch_1_2_1   =  15651
branch_1_2_2   =  0
branch_1_2_3   =  4075
branch_1_2_3_1 =  2551
branch_1_2_3_2 =  1524
..............................
i=  30000 out of  100000
branch_0       =  17
branch_1       =  29983
branch_1_1     =  378
branch_1_2     =  29605
branch_1_2_1   =  23460
branch_1_2_2   =  0
branch_1_2_3   =  6145
branch_1_2_3_1 =  3852
branch_1_2_3_2 =  2293
..............................
i=  40000 out of  100000
branch_0       =  23
branch_1       =  39977
branch_1_1     =  512
branch_1_2     =  39465
branch_1_2_1   =  31303
branch_1_2_2   =  1
branch_1_2_3   =  8161
branch_1_2_3_1 =  5123
branch_1_2_3_2 =  3038
..............................
i=  50000 out of  100000
branch_0       =  30
branch_1       =  49970
branch_1_1     =  632
branch_1_2     =  49338
branch_1_2_1   =  39151
branch_1_2_2   =  1
branch_1_2_3   =  10186
branch_1_2_3_1 =  6369
branch_1_2_3_2 =  3817
..............................
i=  60000 out of  100000
branch_0       =  32
branch_1       =  59968
branch_1_1     =  740
branch_1_2     =  59228
branch_1_2_1   =  46958
branch_1_2_2   =  1
branch_1_2_3   =  12269
branch_1_2_3_1 =  7551
branch_1_2_3_2 =  4718
***********************************************
Start values: 
M= 19.9997 10 10.0003 0 0 0
N= 20 10.0004 19.9996 2.31836e-05 -1.53405e-07 0.0661665
myu= 19.9997 10.0003 10
nyu= 20 20 10
Current values: 
myu= 5.00864 3.01139e-08 -4.99071
nyu= 5.00897 5.00897 0
M= 5.00864 -4.99071 3.02203e-08 9.95662e-12 -2.31834e-05 -2.14337e-06
N= 5.00897 5.00897 0 1.29519e-26 0 0
T= 14.991 10.0002 14.9908 1.1571e-05 -7.65647e-08 0.0330239
T1= 0 0 0 0 0 0
T2= 4.99103 4.99103 0 0 0 0
T3= 10 10 10 0 0 0
myu(M-T)= 5.00864 3.01139e-08 -4.99071
nyu(N-T)= 5.00897 5.00897 -8.01047e-16
PD(M)= 0
PD(N)= 1
branch_0       = 0
branch_1       = 1
branch_1_1     = 0
branch_1_2     = 1
branch_1_2_1   = 0
branch_1_2_2   = 0
branch_1_2_3   = 1
branch_1_2_3_1 = 0
branch_1_2_3_2 = 1
***********************************************
..............................
i=  70000 out of  100000
branch_0       =  36
branch_1       =  69963
branch_1_1     =  858
branch_1_2     =  69105
branch_1_2_1   =  54789
branch_1_2_2   =  1
branch_1_2_3   =  14315
branch_1_2_3_1 =  8705
branch_1_2_3_2 =  5610
..............................
i=  80000 out of  100000
branch_0       =  37
branch_1       =  79962
branch_1_1     =  982
branch_1_2     =  78980
branch_1_2_1   =  62691
branch_1_2_2   =  1
branch_1_2_3   =  16288
branch_1_2_3_1 =  9829
branch_1_2_3_2 =  6459
***********************************************
Start values: 
M= 19.9996 10 10.0004 -0 0 -0
N= 20 10.0055 19.9945 8.66993e-05 0 -0.234903
myu= 19.9996 10.0004 10
nyu= 20 20 10
Current values: 
myu= 5.00966 3.76909e-07 -4.98961
nyu= 5.01002 5.01002 0
M= 5.00966 -4.98961 3.78393e-07 2.9535e-10 8.66722e-05 8.53645e-06
N= 5.01002 5.01002 0 2.03715e-06 0 0
T= 14.99 10.0028 14.9872 4.32389e-05 1.01625e-06 -0.117216
T1= 0 0 0 0 0 0
T2= 4.98998 4.98998 0 0 0 0
T3= 10 10 10 0 0 0
myu(M-T)= 5.00966 3.76909e-07 -4.98961
nyu(N-T)= 5.01002 5.01002 9.63912e-16
PD(M)= 0
PD(N)= 1
branch_0       = 0
branch_1       = 1
branch_1_1     = 0
branch_1_2     = 1
branch_1_2_1   = 0
branch_1_2_2   = 0
branch_1_2_3   = 1
branch_1_2_3_1 = 0
branch_1_2_3_2 = 1
***********************************************
..............................
i=  90000 out of  100000
branch_0       =  42
branch_1       =  89956
branch_1_1     =  1114
branch_1_2     =  88842
branch_1_2_1   =  70495
branch_1_2_2   =  1
branch_1_2_3   =  18346
branch_1_2_3_1 =  10957
branch_1_2_3_2 =  7389
..............................
i=  100000 out of  100000
branch_0       =  44
branch_1       =  99954
branch_1_1     =  1235
branch_1_2     =  98719
branch_1_2_1   =  78288
branch_1_2_2   =  1
branch_1_2_3   =  20430
branch_1_2_3_1 =  12113
branch_1_2_3_2 =  8317
OK:  u+s,u,s: 113.00 112.85 0.15

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tls/tst_tls_refinement_fft.py
random_seed: 1279104071
|-----------------------------------------------------------------------------|
| 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 = 17.09    max = 53.74    mean = 35.10   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|     17.095 -   20.759:      12      |       17.095 -   20.759:      12      |
|     20.759 -   24.423:       0      |       20.759 -   24.423:       0      |
|     24.423 -   28.088:       0      |       24.423 -   28.088:       0      |
|     28.088 -   31.752:       0      |       28.088 -   31.752:       0      |
|     31.752 -   35.416:       8      |       31.752 -   35.416:       8      |
|     35.416 -   39.080:       4      |       35.416 -   39.080:       4      |
|     39.080 -   42.744:       0      |       39.080 -   42.744:       0      |
|     42.744 -   46.409:       0      |       42.744 -   46.409:       0      |
|     46.409 -   50.073:       0      |       46.409 -   50.073:       0      |
|     50.073 -   53.737:      12      |       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                                       |
|-----------------------------------------------------------------------------|
|--(resolution: 1.50 - 11.82 A; n_refl. = 957)--------------------------------|
|                                                                             |
| r_work= 0.0000   r_free= 0.0000   ksol= 0.00   Bsol= 0.00   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:  -0.00 A                  |
| x-ray target function (ls_wunit_k1) for work reflections: 0.000000          |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 11.8227 -  1.5003 1.00    947   10 0.0000 0.0000  2.9276e-31  1.2225e-31|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 11.8227 -  1.5003   947    10  1.00   0.00   1.00     1.00          0.00|
|alpha:            min =        1.00 max =            1.00 mean =         1.00|
|beta:             min =        0.00 max =            0.00 mean =         0.00|
|figures of merit: min =        1.00 max =            1.00 mean =         1.00|
|phase err.(work): min =        0.00 max =            0.00 mean =         0.00|
|phase err.(test): min =        0.00 max =            0.00 mean =         0.00|
|-----------------------------------------------------------------------------|
|--(resolution: 1.50 - 11.82 A; n_refl. = 957)--------------------------------|
|                                                                             |
| r_work= 0.4872   r_free= 0.3832   ksol= 0.00   Bsol= 0.00   scale= 1.066    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ls_wunit_k1) for work reflections: 0.164911          |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 11.8227 -  1.5003 1.00    947   10 0.4872 0.3832      26.991      18.982|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 11.8227 -  1.5003   947    10  0.38  60.73   1.07     0.95         28.51|
|alpha:            min =        0.95 max =            0.95 mean =         0.95|
|beta:             min =       28.51 max =           28.51 mean =        28.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.98 mean =        60.73|
|phase err.(test): min =        0.00 max =           88.11 mean =        55.21|
|-----------------------------------------------------------------------------|
********************************************************************************
 
 None 
 
|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.164911  r_work = 0.4872  r_free = 0.3832       |
|-----------------------------------------------------------------------------|
|-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 = 25.00    max = 25.00    mean = 25.00   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|     25.000 -   25.000:      36      |       25.000 -   25.000:      36      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       0      |       25.000 -   25.000:       0      |
|     25.000 -   25.000:       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=  0.2603 T22=  0.2983 T33=  0.3045 T12=  0.0209 T13=  0.0054 T23= -0.0117|
|L11=  2.0000 L22=  2.0000 L33=  2.0000 L12=  2.0000 L13=  2.0000 L23=  2.0000|
|S11=  0.1402 S22= -0.2801 S33=  0.1399 S12= -0.0936 S13= -0.0276 S21= -0.0453|
|S23= -0.2169 S31= -0.0269 S32=  0.2420                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.2817 T22=  0.2620 T33=  0.3016 T12=  0.0274 T13= -0.0026 T23= -0.0175|
|L11=  2.0000 L22=  2.0000 L33=  2.0000 L12=  2.0000 L13=  2.0000 L23=  2.0000|
|S11= -0.0366 S22= -0.1932 S33=  0.2298 S12= -0.2463 S13= -0.1538 S21= -0.2040|
|S23= -0.2247 S31=  0.0799 S32=  0.4319                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2985 T22=  0.2801 T33=  0.3047 T12=  0.0126 T13= -0.0028 T23= -0.0131|
|L11=  2.0000 L22=  2.0000 L33=  2.0000 L12=  2.0000 L13=  2.0000 L23=  2.0000|
|S11=  0.0075 S22= -0.1145 S33=  0.1069 S12= -0.1756 S13= -0.0750 S21= -0.1185|
|S23= -0.1022 S31=  0.0367 S32=  0.2639                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 0       aniso = 36      pos. def. = 36      non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 15.98    max = 23.20    mean = 19.52   |
| Isotropic B only:              min = 15.98    max = 23.20    mean = 19.52   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|     15.983 -   16.704:       6      |       15.983 -   16.704:       6      |
|     16.704 -   17.426:       6      |       16.704 -   17.426:       6      |
|     17.426 -   18.148:       0      |       17.426 -   18.148:       0      |
|     18.148 -   18.870:       1      |       18.148 -   18.870:       1      |
|     18.870 -   19.592:       9      |       18.870 -   19.592:       9      |
|     19.592 -   20.313:       2      |       19.592 -   20.313:       2      |
|     20.313 -   21.035:       0      |       20.313 -   21.035:       0      |
|     21.035 -   21.757:       0      |       21.035 -   21.757:       0      |
|     21.757 -   22.479:       3      |       21.757 -   22.479:       3      |
|     22.479 -   23.201:       9      |       22.479 -   23.201:       9      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1239 T22=  0.2289 T33=  0.2688 T12=  0.0981 T13=  0.0765 T23=  0.1363|
|L11=  2.0000 L22=  1.9999 L33=  1.9998 L12=  1.9999 L13=  1.9999 L23=  1.9997|
|S11=  0.1415 S22= -0.2814 S33=  0.1399 S12= -0.0943 S13= -0.0272 S21= -0.0402|
|S23= -0.2170 S31= -0.0213 S32=  0.2411                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.1957 T22=  0.2251 T33=  0.2991 T12=  0.1269 T13=  0.0451 T23=  0.1543|
|L11=  2.0000 L22=  1.9999 L33=  1.9999 L12=  1.9997 L13=  1.9999 L23=  1.9997|
|S11= -0.0354 S22= -0.1930 S33=  0.2298 S12= -0.2463 S13= -0.1526 S21= -0.2023|
|S23= -0.2259 S31=  0.0816 S32=  0.4314                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2553 T22=  0.2734 T33=  0.3205 T12=  0.0820 T13=  0.0475 T23=  0.1333|
|L11=  2.0001 L22=  2.0000 L33=  1.9999 L12=  1.9998 L13=  1.9999 L23=  1.9998|
|S11=  0.0079 S22= -0.1151 S33=  0.1069 S12= -0.1754 S13= -0.0739 S21= -0.1170|
|S23= -0.1030 S31=  0.0382 S32=  0.2636                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0426172  r_work = 0.2472  r_free = 0.1737      |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =    5.4095    5.5841    7.5222                |
|T11=  0.1239 T22=  0.2289 T33=  0.2688 T12=  0.0981 T13=  0.0765 T23=  0.1363|
|L11=  2.0000 L22=  1.9999 L33=  1.9998 L12=  1.9999 L13=  1.9999 L23=  1.9997|
|S11=  0.1415 S22= -0.2814 S33=  0.1399 S12= -0.0943 S13= -0.0272 S21= -0.0402|
|S23= -0.2170 S31= -0.0213 S32=  0.2411                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   10.8834    4.8200    7.3685                |
|T11=  0.1957 T22=  0.2251 T33=  0.2991 T12=  0.1269 T13=  0.0451 T23=  0.1543|
|L11=  2.0000 L22=  1.9999 L33=  1.9999 L12=  1.9997 L13=  1.9999 L23=  1.9997|
|S11= -0.0354 S22= -0.1930 S33=  0.2298 S12= -0.2463 S13= -0.1526 S21= -0.2023|
|S23= -0.2259 S31=  0.0816 S32=  0.4314                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =   10.4142   10.1560    8.5901                |
|T11=  0.2553 T22=  0.2734 T33=  0.3205 T12=  0.0820 T13=  0.0475 T23=  0.1333|
|L11=  2.0001 L22=  2.0000 L33=  1.9999 L12=  1.9998 L13=  1.9999 L23=  1.9998|
|S11=  0.0079 S22= -0.1151 S33=  0.1069 S12= -0.1754 S13= -0.0739 S21= -0.1170|
|S23= -0.1030 S31=  0.0382 S32=  0.2636                                       |
|-----------------------------------------------------------------------------|
u+s,u,s: 15.62 15.45 0.17

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/examples/f_model_manager.py
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
|                                                                             |
| r_work= 0.2715   r_free= 0.2582   ksol= 0.00   Bsol= 0.00   scale= 0.996    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.094793                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.8046 -  3.4193 1.00   1379  144 0.2703 0.2757      5.4467      5.4664|
|  2:  3.4193 -  2.7143 1.00   1296  139 0.2607 0.2385      5.2158      5.1916|
|  3:  2.7143 -  2.3713 1.00   1261  153 0.2707 0.2585      5.0201      5.0422|
|  4:  2.3713 -  2.1545 1.00   1258  147 0.2772 0.2290      4.9312      4.7391|
|  5:  2.1545 -  2.0001 1.00   1257  134 0.2861 0.2886      4.8226       4.811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.8046 -  3.4193  1379   144  0.80  24.42   0.99     0.97       7091.12|
|  2:  3.4193 -  2.7143  1296   139  0.81  24.45   1.00     0.98       4750.46|
|  3:  2.7143 -  2.3713  1261   153  0.82  24.56   1.00     0.98       3124.95|
|  4:  2.3713 -  2.1545  1258   147  0.83  23.75   0.99     0.96       2335.56|
|  5:  2.1545 -  2.0001  1257   134  0.81  25.26   0.99     0.96       2114.06|
|alpha:            min =        0.96 max =            0.98 mean =         0.97|
|beta:             min =     2114.06 max =         7091.12 mean =      3948.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           90.00 mean =        24.49|
|phase err.(test): min =        0.00 max =           89.65 mean =        24.18|
|-----------------------------------------------------------------------------|
0.271520875931
0.258211729842
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
|                                                                             |
| r_work= 0.2715   r_free= 0.2582   ksol= 0.00   Bsol= 0.00   scale= 0.996    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.094793                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.8046 -  3.4193 1.00   1379  144 0.2703 0.2757      5.4467      5.4664|
|  2:  3.4193 -  2.7143 1.00   1296  139 0.2607 0.2385      5.2158      5.1916|
|  3:  2.7143 -  2.3713 1.00   1261  153 0.2707 0.2585      5.0201      5.0422|
|  4:  2.3713 -  2.1545 1.00   1258  147 0.2772 0.2290      4.9312      4.7391|
|  5:  2.1545 -  2.0001 1.00   1257  134 0.2861 0.2886      4.8226       4.811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.8046 -  3.4193  1379   144  0.80  24.42   0.99     0.97       7091.12|
|  2:  3.4193 -  2.7143  1296   139  0.81  24.45   1.00     0.98       4750.46|
|  3:  2.7143 -  2.3713  1261   153  0.82  24.56   1.00     0.98       3124.95|
|  4:  2.3713 -  2.1545  1258   147  0.83  23.75   0.99     0.96       2335.56|
|  5:  2.1545 -  2.0001  1257   134  0.81  25.26   0.99     0.96       2114.06|
|alpha:            min =        0.96 max =            0.98 mean =         0.97|
|beta:             min =     2114.06 max =         7091.12 mean =      3948.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           90.00 mean =        24.49|
|phase err.(test): min =        0.00 max =           89.65 mean =        24.18|
|-----------------------------------------------------------------------------|
|--(resolution: 2.00 - 36.80 A; n_refl. = 7168)-------------------------------|
|                                                                             |
| r_work= 0.5013   r_free= 0.4699   ksol= 1.20   Bsol= 30.00   scale= 0.646   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.300042                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.8046 -  3.4193 1.00   1379  144 0.6257 0.6350      5.9193      5.8373|
|  2:  3.4193 -  2.7143 1.00   1296  139 0.3667 0.4064       5.564      5.6956|
|  3:  2.7143 -  2.3713 1.00   1261  153 0.2870 0.2733       5.159      5.1916|
|  4:  2.3713 -  2.1545 1.00   1258  147 0.2814 0.2368      4.9455      4.7852|
|  5:  2.1545 -  2.0001 1.00   1257  134 0.2944 0.2921      4.8448       4.815|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 36.8046 -  3.4193  1379   144  0.34  63.37   0.47     0.39      29597.42|
|  2:  3.4193 -  2.7143  1296   139  0.53  49.41   1.28     0.84      14636.65|
|  3:  2.7143 -  2.3713  1261   153  0.74  31.27   0.92     0.98       5543.60|
|  4:  2.3713 -  2.1545  1258   147  0.81  25.07   0.85     0.83       2619.18|
|  5:  2.1545 -  2.0001  1257   134  0.81  25.51   0.85     0.83       2132.04|
|alpha:            min =        0.39 max =            0.98 mean =         0.77|
|beta:             min =     2132.04 max =        29597.42 mean =     11277.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           90.00 mean =        39.44|
|phase err.(test): min =        0.00 max =           89.75 mean =        39.35|
|-----------------------------------------------------------------------------|
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling.py
OK:  u+s,u,s: 372.24 361.50 10.74

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/alignment.py
D
                A     A     A     T     T
        0.0   0.0   0.0   0.0   0.0   0.0
    A   0.0  -4.0  -5.0  -6.0  -7.0  -8.0
    A   0.0  -1.0  -3.0  -4.0  -5.0  -6.0
    A   0.0  -2.0   0.0  -2.0  -3.0  -4.0
    G   0.0  -3.0  -1.0   1.0  -1.0  -2.0
    G   0.0  -4.0  -2.0   0.0   1.0  -1.0
    T   0.0  -5.0  -3.0  -1.0   0.0   1.0
    T   0.0  -6.0  -4.0  -2.0  -1.0   0.0
I
                A     A     A     T     T
        0.0   0.0   0.0   0.0   0.0   0.0
    A   0.0  -4.0  -1.0  -2.0  -3.0  -4.0
    A   0.0  -5.0  -3.0   0.0  -1.0  -2.0
    A   0.0  -6.0  -4.0  -2.0   1.0   0.0
    G   0.0  -7.0  -5.0  -3.0  -1.0   1.0
    G   0.0  -8.0  -6.0  -4.0  -2.0  -1.0
    T   0.0  -9.0  -7.0  -5.0  -3.0  -1.0
    T   0.0 -10.0  -8.0  -6.0  -4.0  -2.0
M
                A     A     A     T     T
        0.0  -2.0  -3.0  -4.0  -5.0  -6.0
    A  -2.0   1.0  -1.0  -2.0  -3.0  -4.0
    A  -3.0  -1.0   2.0   0.0  -1.0  -2.0
    A  -4.0  -2.0   0.0   3.0   1.0   0.0
    G  -5.0  -3.0  -1.0   1.0   3.0   1.0
    G  -6.0  -4.0  -2.0   0.0   1.0   3.0
    T  -7.0  -5.0  -3.0  -1.0   1.0   2.0
    T  -8.0  -6.0  -4.0  -2.0   0.0   2.0
E
                A     A     A     T     T
        0.0   0.0   0.0   0.0   0.0   0.0
    A   0.0   0.0  -1.0  -1.0  -1.0  -1.0
    A   0.0   1.0   0.0  -1.0  -1.0  -1.0
    A   0.0   1.0   1.0   0.0  -1.0  -1.0
    G   0.0   1.0   1.0   1.0   0.0  -1.0
    G   0.0   1.0   1.0   1.0   1.0   0.0
    T   0.0   1.0   1.0   1.0   0.0   0.0
    T   0.0   1.0   1.0   1.0   0.0   0.0
score=2.0
mmmddmm
AAAGGTT
|||  ||
AAA--TT

1rra vs. 1bli; GLOBAL allignment; mdm78
score=1773.0
mmmmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii
AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----
**|    |  || |*  *****  ||* *|*|*|*| **|| *|||*|*   ***||| ***   *  |*| * | |****| |*| |*|  | |*| *|** *****||* |  *|||*| |*    
DNSRYTHFLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP

1rra vs. 1bli; LOCAL allignment; mdm78
score=2009.0
mmmmmmmmmmmmmmmmdmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmmdmmmmmdmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm
FKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV
|  || |*  *****  ||* *|*|*|*| **|| *|||*|*   ***||| ***   *  |*| * | |****| |*| |*|  | |*| *|** *****||* |  *|||*| |*
FLTQHYDAKPQGRDDR-YCESIMRRRGLT-SPCKDINTFIHGNKRSIKAIC-ENKNG-NPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSI

1rra vs. 1bli; GLOBAL allignment; blosum50
score=267.0
mmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmmiiii
AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----
  |    |  || | * |      ||  *|*|*|*|   || *|||*|     **||| *     |||   | |   | |****| |*| | | *| | |  |   *****||* |  *|||*| |*    
DNSRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSIFRRP

1rra vs. 1bli; LOCAL allignment; blosum50
score=287.0
mmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmmmmmmmmmmmmmmmmmmmdmmddddmmmiiimmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmmdmmdmmmmmmmmm
SSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV
|    |  || | * |      ||  *|*|*|*|   || *|||*|     **||| *     |||   | |   | |****| |*| | | *| | |  |   *****||* |  *|||*| |*
SRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKRSIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACE-NG-LPVHLDQSI

pretty_print is pretty pretty
              12345678901234567890123456789012345678901234567890     

1rra          SSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLE    
              |    |  || | * |      ||  *|*|*|*|   || *|||*|        
1bli          SRYTHFLTQHYDAK-PQGRDDRYCESIMRRRGLTS-PCKDINTFIHGNKR    

1rra          DVQAICSQGQVTCKNG---RNNCHKSSSTLRITDCRLKGSSKYPNCDYTT    
               **||| *     |||   | |   | |****| |*| | | *| | |      
1bli          SIKAIC-EN----KNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRA    

1rra          TDSQKHIIIACDGNPYVPVHFDASV    
              |   *****||* |  *|||*| |*    
1bli          TAGFRNVVVACE-NG-LPVHLDQSI    

OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/invariant_domain.py
OK

libtbx.python /net/longnose/scratch1/rwgk/auto_build/sources/mmtbx/tst_bioinformatics.py
testEquality (__main__.test_sequence) ... ok
testNonEquality (__main__.test_sequence) ... ok
testFormat (__main__.test_fasta_sequence) ... ok
testStr (__main__.test_fasta_sequence) ... ok
testFormat (__main__.test_pir_sequence) ... ok
testStr (__main__.test_pir_sequence) ... ok
testConservationCode (__main__.test_midline) ... ok
testMidline (__main__.test_midline) ... ok
testError (__main__.test_alignment) ... ok
testIdentityCount (__main__.test_alignment) ... ok
testError (__main__.test_fasta_alignment) ... ok
testFormat (__main__.test_fasta_alignment) ... ok
testStr (__main__.test_fasta_alignment) ... ok
testError (__main__.test_pir_alignment) ... ok
testFormat (__main__.test_pir_alignment) ... ok
testStr (__main__.test_pir_alignment) ... ok
testFormat (__main__.test_clustal_alignment) ... ok
testStr (__main__.test_clustal_alignment) ... ok
testFasta (__main__.test_sequence_parse) ... ok
testPir (__main__.test_sequence_parse) ... ok
testSequence (__main__.test_sequence_parse) ... ok
test_filename_selection (__main__.test_sequence_parse) ... ok
test_known_formats (__main__.test_sequence_parse) ... ok
testAli (__main__.test_alignment_parse) ... ok
testClustal (__main__.test_alignment_parse) ... ok
testFasta (__main__.test_alignment_parse) ... ok
testPir (__main__.test_alignment_parse) ... ok
test_filename_selection (__main__.test_alignment_parse) ... ok
test_known_formats (__main__.test_alignment_parse) ... ok

----------------------------------------------------------------------
Ran 29 tests in 0.016s

OK

endif
endif
libtbx.show_date_and_time -v
Date 2009-02-03 Time 01:15:16 PST -0800 (1233652516.46 s) Seconds since the Epoch 1233652516.46