# Date 2006-07-10 Time 19:52:02 PDT -0700
#phil __OFF__

HOST = sharptail.lbl.gov
HOSTTYPE = i386-linux
USER = phzwart

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.generate_r_free_flags = True

Crystal symmetry:
  Unit cell: (155.88, 156.25, 199.75, 90, 90, 90)
  Space group: C 2 2 21 (No. 20)

1upp.pdb
  Monomer Library directory:
    "/net/sharptail/scratch1/phzwart/Sources/mon_lib"
  Total number of atoms: 19504
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 19504
      Number of chains: 20
        Number of residues, atoms: 467, 3656
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 21, 'TRANS': 445}
        Number of residues, atoms: 467, 3656
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 20, 'TRANS': 445, 'PCIS': 1}
        Number of residues, atoms: 467, 3656
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 21, 'TRANS': 445}
        Number of residues, atoms: 467, 3656
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 21, 'TRANS': 445}
        Number of residues, atoms: 123, 1032
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
        Number of residues, atoms: 123, 1032
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
        Number of residues, atoms: 123, 1032
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
        Number of residues, atoms: 123, 1032
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
        Number of residues, atoms: 2, 22
          Unusual residues: {' CA': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
        Number of residues, atoms: 2, 22
          Unusual residues: {' CA': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
        Number of residues, atoms: 2, 22
          Unusual residues: {' CA': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
        Number of residues, atoms: 2, 22
          Unusual residues: {' CA': 1, 'CAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
        Number of residues, atoms: 47, 47
          Classifications: {'water': 47}
          Link IDs: {None: 46}
        Number of residues, atoms: 41, 41
          Classifications: {'water': 41}
          Link IDs: {None: 40}
        Number of residues, atoms: 43, 43
          Classifications: {'water': 43}
          Link IDs: {None: 42}
        Number of residues, atoms: 34, 34
          Classifications: {'water': 34}
          Link IDs: {None: 33}
        Number of residues, atoms: 133, 133
          Classifications: {'water': 133}
          Link IDs: {None: 132}
        Number of residues, atoms: 133, 133
          Classifications: {'water': 133}
          Link IDs: {None: 132}
        Number of residues, atoms: 121, 121
          Classifications: {'water': 121}
          Link IDs: {None: 120}
        Number of residues, atoms: 112, 112
          Classifications: {'water': 112}
          Link IDs: {None: 111}
  Time building chain proxies: 28.43, per 1000 atoms: 1.46

F-obs:
  1upp.mtz:F,SIGF

*******************************************************************************
Generating a new array of R-free flags.
*******************************************************************************


No array of experimental phases found.

Writing MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_data.mtz

  Number of scatterers: 19504
  At special positions: 0
  Unit cell: (155.88, 156.25, 199.75, 90, 90, 90)
  Space group: C 2 2 21 (No. 20)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      4     19.99
     S     100     16.00
     P       8     15.00
     O    4172      8.00
     N    3228      7.00
     C   11992      6.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=3
    Symmetry disulfide: " SG  CYS A 247 " - " SG  CYS E 247 " distance=2.58 -x,y,-z+1/2
    Symmetry disulfide: " SG  CYS C 247 " - " SG  CYS C 247 " distance=2.69 -x,y,-z+1/2
    Symmetry disulfide: " SG  CYS G 247 " - " SG  CYS G 247 " distance=2.54 -x,y,-z+1/2
  Time building geometry restraints manager: 2.20 seconds
  Histogram of bond lengths:
        1.17 -     1.47: 10662
        1.47 -     1.78: 8542
        1.78 -     2.08: 128
        2.08 -     2.39: 0
        2.39 -     2.69: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual sym.op. j
  " SG  CYS C 247 " - " SG  CYS C 247 " 2.031  2.691 -0.660 2.50e+03 1.09e+03 -x,y,-z+1/2
  " SG  CYS A 247 " - " SG  CYS E 247 " 2.031  2.580 -0.549 2.50e+03 7.53e+02 -x,y,-z+1/2
  " SG  CYS G 247 " - " SG  CYS G 247 " 2.031  2.537 -0.506 2.50e+03 6.39e+02 -x,y,-z+1/2
  " N   PRO C 176 " - " CD  PRO C 176 " 1.473  1.580 -0.107 5.10e+03 5.85e+01
  " CE1 HIS A 294 " - " NE2 HIS A 294 " 1.321  1.391 -0.070 1.00e+04 4.91e+01
  ... (remaining 19330 not shown)
  Histogram of nonbonded interaction distances:
        1.65 -     2.36: 20
        2.36 -     3.07: 14234
        3.07 -     3.78: 42306
        3.78 -     4.49: 71274
        4.49 -     5.20: 106356
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH T  77 " - " O   HOH T  77 "  1.648 3.400 -x,y,-z+1/2
  " O   HOH T  81 " - " O   HOH T  81 "  1.886 3.400 -x,y,-z+1/2
  " OD1 ASP L  24 " - " NH2 ARG L  28 "  2.050 3.070 x,-y,-z
  " CD  LYS A 177 " - " O   HOH Z  40 "  2.099 3.600
  " O   HOH T  86 " - " O   HOH T  86 "  2.117 3.400 -x,y,-z+1/2
  ... (remaining 234185 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    20.19: 5631
       20.19 -    40.37: 861
       40.37 -    60.55: 312
       60.55 -    80.73: 69
       80.73 -   100.91: 31
  Dihedral angle restraints sorted by residual:
  " CA  LYS A 175 "
  " C   LYS A 175 "
  " N   PRO A 176 "
  " CA  PRO A 176 "
      ideal   model   delta periodicty    weight residual
     180.00  -79.09 -100.91     1       4.00e-02 4.07e+02
  " CA  LYS E 175 "
  " C   LYS E 175 "
  " N   PRO E 176 "
  " CA  PRO E 176 "
      ideal   model   delta periodicty    weight residual
     180.00  -80.07  -99.93     1       4.00e-02 3.99e+02
  " CA  LYS G 175 "
  " C   LYS G 175 "
  " N   PRO G 176 "
  " CA  PRO G 176 "
      ideal   model   delta periodicty    weight residual
     180.00  -85.52  -94.48     1       4.00e-02 3.57e+02
  ... (remaining 6901 not shown)

From PDB header: deposition year: 03
From PDB remark 2: resolution: 2.3
From PDB remark 3: program(s) used: REFMAC


================================== X-ray data =================================

Miller array info: 1upp.mtz:F,SIGF
Observation type: xray.amplitude
Type of data: double, size=108166
Type of sigmas: double, size=108166
Number of Miller indices: 108166
Anomalous flag: False
Unit cell: (155.88, 156.25, 199.75, 90, 90, 90)
Space group: C 2 2 21 (No. 20)
Systematic absences: 0
Centric reflections: 4807
Resolution range: 74.0507 2.09391
Completeness in resolution range: 0.758469
Completeness with d_max=infinity: 0.758442

Number of F-obs in resolution range:                   108166
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  74.0507
                             d_min =   2.0939


================================= R-free flags ================================

Miller array info: R-free-flags
Observation type: None
Type of data: bool, size=108166
Type of sigmas: None
Number of Miller indices: 108166
Anomalous flag: False
Unit cell: (155.88, 156.25, 199.75, 90, 90, 90)
Space group: C 2 2 21 (No. 20)
Systematic absences: 0
Centric reflections: 4807
Resolution range: 74.0507 2.09391
Completeness in resolution range: 0.758469
Completeness with d_max=infinity: 0.758442

Test flag value: True

Number of work/free reflections by resolution:
                                            work   free  %free
  bin  1: 74.0970 -  4.5109 [14554/14714]  14285    269   1.8%
  bin  2:  4.5109 -  3.5804 [12122/14340]  11898    224   1.8%
  bin  3:  3.5804 -  3.1278 [10438/14284]  10245    193   1.8%
  bin  4:  3.1278 -  2.8418 [10273/14256]  10083    190   1.8%
  bin  5:  2.8418 -  2.6381 [10193/14220]  10004    189   1.9%
  bin  6:  2.6381 -  2.4826 [10116/14180]   9930    186   1.8%
  bin  7:  2.4826 -  2.3583 [10204/14169]  10014    190   1.9%
  bin  8:  2.3583 -  2.2556 [10170/14154]   9983    187   1.8%
  bin  9:  2.2556 -  2.1688 [10297/14128]  10107    190   1.8%
  bin 10:  2.1688 -  2.0939 [ 9799/14166]   9617    182   1.9%
                                  overall 106166   2000   1.8%
*******************************************************************************
Automatic adjustment. Reason: not enough test/work flags in some bins.
   old value:
      refinement.alpha_beta.test_ref_in_bin=100
   new value:
      refinement.alpha_beta.test_ref_in_bin=120
*******************************************************************************


============================== Scattering factors =============================

Number of scattering types: 6
  Type Number    sf(0)   Gaussians
   Ca      4     19.92       2
   S     100     15.96       2
   P       8     14.95       2
   O    4172      7.97       2
   N    3228      6.97       2
   C   11992      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


======================= NCS restraints before refinement ======================

No NCS restraint groups specified.

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001.geo


===================== Complete set of effective parameters ====================

#phil __ON__
refinement.crystal_symmetry {
  unit_cell = 155.88 156.25 199.75 90 90 90
  space_group = "C 2 2 21"
}
refinement.input {
  pdb {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp.pdb"
  }
  neutron_data {
    file_name = None
    labels = None
  }
  neutron_r_free_flags {
    file_name = None
    label = None
    test_flag_value = None
    disable_suitability_test = False
  }
  xray_data {
    file_name = "1upp.mtz"
    labels = "F,SIGF"
  }
  r_free_flags {
    file_name = None
    label = "R-free-flags"
    test_flag_value = True
    disable_suitability_test = False
  }
  experimental_phases {
    file_name = None
    labels = None
  }
  monomers {
    file_name = None
  }
}
refinement.output {
  prefix = "1upp_refine"
  serial = 1
  serial_format = "%03d"
  write_eff_file = True
  write_geo_file = True
  write_def_file = True
  write_refined_mtz_file = True
  write_refined_hkl_file = False
  write_maps = True
  write_map_coefficients = True
  refined_fmodel_data_labels {
    f_obs = "FOBS"
    f_model_amplitudes = "FMODEL"
    f_model_phases = "PHMODEL"
    figures_of_merit = "FOM"
    alpha = "D"
    cross_validation_flags = "CVFLAGS"
  }
}
refinement.electron_density_map {
  map_types = k*Fobs-n*Fmodel *2m*Fobs-D*Fmodel *m*Fobs-D*Fmodel
  map_format = *xplor
  map_coefficients_format = *mtz phs
  mtz_labels {
    map_type = "2m*Fobs-D*Fmodel"
    amplitudes = "2FOFCWT"
    phases = "PH2FOFCWT"
  }
  mtz_labels {
    map_type = "m*Fobs-D*Fmodel"
    amplitudes = "FOFCWT"
    phases = "PHFOFCWT"
  }
  mtz_labels {
    map_type = "k*Fobs-n*Fmodel"
    amplitudes = "oFOoFCWT"
    phases = "oPHFOoFCWT"
  }
  grid_resolution_factor = 0.3333333333
  region = *selection cell
  atom_selection = None
  atom_selection_buffer = 3
}
refinement.main {
  refine_adp_individual = True
  refine_adp_group = False
  refine_tls = False
  high_resolution = None
  low_resolution = None
  bulk_solvent_and_scale = True
  simulated_annealing = False
  fcalc_accuracy_check = False
  scale_adp = True
  ordered_solvent = False
  ls_bulk_solvent_and_scale_if_r_greater_then = 0.99
  put_water_after_macro_cycle_number = True
  number_of_macro_cycles = 3
  max_number_of_iterations = 25
  use_experimental_sigmas = False
  generate_neutron_r_free_flags = False
  generate_r_free_flags = True
  r_free_flags_fraction = 0.1
  r_free_flags_max_free = 2000
  remove_test_set_memory = None
  use_form_factor_weights = False
  refine_site = True
  number_of_macro_cycles_for_uiso_site_refinement = 1
  tan_u_iso = False
  sf_algorithm = *fft direct
  use_convergence_test = False
  target = *ml mlhl ls
  min_number_of_test_set_reflections_for_max_likelihood_target = 50
  max_number_of_resolution_bins = 20
  sigma_fobs_rejection_criterion = 0
  reference_xray_structure = None
  use_experimental_phases = None
  force_anomalous_flag_to_be_equal_to = None
  compute_optimal_errors = False
  update_target_functors = True
  random_seed = 2679941
  scattering_table = wk1995 it1992 *n_gaussian neutron
  use_normalized_geometry_target = True
  stop_refinement_if_resolution_higher_than = 0
  remove_hydrogens = True
  target_weights_only = False
  rigid_body = False
  max_f_obs = 50000000
  max_d_min = 0.1
  shake_start_model = None
  sf_cos_sin_table = True
  rigid_body_shift {
    apply = False
    write_shifted = False
    t_x = 0
    t_y = 0
    t_z = 0
    r_1 = 0
    r_2 = 0
    r_3 = 0
  }
}
refinement.modify_start_model {
  randomize_adp = False
  fake_f_obs = False
  write_modified_model = False
  k_sol = 0
  b_sol = 0
}
refinement.pdb_interpretation {
  link_distance_cutoff = 3
  disulfide_distance_cutoff = 3
  nonbonded_distance_cutoff = None
  default_vdw_distance = 1
  min_vdw_distance = 1
  nonbonded_buffer = 1
  vdw_1_4_factor = 0.6666666667
  translate_cns_dna_rna_residue_names = True
  clash_guard {
    nonbonded_distance_threshold = 0.5
    max_number_of_distances_below_threshold = 100
    max_fraction_of_distances_below_threshold = 0.1
  }
}
refinement.group_b_iso {
  number_of_macro_cycles = 5
  max_number_of_iterations = 50
  one_residue_one_group = True
  convergence_test = True
  selection = None
}
refinement.adp {
  convert_to_isotropic = True
  iso {
    max_number_of_iterations = 25
    shake_biso = None
    set_biso = None
    set_biso_random = False
    set_biso_to_wilson_b = False
    scaling {
      scale_max = 3
      scale_min = 10
    }
  }
  aniso {
    selection = None
  }
}
refinement.tls {
  selection = None
  one_residue_one_group = None
  refine_T = True
  refine_L = True
  refine_S = True
  number_of_macro_cycles = 2
  max_number_of_iterations = 50
  start_tls_value = None
  run_finite_differences_test = False
  eps = 1e-06
}
refinement.adp_restraints {
  iso {
    use_u_local_only = False
    sphere_radius = 5
    distance_power = 1.69
    average_power = 1.03
    wilson_b_weight_auto = False
    wilson_b_weight = None
    plain_pairs_radius = 5
    refine_ap_and_dp = False
    b_iso_max = None
  }
}
refinement.rigid_body {
  target = *ls_wunit_k1 ml
  refine_rotation = True
  refine_translation = True
  min_number_of_reflections = 1000
  max_iterations = 50
  convergence_test = True
  max_shift_for_bulk_solvent_and_scale_update = 0.3
  convergence_delta = 1e-05
  bulk_solvent_and_scale = True
  euler_angle_convention = *xyz zyz
  selection = None
}
refinement.ncs_restraint_group {
  reference = None
  selection = None
  coordinate_sigma = 0.05
  b_factor_weight = 10
}
refinement.geometry_restraints.remove {
  angles = None
  dihedrals = None
  chiralities = None
  planarities = None
}
refinement.ordered_solvent {
  low_resolution = 2.8
  filter_only = False
  output_residue_name = "HOH"
  output_chain_id = "S"
  output_atom_name = "O"
  output_record_name = "HETATM"
  b_iso_min = 1
  b_iso_max = 50
  b_iso = None
  scattering_type = "O"
  occupancy_min = 1
  occupancy_max = 1
  occupancy = 1
  use_sigma_scaled_maps = True
  primary_map_type = "m*Fobs-D*Fmodel"
  primary_map_k = None
  primary_map_n = None
  primary_map_cutoff = 3
  secondary_map_type = "2m*Fobs-D*Fmodel"
  secondary_map_k = None
  secondary_map_n = None
  secondary_map_cutoff = 1
  peak_map_matching_tolerance = 2
  resolution_factor = 0.25
  min_solv_macromol_dist = 1.8
  max_solv_macromol_dist = 6
  max_number_of_peaks = None
  verbose = 1
  peak_search {
    peak_search_level = 1
    max_peaks = 0
    interpolate = True
    min_distance_sym_equiv = 1e-06
    general_positions_only = False
    min_cross_distance = 2
  }
}
refinement.bulk_solvent_and_scale {
  bulk_solvent = True
  anisotropic_scaling = True
  statistical_solvent = False
  k_sol_b_sol_grid_search = True
  minimization_k_sol_b_sol = True
  minimization_b_cart = True
  target = ls_wunit_k1 *ml
  symmetry_constraints_on_b_cart = True
  k_sol_max = 0.6
  k_sol_min = 0
  b_sol_max = 80
  b_sol_min = 10
  k_sol_step = 0.05
  b_sol_step = 5
  number_of_macro_cycles = 2
  number_of_minimization_macro_cycles = 3
  number_of_cycles_for_anisotropic_scaling = 3
  fix_k_sol = None
  fix_b_sol = None
  fix_b_cart {
    u11 = None
    u22 = None
    u33 = None
    u12 = None
    u13 = None
    u23 = None
  }
  apply_back_trace_of_b_cart = False
  start_minimization_from_k_sol = 0.35
  start_minimization_from_b_sol = 46
  start_minimization_from_b_cart {
    u11 = 0
    u22 = 0
    u33 = 0
    u12 = 0
    u13 = 0
    u23 = 0
  }
  nu_fix_n_atoms = None
  nu_fix_b_atoms = None
  verbose = 1
}
refinement.fcalc_accuracy_check {
  nref_in_bin = 100
  r_lim = 1
  r_lim_high = 0.5
  scat_table = *wk1995 it1992
}
refinement.alpha_beta {
  test_ref_in_bin = 120
  keep_test_ref_in_bin = True
  number_of_macromolecule_atoms_absent = 225
  n_atoms_included = 0
  bf_atoms_absent = 15
  final_error = 0
  absent_atom_type = "O"
  method = *est calc
  verbose = -1
  interpolation = True
  fix_scale_for_calc_option = None
  number_of_waters_absent = 613
}
refinement.mask {
  solvent_radius = 1
  shrink_truncation_radius = 1
  grid_step_factor = 4
  verbose = 1
}
refinement.cartesian_dynamics {
  temperature = 300
  number_of_steps = 200
  time_step = 0.0005
  n_print = 100
  verbose = -1
}
refinement.simulated_annealing {
  start_temperature = 5000
  final_temperature = 300
  cool_rate = 100
  number_of_steps = 25
  time_step = 0.0005
  n_print = 100
  update_grads_shift = 0.3
  refine_sites = True
  refine_adp = False
  max_number_of_iterations = 25
  mode = every_macro_cycle *second_and_before_last
  verbose = -1
}
refinement.target_weights {
  wxc_scale = 0.5
  wxu_scale = 1
  wc = 1
  wu = 1
  fix_wxc = None
  fix_wxu = None
  allow_automatic_adjustment = False
  delta_r_free_r_work = 6
  wxc_scale_drop = 3
  wxu_scale_drop = 3
  max_number_of_macro_cycles = 12
  optimize_wxc = False
  optimization_criterion = *r_free gradient_angle
  optimize_wxu = False
  shake_sites = True
  shake_adp = 10
  regularize_ncycles = 50
  gradient_filtering = True
  gradient_filtering_method = *cns new
  rmsd_cutoff_for_gradient_filtering = 3
  verbose = 1
}
refinement.dbe {
  b_iso_cutoff = 10
  occupancy_cutoff = 0.8
  resolution = 0.7
}
refinement.ls_target_names {
  target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \
                ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \
                ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \
                ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \
                lsm_k1ask3_fixed
}
refinement.neutron {
  low_resolution = None
  high_resolution = None
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  

|-----------------------------------------------------------------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.3208      r_work = 0.2740            r_work = 0.4216             |
| r_free = 0.3090      r_free = 0.2807            r_free = 0.4092             |
|                                                                             |
| scale (work) = 0.9634  scale (free) = 1.0076  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ml:  work = 7.541622E+00  free = 7.535708E+00                        |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 74.0970 -  5.3834 0.99   8507  160 0.3938 0.3648  8.3912E+00  8.3241E+00|
|  2:  5.3834 -  4.2731 0.98   8159  154 0.2480 0.2633  8.1106E+00  8.0283E+00|
|  3:  4.2731 -  3.7329 0.85   7000  132 0.2506 0.2657  8.1091E+00  8.1864E+00|
|  4:  3.7329 -  3.3916 0.75   6206  117 0.2507 0.2590  7.9690E+00  7.8888E+00|
|  5:  3.3916 -  3.1485 0.72   5963  112 0.2588 0.2513  7.8133E+00  7.7397E+00|
|  6:  3.1485 -  2.9629 0.72   5944  112 0.2691 0.2501  7.6404E+00  7.6148E+00|
|  7:  2.9629 -  2.8145 0.72   5910  111 0.2637 0.2305  7.5061E+00  7.4310E+00|
|  8:  2.8145 -  2.6920 0.72   5875  111 0.2669 0.2848  7.4200E+00  7.4079E+00|
|  9:  2.6920 -  2.5884 0.71   5864  110 0.2646 0.2769  7.3181E+00  7.4102E+00|
| 10:  2.5884 -  2.4990 0.72   5852  111 0.2681 0.2304  7.2620E+00  7.2767E+00|
| 11:  2.4990 -  2.4209 0.72   5865  110 0.2749 0.2919  7.2139E+00  7.2210E+00|
| 12:  2.4209 -  2.3517 0.72   5887  112 0.2741 0.2757  7.2031E+00  7.1896E+00|
| 13:  2.3517 -  2.2898 0.72   5892  110 0.2822 0.3022  7.1799E+00  7.2498E+00|
| 14:  2.2898 -  2.2339 0.72   5919  112 0.2794 0.3075  7.1260E+00  7.1438E+00|
| 15:  2.2339 -  2.1831 0.73   5927  111 0.2849 0.3022  7.0893E+00  7.1322E+00|
| 16:  2.1831 -  2.1367 0.73   5988  113 0.2779 0.3362  7.0567E+00  7.1375E+00|
| 17:  2.1367 -  2.0939 0.71   5408  102 0.2950 0.3432  7.0351E+00  7.0059E+00|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 74.0970 -  5.3834  8507   160 0.570  45.912  46.935   0.627 3039380.845 |
|  2:  5.3834 -  4.2731  8159   154 0.778  29.187  31.843   0.867 2187600.683 |
|  3:  4.2731 -  3.7329  7000   132 0.845  23.317  23.492   1.016 1564147.330 |
|  4:  3.7329 -  3.3916  6206   117 0.863  21.939  21.576   1.086 1156276.830 |
|  5:  3.3916 -  3.1485  5963   112 0.862  22.045  22.765   1.118  861620.383 |
|  6:  3.1485 -  2.9629  5944   112 0.847  23.437  23.190   1.130  634829.277 |
|  7:  2.9629 -  2.8145  5910   111 0.845  23.622  22.942   1.120  511809.090 |
|  8:  2.8145 -  2.6920  5875   111 0.831  24.855  26.468   1.116  446391.897 |
|  9:  2.6920 -  2.5884  5864   110 0.821  25.814  26.491   1.115  400787.664 |
| 10:  2.5884 -  2.4990  5852   111 0.822  25.875  22.933   1.107  352380.462 |
| 11:  2.4990 -  2.4209  5865   110 0.813  26.687  27.887   1.097  319908.920 |
| 12:  2.4209 -  2.3517  5887   112 0.813  26.715  26.406   1.122  307394.264 |
| 13:  2.3517 -  2.2898  5892   110 0.797  28.079  28.572   1.138  302025.502 |
| 14:  2.2898 -  2.2339  5919   112 0.792  28.567  31.150   1.170  295968.685 |
| 15:  2.2339 -  2.1831  5927   111 0.782  29.517  28.772   1.183  284372.794 |
| 16:  2.1831 -  2.1367  5988   113 0.784  29.377  30.625   1.190  271657.905 |
| 17:  2.1367 -  2.0939  5408   102 0.769  30.705  33.276   1.142  242920.215 |
|alpha:            min =       0.6270 max =       1.1903 mean =       1.0626  |
|beta:             min =  242920.2145 max = 3039380.8449 mean =  872628.8885  |
|figures of merit: min =       0.0001 max =       1.0000 mean =       0.7966  |
|phase err.(work): min =       0.0000 max =      89.9942 mean =      27.8101  |
|phase err.(test): min =       0.0000 max =      89.9681 mean =      28.4175  |
|-----------------------------------------------------------------------------|

                          ----------Wilson B----------                         

Wilson B = 17.862    

             ----------Target weights (before refinement)----------            


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            3.620143 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.064188 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.277 (deg)            |
| angle between Xray and ADP gradient vectors:        91.860 (deg)            |
|-----------------------------------------------------------------------------|

|-target weights and weight scales : after gradient filtering-----------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            4.047218 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.064188 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.220 (deg)            |
| angle between Xray and ADP gradient vectors:        91.860 (deg)            |
| Number of Xray gradient terms excluded =     356 from total =   19148       |
|-----------------------------------------------------------------------------|

        ----------Initial model statistics (before refinement)----------       


|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.012   0.660  0.000|   15462.678||            ||  mean   max    min  |
|angl|  2.298  24.156  0.000|   71406.206||            ||                     |
|chir|  0.106   0.737  0.000|    1345.860||  118113.230||  0.000  0.000  0.000|
|plan|  0.012   0.143  0.000|    7631.936||            ||                     |
|dihe| 12.679 100.906  0.008|   14937.064||            ||                     |
|repu|  4.179   5.050  1.648|    7329.486||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.066: 19307/19307|  0.00-  2.42: 16406/16406| 1.65- 2.00:     2/    2 |
|0.066-0.132:    25/   25|  2.42-  4.83:  7027/ 7027| 2.00- 2.36:    18/   18 |
|0.132-0.198:     0/    0|  4.83-  7.25:  2172/ 2172| 2.36- 2.71:  1712/ 1712 |
|0.198-0.264:     0/    0|  7.25-  9.66:   496/  496| 2.71- 3.07: 12522/12522 |
|0.264-0.330:     0/    0|  9.66- 12.08:   103/  103| 3.07- 3.42: 16163/16163 |
|0.330-0.396:     0/    0| 12.08- 14.49:    38/   38| 3.42- 3.78: 26143/26143 |
|0.396-0.462:     0/    0| 14.49- 16.91:    11/   11| 3.78- 4.13: 31407/31407 |
|0.462-0.528:     1/    1| 16.91- 19.32:     3/    3| 4.13- 4.49: 39867/39867 |
|0.528-0.594:     1/    1| 19.32- 21.74:     5/    5| 4.49- 4.84: 50611/50611 |
|0.594-0.660:     1/    1| 21.74- 24.16:     3/    3| 4.84- 5.20: 55745/32596 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Wilson B =  17.862 | target =      0.00256 | norm of gradient =     0.00064 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   2.310   85.290    25.368            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|      2.310 -   10.608:     359      |        2.310 -   10.608:     359      |
|     10.608 -   18.906:    6522      |       10.608 -   18.906:    6522      |
|     18.906 -   27.204:    6597      |       18.906 -   27.204:    6597      |
|     27.204 -   35.502:    2611      |       27.204 -   35.502:    2611      |
|     35.502 -   43.800:    1705      |       35.502 -   43.800:    1705      |
|     43.800 -   52.098:     939      |       43.800 -   52.098:     939      |
|     52.098 -   60.396:     379      |       52.098 -   60.396:     379      |
|     60.396 -   68.694:     241      |       60.396 -   68.694:     241      |
|     68.694 -   76.992:      67      |       68.694 -   76.992:      67      |
|     76.992 -   85.290:      84      |       76.992 -   85.290:      84      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 1.00   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|-macro cycle = 1-------------------------------------------------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.3208      r_work = 0.2740            r_work = 0.4216             |
| r_free = 0.3090      r_free = 0.2807            r_free = 0.4092             |
|                                                                             |
| scale (work) = 0.9634  scale (free) = 1.0076  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ml:  work = 7.541622E+00  free = 7.535708E+00                        |
|-----------------------------------------------------------------------------|

===================== bulk solvent correction and scaling =====================

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 46.6 %           grid_step                = 0.523 A | 
| number of grid points = (300, 300, 384)                                     |
|-----------------------------------------------------------------------------|

|-macro cycle = 1: after bulk solvent correction and scaling------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.2601      r_work = 0.2618            r_work = 0.2428             |
| r_free = 0.2658      r_free = 0.2704            r_free = 0.2183             |
|                                                                             |
| scale (work) = 1.0901  scale (free) = 1.0684  ksol = 0.35  Bsol = 64.14     |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (-2.24,-2.01,-4.62,-0.00,-0.00,-0.00)            |
| (B11+B22+B33)/3 = -2.96                                                     |
|                                                                             |
| Target ml:  work = 7.491196E+00  free = 7.487181E+00                        |
|-----------------------------------------------------------------------------|

|-macro cycle = 1: isotropic adp statistics-----------------------------------|
|                             Wilson B = 17.86                                |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   5.074   76.110    25.345            |
| number of B <   1.0: 0              |  number of B <   1.0: 0               |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


================================ Target weights ===============================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            3.269488 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.061470 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.295 (deg)            |
| angle between Xray and ADP gradient vectors:        91.096 (deg)            |
|-----------------------------------------------------------------------------|

|-target weights and weight scales : after gradient filtering-----------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            3.589200 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.061470 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.248 (deg)            |
| angle between Xray and ADP gradient vectors:        91.096 (deg)            |
| Number of Xray gradient terms excluded =     302 from total =   19202       |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2601      final r-factor (work) = 0.2590          |
| start r-factor (free) = 0.2658      final r-factor (free) = 0.2964          |
|-----------------------------------------------------------------------------|
| T_start   = wxc      * Exray    + wc  * Echem                               |
| 13.881590 = 1.794599 * 7.491196 + 1.0 * 0.437891                            |
|-----------------------------------------------------------------------------|
| T_final   = wxc      * Exray    + wc  * Echem                               |
| 13.552464 = 1.794599 * 7.497381 + 1.0 * 0.097665                            |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   26   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.005   0.118  0.000|    2134.489||            ||  mean   max    min  |
|angl|  0.747  26.477  0.000|    6820.454||            ||                     |
|chir|  0.057   0.416  0.000|     419.251||   26343.502||  0.101  0.910  0.003|
|plan|  0.004   0.187  0.000|     771.970||            ||                     |
|dihe| 11.211  88.548  0.001|    9959.445||            ||                     |
|repu|  4.180   5.809  1.816|    6237.892||            ||                     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2590      final r-factor (work) = 0.2531          |
| start r-factor (free) = 0.2964      final r-factor (free) = 0.3016          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.464545 = 0.061469 * 7.515989 + 1.0 * 0.002540                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.462185 = 0.061469 * 7.497401 + 1.0 * 0.001322                             |
|-----------------------------------------------------------------------------|
| number of iterations =    9    |    number of function evaluations =   10   |
|-----------------------------------------------------------------------------|

|-macro cycle 1: -------------------------------------------------------------|
|                             Wilson B = 17.86                                |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   7.240   66.281    22.093            |
| number of B <   1.0: 0              |  number of B <   1.0: 0               |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|-macro cycle = 2-------------------------------------------------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.2531      r_work = 0.2551            r_work = 0.2323             |
| r_free = 0.3016      r_free = 0.3074            r_free = 0.2366             |
|                                                                             |
| scale (work) = 1.0557  scale (free) = 1.0156  ksol = 0.35  Bsol = 64.14     |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (-2.24,-2.01,-4.62,-0.00,-0.00,-0.00)            |
| (B11+B22+B33)/3 = -2.96                                                     |
|                                                                             |
| Target ml:  work = 7.508726E+00  free = 7.598079E+00                        |
|-----------------------------------------------------------------------------|

===================== bulk solvent correction and scaling =====================

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 46.7 %           grid_step                = 0.523 A | 
| number of grid points = (300, 300, 384)                                     |
|-----------------------------------------------------------------------------|

|-macro cycle = 2: after bulk solvent correction and scaling------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.2535      r_work = 0.2551            r_work = 0.2367             |
| r_free = 0.3010      r_free = 0.3072            r_free = 0.2341             |
|                                                                             |
| scale (work) = 1.0677  scale (free) = 1.0276  ksol = 0.35  Bsol = 60.00     |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (-1.94,-2.02,-3.72,-0.00,-0.00,-0.00)            |
| (B11+B22+B33)/3 = -2.56                                                     |
|                                                                             |
| Target ml:  work = 7.510441E+00  free = 7.597362E+00                        |
|-----------------------------------------------------------------------------|

|-macro cycle = 2: isotropic adp statistics-----------------------------------|
|                             Wilson B = 17.86                                |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   7.240   66.279    22.093            |
| number of B <   1.0: 0              |  number of B <   1.0: 0               |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


================================ Target weights ===============================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            4.801237 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.073746 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.221 (deg)            |
| angle between Xray and ADP gradient vectors:       119.784 (deg)            |
|-----------------------------------------------------------------------------|

|-target weights and weight scales : after gradient filtering-----------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            5.195765 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.073746 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.220 (deg)            |
| angle between Xray and ADP gradient vectors:       119.784 (deg)            |
| Number of Xray gradient terms excluded =     269 from total =   19235       |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2535      final r-factor (work) = 0.2497          |
| start r-factor (free) = 0.3010      final r-factor (free) = 0.3084          |
|-----------------------------------------------------------------------------|
| T_start   = wxc      * Exray    + wc  * Echem                               |
| 19.608563 = 2.597882 * 7.510441 + 1.0 * 0.097318                            |
|-----------------------------------------------------------------------------|
| T_final   = wxc      * Exray    + wc  * Echem                               |
| 19.571854 = 2.597882 * 7.496969 + 1.0 * 0.095607                            |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   29   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.005   0.081  0.000|    2009.369||            ||  mean   max    min  |
|angl|  0.770  21.578  0.000|    7127.320||            ||                     |
|chir|  0.056   0.363  0.000|     405.955||   25880.362||  0.143  1.063  0.003|
|plan|  0.003   0.185  0.000|     736.494||            ||                     |
|dihe| 10.949  88.809  0.001|    9424.293||            ||                     |
|repu|  4.180   5.426  1.899|    6176.929||            ||                     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2497      final r-factor (work) = 0.2510          |
| start r-factor (free) = 0.3084      final r-factor (free) = 0.3103          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.554924 = 0.073746 * 7.506878 + 1.0 * 0.001320                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.554390 = 0.073746 * 7.501566 + 1.0 * 0.001179                             |
|-----------------------------------------------------------------------------|
| number of iterations =   10    |    number of function evaluations =   11   |
|-----------------------------------------------------------------------------|

|-macro cycle 2: -------------------------------------------------------------|
|                             Wilson B = 17.86                                |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   4.842   59.663    19.887            |
| number of B <   1.0: 0              |  number of B <   1.0: 0               |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|-macro cycle = 3-------------------------------------------------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.2510      r_work = 0.2533            r_work = 0.2226             |
| r_free = 0.3103      r_free = 0.3164            r_free = 0.2385             |
|                                                                             |
| scale (work) = 1.0307  scale (free) = 0.9897  ksol = 0.35  Bsol = 60.00     |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (-1.94,-2.02,-3.72,-0.00,-0.00,-0.00)            |
| (B11+B22+B33)/3 = -2.56                                                     |
|                                                                             |
| Target ml:  work = 7.508448E+00  free = 7.619985E+00                        |
|-----------------------------------------------------------------------------|

===================== bulk solvent correction and scaling =====================

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 46.8 %           grid_step                = 0.523 A | 
| number of grid points = (300, 300, 384)                                     |
|-----------------------------------------------------------------------------|

|-macro cycle = 3: after bulk solvent correction and scaling------------------|
|                                                                             |
| all data [74.1-2.09] high resolution [6.0-2.09] low resolution [74.1-6.00]  |
| r_work = 0.2508      r_work = 0.2529            r_work = 0.2287             |
| r_free = 0.3097      r_free = 0.3161            r_free = 0.2403             |
|                                                                             |
| scale (work) = 1.0673  scale (free) = 1.0258  ksol = 0.35  Bsol = 61.18     |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (-0.26,-0.46,-1.98,-0.00,-0.00,-0.00)            |
| (B11+B22+B33)/3 = -0.90                                                     |
|                                                                             |
| Target ml:  work = 7.510476E+00  free = 7.619344E+00                        |
|-----------------------------------------------------------------------------|

|-macro cycle = 3: isotropic adp statistics-----------------------------------|
|                             Wilson B = 17.86                                |
|                                                                             |
| Reference model:                    | Current model:                        |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   4.842   59.662    19.887            |
| number of B <   1.0: 0              |  number of B <   1.0: 0               |
| number of B < 100.0: 0              |  number of B < 100.0: 0               |
|                                                                             |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


================================ Target weights ===============================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            4.887850 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.082350 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.922 (deg)            |
| angle between Xray and ADP gradient vectors:       122.034 (deg)            |
|-----------------------------------------------------------------------------|

|-target weights and weight scales : after gradient filtering-----------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            5.253576 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.082350 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.914 (deg)            |
| angle between Xray and ADP gradient vectors:       122.034 (deg)            |
| Number of Xray gradient terms excluded =     239 from total =   19265       |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2508      final r-factor (work) = 0.2505          |
| start r-factor (free) = 0.3097      final r-factor (free) = 0.3145          |
|-----------------------------------------------------------------------------|
| T_start   = wxc      * Exray    + wc  * Echem                               |
| 19.823923 = 2.626787 * 7.510475 + 1.0 * 0.095498                            |
|-----------------------------------------------------------------------------|
| T_final   = wxc      * Exray    + wc  * Echem                               |
| 19.811851 = 2.626787 * 7.509724 + 1.0 * 0.085399                            |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   28   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.005   0.058  0.000|    1546.213||            ||  mean   max    min  |
|angl|  0.676  19.879  0.000|    5561.185||            ||                     |
|chir|  0.053   0.352  0.000|     354.960||   23143.734||  0.169  1.126  0.005|
|plan|  0.003   0.187  0.000|     579.976||            ||                     |
|dihe| 10.806  87.055  0.000|    9053.503||            ||                     |
|repu|  4.180   5.603  1.973|    6047.898||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.066: 19307/19335|  0.00-  2.42: 16406/25154| 1.65- 2.00:     2/    1 |
|0.066-0.132:    25/    0|  2.42-  4.83:  7027/  989| 2.00- 2.36:    18/   13 |
|0.132-0.198:     0/    0|  4.83-  7.25:  2172/  107| 2.36- 2.71:  1712/ 1123 |
|0.198-0.264:     0/    0|  7.25-  9.66:   496/    7| 2.71- 3.07: 12522/13356 |
|0.264-0.330:     0/    0|  9.66- 12.08:   103/    3| 3.07- 3.42: 16163/16366 |
|0.330-0.396:     0/    0| 12.08- 14.49:    38/    2| 3.42- 3.78: 26143/25426 |
|0.396-0.462:     0/    0| 14.49- 16.91:    11/    0| 3.78- 4.13: 31407/31627 |
|0.462-0.528:     1/    0| 16.91- 19.32:     3/    1| 4.13- 4.49: 39867/41056 |
|0.528-0.594:     1/    0| 19.32- 21.74:     5/    1| 4.49- 4.84: 50611/51126 |
|0.594-0.660:     1/    0| 21.74- 24.16:     3/    0| 4.84- 5.20: 55745/32018 |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2505      final r-factor (work) = 0.2519          |
| start r-factor (free) = 0.3145      final r-factor (free) = 0.3153          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.620034 = 0.082349 * 7.514904 + 1.0 * 0.001183                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.619581 = 0.082349 * 7.509297 + 1.0 * 0.001191                             |
|-----------------------------------------------------------------------------|
| number of iterations =   11    |    number of function evaluations =   12   |
|-----------------------------------------------------------------------------|

|-macro cycle 3: -------------------------------------------------------------|
| Wilson B =  17.862 | target =      0.00119 | norm of gradient =     0.00052 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|   2.310   85.290    25.368          |   3.604   53.917    17.972            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|      2.310 -   10.608:     359      |        3.604 -    8.635:     102      |
|     10.608 -   18.906:    6522      |        8.635 -   13.666:    5293      |
|     18.906 -   27.204:    6597      |       13.666 -   18.698:    7413      |
|     27.204 -   35.502:    2611      |       18.698 -   23.729:    3742      |
|     35.502 -   43.800:    1705      |       23.729 -   28.760:    1578      |
|     43.800 -   52.098:     939      |       28.760 -   33.792:     695      |
|     52.098 -   60.396:     379      |       33.792 -   38.823:     339      |
|     60.396 -   68.694:     241      |       38.823 -   43.855:     163      |
|     68.694 -   76.992:      67      |       43.855 -   48.886:      88      |
|     76.992 -   85.290:      84      |       48.886 -   53.917:      91      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 19504 total              |
|-----------------------------------------------------------------------------|


================= overall refinement statistics: step by step =================

************************************************************************
Refinement target            :  ml
Number of atoms              :   19504
Number of geometry restraints:  271004
Unit cell volume             :     4865160.938
Space group                  :   20 (C 2 2 21)
Number of symmetries         :    4
Wilson B-factor              :     17.862
Isotropic ADP: distance_power:  1.69
Isotropic ADP: average_power :  1.03
****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_sar: simulated annealing refinement of x,y,z                          
1_wat: ordered solvent update (add / remove)                            
1_rbr: rigid body refinement                                            
1_gbr: group B-factor refinement                                        
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t         |grad|
   0    :  0.3208 0.3090   7.541622e+00   7.535708e+00   8.753458e-03
   1_bss:  0.2601 0.2658   7.491196e+00   7.487181e+00   9.330332e-03
   1_xyz:  0.2590 0.2964   7.515989e+00   7.582803e+00   6.821734e-03
   1_adp:  0.2531 0.3016   7.508726e+00   7.598079e+00   6.390885e-03
   2_bss:  0.2535 0.3010   7.510441e+00   7.597362e+00   6.428320e-03
   2_xyz:  0.2497 0.3084   7.506878e+00   7.616861e+00   5.566909e-03
   2_adp:  0.2510 0.3103   7.508448e+00   7.619985e+00   5.534262e-03
   3_bss:  0.2508 0.3097   7.510476e+00   7.619344e+00   5.559221e-03
   3_xyz:  0.2505 0.3145   7.514905e+00   7.629214e+00   5.358564e-03
   3_adp:  0.2519 0.3153   7.516380e+00   7.630475e+00   5.338475e-03
------------------------------------------------------------------------
 Weights for target T = Exray * wxc * wxc_scale + Echem * wc and
 angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites)
 stage              wxc          wxu  wxc_sc  wxu_sc /_gxc,gc /_gxu,gu
   0    :    2.0236e+00   6.4188e-02   0.500   1.000   90.220   91.860
   1_bss:    2.0236e+00   6.4188e-02   0.500   1.000   90.220   91.860
   1_xyz:    1.7946e+00   6.1470e-02   0.500   1.000   90.248   91.096
   1_adp:    1.7946e+00   6.1470e-02   0.500   1.000   90.248   91.096
   2_bss:    1.7946e+00   6.1470e-02   0.500   1.000   90.248   91.096
   2_xyz:    2.5979e+00   7.3746e-02   0.500   1.000   90.220  119.784
   2_adp:    2.5979e+00   7.3746e-02   0.500   1.000   90.220  119.784
   3_bss:    2.5979e+00   7.3746e-02   0.500   1.000   90.220  119.784
   3_xyz:    2.6268e+00   8.2350e-02   0.500   1.000   89.914  122.034
   3_adp:    2.6268e+00   8.2350e-02   0.500   1.000   89.914  122.034
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.351  64.136  -2.244  -2.011  -4.622  -0.000  -0.000  -0.000
   1_xyz:  0.351  64.136  -2.244  -2.011  -4.622  -0.000  -0.000  -0.000
   1_adp:  0.351  64.136  -2.244  -2.011  -4.622  -0.000  -0.000  -0.000
   2_bss:  0.350  60.000  -1.940  -2.021  -3.717  -0.000  -0.000  -0.000
   2_xyz:  0.350  60.000  -1.940  -2.021  -3.717  -0.000  -0.000  -0.000
   2_adp:  0.350  60.000  -1.940  -2.021  -3.717  -0.000  -0.000  -0.000
   3_bss:  0.350  61.180  -0.263  -0.462  -1.982  -0.000  -0.000  -0.000
   3_xyz:  0.350  61.180  -0.263  -0.462  -1.982  -0.000  -0.000  -0.000
   3_adp:  0.350  61.180  -0.263  -0.462  -1.982  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.821 0.7966  1.0626   872628.889
   1_bss:  24.944 0.8282  1.0049   585544.803
   1_xyz:  29.402 0.7795  0.9505   740545.444
   1_adp:  30.418 0.7676  0.9027   771148.578
   2_bss:  30.394 0.7678  0.9171   768008.105
   2_xyz:  31.767 0.7517  0.9036   816746.016
   2_adp:  31.940 0.7497  0.8597   824708.907
   3_bss:  31.935 0.7498  0.9058   823245.471
   3_xyz:  32.557 0.7427  0.8986   852404.384
   3_adp:  32.640 0.7417  0.8516   856553.741
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target     wc
   0    :   2.298  0.012  0.106 12.679  0.012  4.179   1.1811e+05   1.00
   1_bss:   2.298  0.012  0.106 12.679  0.012  4.179   1.1811e+05   1.00
   1_xyz:   0.747  0.005  0.057 11.211  0.004  4.180   2.6344e+04   1.00
   1_adp:   0.747  0.005  0.057 11.211  0.004  4.180   2.6344e+04   1.00
   2_bss:   0.747  0.005  0.057 11.211  0.004  4.180   2.6344e+04   1.00
   2_xyz:   0.770  0.005  0.056 10.949  0.003  4.180   2.5880e+04   1.00
   2_adp:   0.770  0.005  0.056 10.949  0.003  4.180   2.5880e+04   1.00
   3_bss:   0.770  0.005  0.056 10.949  0.003  4.180   2.5880e+04   1.00
   3_xyz:   0.676  0.005  0.053 10.806  0.003  4.180   2.3144e+04   1.00
   3_adp:   0.676  0.005  0.053 10.806  0.003  4.180   2.3144e+04   1.00
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  24.156  0.660  0.737100.906  0.143  1.648   1.5203e-01
   1_bss:  24.156  0.660  0.737100.906  0.143  1.648   1.5203e-01
   1_xyz:  26.477  0.118  0.416 88.548  0.187  1.816   2.2156e-02
   1_adp:  26.477  0.118  0.416 88.548  0.187  1.816   2.2156e-02
   2_bss:  26.477  0.118  0.416 88.548  0.187  1.816   2.2156e-02
   2_xyz:  21.578  0.081  0.363 88.809  0.185  1.899   1.9583e-02
   2_adp:  21.578  0.081  0.363 88.809  0.185  1.899   1.9583e-02
   3_bss:  21.578  0.081  0.363 88.809  0.185  1.899   1.9583e-02
   3_xyz:  19.879  0.058  0.352 87.055  0.187  1.973   1.5424e-02
   3_adp:  19.879  0.058  0.352 87.055  0.187  1.973   1.5424e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  85.29   2.31  25.37  85.29   4.90  25.66  65.25   2.31  17.02
   1_bss:  76.11   5.07  25.35  76.11   5.07  25.64  65.25   5.07  17.07
   1_xyz:  76.11   5.07  25.35  76.11   5.07  25.64  65.25   5.07  17.07
   1_adp:  66.28   7.24  22.09  66.28   7.80  22.16  51.68   7.24  20.12
   2_bss:  66.28   7.24  22.09  66.28   7.80  22.16  51.68   7.24  20.12
   2_xyz:  66.28   7.24  22.09  66.28   7.80  22.16  51.68   7.24  20.12
   2_adp:  59.66   4.84  19.89  59.66   7.30  19.92  49.60   4.84  19.02
   3_bss:  59.66   4.84  19.89  59.66   7.30  19.92  49.60   4.84  19.02
   3_xyz:  59.66   4.84  19.89  59.66   7.30  19.92  49.60   4.84  19.02
   3_adp:  53.92   3.60  17.97  53.92   6.57  18.00  47.31   3.60  17.27
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.910    0.003    0.101
   1_adp:    0.910    0.003    0.101
   2_bss:    0.910    0.003    0.101
   2_xyz:    1.063    0.003    0.143
   2_adp:    1.063    0.003    0.143
   3_bss:    1.063    0.003    0.143
   3_xyz:    1.126    0.005    0.169
   3_adp:    1.126    0.005    0.169
------------------------------------------------------------------------
 stage         k1_w     k1_t     k3_w     k3_t scale_ml
   0    :    0.9634   1.0076   1.0752   1.1030   1.0000
   1_bss:    1.0901   1.0684   1.1424   1.1253   1.0000
   1_xyz:    1.0927   1.0560   1.1439   1.1248   1.0000
   1_adp:    1.0557   1.0156   1.1032   1.0833   1.0000
   2_bss:    1.0677   1.0276   1.1159   1.0959   1.0000
   2_xyz:    1.0689   1.0261   1.1146   1.0972   1.0000
   2_adp:    1.0307   0.9897   1.0749   1.0589   1.0000
   3_bss:    1.0673   1.0258   1.1136   1.0975   1.0000
   3_xyz:    1.0678   1.0244   1.1137   1.0977   1.0000
   3_adp:    1.0287   0.9865   1.0731   1.0575   1.0000
------------------------------------------------------------------------
 stage      adp_target      wu
   0    :   2.5642e-03   1.000
   1_bss:   2.5421e-03   1.000
   1_xyz:   2.5405e-03   1.000
   1_adp:   1.3226e-03   1.000
   2_bss:   1.3226e-03   1.000
   2_xyz:   1.3210e-03   1.000
   2_adp:   1.1791e-03   1.000
   3_bss:   1.1791e-03   1.000
   3_xyz:   1.1837e-03   1.000
   3_adp:   1.1918e-03   1.000
------------------------------------------------------------------------

============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001.pdb

Writing refined f_model, FOM, alpha, cv_set to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001.mtz

Writing 2m*Fobs-D*Fmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001_2mFobs-DFmodel.map
Writing m*Fobs-D*Fmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/1upp/1upp_refine_002.def

# Date 2006-07-10 Time 20:35:10 PDT -0700
Start R-work = 0.2601, R-free = 0.2658
Final R-work = 0.2519, R-free = 0.3153
Time per interpreted Python bytecode instruction: 10.677 micro seconds
Total CPU time: 43.13 minutes