# Date 2006-07-10 Time 23:05:51 PDT -0700
#phil __OFF__

------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.24.1b
  Platform: intel-linux-2.6 linux
  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.

Crystal symmetry:
  Unit cell: (101.5, 101.5, 104.2, 90, 90, 90)
  Space group: P 43 (No. 78)

1rfq.pdb
  Monomer Library directory:
    "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/ext_ref_files/mon_lib"
  Total number of atoms: 5824
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 5824
      Number of chains: 3
        Number of residues, atoms: 361, 2829
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 19, 'TRANS': 341}
          Chain breaks: 1
        Number of residues, atoms: 361, 2829
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 19, 'TRANS': 341}
          Chain breaks: 1
        Number of residues, atoms: 50, 166
          Unusual residues: {' MG': 2, 'LAR': 2, 'ATP': 2}
          Classifications: {'undetermined': 6, 'water': 44}
          Link IDs: {None: 49}
  Time building chain proxies: 8.13, per 1000 atoms: 1.40

F-obs:
  1rfq-sf.mtz:FP,SIGFP

R-free flags:
  1rfq-sf.mtz:FREE


No array of experimental phases found.

  Number of scatterers: 5824
  At special positions: 0
  Unit cell: (101.5, 101.5, 104.2, 90, 90, 90)
  Space group: P 43 (No. 78)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number   Weight
     S      40     16.00
     P       6     15.00
     Mg      2     11.99
     O    1160      8.00
     N     964      7.00
     C    3652      6.00
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.62 seconds
  Histogram of bond lengths:
        1.18 -     1.46: 3048
        1.46 -     1.75: 2788
        1.75 -     2.03: 70
        2.03 -     2.32: 0
        2.32 -     2.61: 4
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " C5  LAR   387 " - " C7  LAR   387 " 1.517  2.606 -1.090 2.50e+03 2.97e+03
  " C5  LAR   377 " - " C7  LAR   377 " 1.517  2.572 -1.055 2.50e+03 2.78e+03
  " C6  LAR   377 " - " C8  LAR   377 " 1.487  2.451 -0.965 2.50e+03 2.33e+03
  " C6  LAR   387 " - " C8  LAR   387 " 1.487  2.446 -0.959 2.50e+03 2.30e+03
  " N   SER A 235 " - " CA  SER A 235 " 1.458  1.787 -0.329 2.77e+03 3.00e+02
  ... (remaining 5905 not shown)
  Histogram of nonbonded interaction distances:
        0.32 -     1.30: 4
        1.30 -     2.27: 65
        2.27 -     3.25: 8147
        3.25 -     4.22: 21461
        4.22 -     5.20: 37529
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " NH1 ARG B  39 " - " O   HOH     7 "  0.325 3.070
  " CE1 TYR A 169 " - " O   HOH    26 "  0.912 3.600
  " C   CYS A 374 " - " CD1 PHE A 375 "  1.014 3.700
  " CE  LYS A 373 " - " O   ARG B 372 "  1.075 3.500
  " CZ  ARG B  39 " - " O   HOH     7 "  1.312 3.500
  ... (remaining 67201 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.87: 1886
       32.87 -    65.73: 247
       65.73 -    98.60: 48
       98.60 -   131.47: 1
      131.47 -   164.33: 8
  Dihedral angle restraints sorted by residual:
  " CA  HIS A  40 "
  " C   HIS A  40 "
  " N   ASP A  51 "
  " CA  ASP A  51 "
      ideal   model   delta periodicty    weight residual
     180.00  -60.60 -119.40     1       4.00e-02 5.70e+02
  " CA  SER A 234 "
  " C   SER A 234 "
  " N   SER A 235 "
  " CA  SER A 235 "
      ideal   model   delta periodicty    weight residual
     180.00 -137.95  -42.05     1       4.00e-02 7.07e+01
  " N1  LAR   387 "
  " C17 LAR   387 "
  " C18 LAR   387 "
  " O4  LAR   387 "
      ideal   model   delta periodicty    weight residual
     -83.71   80.62 -164.33     1       2.50e-03 6.75e+01
  ... (remaining 2187 not shown)

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


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

Miller array info: 1rfq-sf.mtz:FP,SIGFP
Observation type: xray.amplitude
Type of data: double, size=20909
Type of sigmas: double, size=20909
Number of Miller indices: 20909
Anomalous flag: False
Unit cell: (101.5, 101.5, 104.2, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 850
Resolution range: 46.3505 3.00333
Completeness in resolution range: 0.986599
Completeness with d_max=infinity: 0.986367

Number of F-obs in resolution range:                   20909
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  46.3505
                             d_min =   3.0033


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

Miller array info: 1rfq-sf.mtz:FREE
Observation type: None
Type of data: int, size=21195
Type of sigmas: None
Number of Miller indices: 21195
Anomalous flag: False
Unit cell: (101.5, 101.5, 104.2, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 891
Resolution range: 46.3505 3.00315
Completeness in resolution range: 1
Completeness with d_max=infinity: 0.999764

Test flag value: 0

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 46.3560 -  6.4652 [2168/2176]  1906   262  12.1%
  bin  2:  6.4652 -  5.1338 [2123/2125]  1832   291  13.7%
  bin  3:  5.1338 -  4.4854 [2127/2132]  1835   292  13.7%
  bin  4:  4.4854 -  4.0756 [2108/2112]  1843   265  12.6%
  bin  5:  4.0756 -  3.7836 [2102/2106]  1800   302  14.4%
  bin  6:  3.7836 -  3.5606 [2120/2126]  1822   298  14.1%
  bin  7:  3.5606 -  3.3824 [2074/2093]  1773   301  14.5%
  bin  8:  3.3824 -  3.2352 [2093/2111]  1772   321  15.3%
  bin  9:  3.2352 -  3.1106 [2069/2117]  1772   297  14.4%
  bin 10:  3.1106 -  3.0033 [1925/2095]  1696   229  11.9%
                                overall 18051  2858  13.7%
*******************************************************************************
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=130
*******************************************************************************


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

Number of scattering types: 6
  Type Number   Weight   Gaussians
   S      40     15.96       2
   P       6     14.95       2
   Mg      2     11.95       2
   O    1160      7.97       1
   N     964      6.97       1
   C    3652      5.97       2


======================= 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/bastard/1rfq_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq_refine_001.geo

Complete set of effective parameters:
#phil __ON__
refinement.crystal_symmetry {
  unit_cell = 101.5 101.5 104.2 90 90 90
  space_group = "P 43"
}
refinement.input {
  pdb {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq.pdb"
  }
  xray_data {
    file_name = "1rfq-sf.mtz"
    labels = "FP,SIGFP"
  }
  r_free_flags {
    file_name = "1rfq-sf.mtz"
    label = "FREE"
    test_flag_value = 0
    disable_suitability_test = False
  }
  experimental_phases {
    file_name = None
    labels = None
  }
  monomers {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/elbow.LAR.001.cif"
  }
}
refinement.output {
  prefix = "1rfq_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_r_free_flags = False
  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 lsm
  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 {
  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 = 130
  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
}
#phil __OFF__


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


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

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.4343  scale (work) =  1.0000  ksol=  0.00  bsol=   0.00 |
| r-factor (free) = 0.3850  scale (free) =  1.2427                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    0.000 B12=    0.000 B13=    0.000 |target name=                 ml |
|                B22=    0.000 B23=    0.000 |target (work) =  4.034525E+00   |
|                              B33=    0.000 |target (free) =  4.010795E+00   |
| (B11+B22+B33)/3 =    0.000                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 46.3560 -  8.1383 0.99    963  128 0.5049 0.3877  5.7279E+00  5.1156E+00|
|  2:  8.1383 -  6.4652 1.00    943  134 0.3178 0.3647  4.6640E+00  4.7027E+00|
|  3:  6.4652 -  5.6496 1.00    913  146 0.3184 0.3624  4.4170E+00  4.4300E+00|
|  4:  5.6496 -  5.1338 1.00    919  145 0.3039 0.3689  4.3113E+00  4.4176E+00|
|  5:  5.1338 -  4.7662 1.00    934  125 0.2939 0.3049  4.3301E+00  4.3373E+00|
|  6:  4.7662 -  4.4854 1.00    901  167 0.2783 0.2917  4.3511E+00  4.4443E+00|
|  7:  4.4854 -  4.2610 1.00    916  142 0.2947 0.3423  4.2970E+00  4.3899E+00|
|  8:  4.2610 -  4.0756 1.00    927  123 0.3181 0.2950  4.2206E+00  4.1903E+00|
|  9:  4.0756 -  3.9188 1.00    901  136 0.3178 0.3698  4.1322E+00  4.0687E+00|
| 10:  3.9188 -  3.7836 1.00    899  166 0.3291 0.3615  3.9888E+00  4.0608E+00|
| 11:  3.7836 -  3.6654 1.00    908  154 0.3387 0.3950  3.9215E+00  4.0640E+00|
| 12:  3.6654 -  3.5606 1.00    914  144 0.3487 0.3570  3.8761E+00  3.8264E+00|
| 13:  3.5606 -  3.4669 0.99    882  151 0.3727 0.3860  3.8116E+00  3.8400E+00|
| 14:  3.4669 -  3.3824 0.99    891  150 0.3773 0.3752  3.7450E+00  3.6279E+00|
| 15:  3.3824 -  3.3055 0.99    889  155 0.3719 0.3736  3.6354E+00  3.6899E+00|
| 16:  3.3055 -  3.2352 0.99    883  166 0.3909 0.3946  3.5400E+00  3.6106E+00|
| 17:  3.2352 -  3.1705 0.98    891  125 0.3933 0.4525  3.4570E+00  3.4861E+00|
| 18:  3.1705 -  3.1106 0.98    881  172 0.4135 0.4070  3.4228E+00  3.3726E+00|
| 19:  3.1106 -  3.0551 0.97    891  110 0.4083 0.4596  3.2984E+00  3.3442E+00|
| 20:  3.0551 -  3.0033 0.91    805  119 0.4153 0.4371  3.2320E+00  3.2277E+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: 46.3560 -  8.1383   963   128 0.687  36.245  42.075   0.825    6134.567 |
|  2:  8.1383 -  6.4652   943   134 0.599  44.427  44.062   0.991    3317.495 |
|  3:  6.4652 -  5.6496   913   146 0.666  39.569  38.458   1.056    1795.907 |
|  4:  5.6496 -  5.1338   919   145 0.700  36.607  36.328   1.115    1373.887 |
|  5:  5.1338 -  4.7662   934   125 0.744  32.833  32.726   1.247    1235.490 |
|  6:  4.7662 -  4.4854   901   167 0.799  28.765  24.818   1.356    1155.352 |
|  7:  4.4854 -  4.2610   916   142 0.783  29.434  30.614   1.395    1039.418 |
|  8:  4.2610 -  4.0756   927   123 0.732  34.005  33.474   1.342     924.745 |
|  9:  4.0756 -  3.9188   901   136 0.705  35.770  39.900   1.257     810.453 |
| 10:  3.9188 -  3.7836   899   166 0.660  40.398  38.524   1.228     743.945 |
| 11:  3.7836 -  3.6654   908   154 0.645  41.400  40.583   1.214     654.574 |
| 12:  3.6654 -  3.5606   914   144 0.655  40.539  39.565   1.237     540.318 |
| 13:  3.5606 -  3.4669   882   151 0.665  39.842  38.635   1.214     425.003 |
| 14:  3.4669 -  3.3824   891   150 0.649  40.971  41.600   1.207     355.131 |
| 15:  3.3824 -  3.3055   889   155 0.627  43.182  40.472   1.157     329.341 |
| 16:  3.3055 -  3.2352   883   166 0.571  47.627  45.241   1.089     311.819 |
| 17:  3.2352 -  3.1705   891   125 0.512  51.859  51.323   1.016     286.704 |
| 18:  3.1705 -  3.1106   881   172 0.491  53.056  55.059   0.939     244.759 |
| 19:  3.1106 -  3.0551   891   110 0.488  53.524  54.937   0.917     215.832 |
| 20:  3.0551 -  3.0033   805   119 0.482  54.184  53.719   0.888     178.646 |
|alpha:            min =       0.8110 max =       1.3979 mean =       1.1362  |
|beta:             min =     175.0125 max =    6370.7944 mean =    1126.3938  |
|figures of merit: min =       0.0010 max =       1.0000 mean =       0.6449  |
|phase err.(work): min =       0.0000 max =      89.9136 mean =      41.0598  |
|phase err.(test): min =       0.0000 max =      89.5515 mean =      40.8744  |
|-----------------------------------------------------------------------------|

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

Wilson B =     77.122

             ----------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 =            0.770720 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.009637 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.925 (deg)            |
| angle between Xray and ADP gradient vectors:        91.238 (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 =            0.805443 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.009637 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.001 (deg)            |
| angle between Xray and ADP gradient vectors:        91.238 (deg)            |
| Number of Xray gradient terms excluded =      42 from total =    5782       |
|-----------------------------------------------------------------------------|

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


| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.009   1.090  0.000|   14982.029||            ||  mean   max    min  |
|angl|  1.439 136.884  0.000|   27023.123||            ||                     |
|chir|  0.082   0.614  0.001|     269.360||   65846.534||  0.000  0.000  0.000|
|plan|  0.005   0.190  0.000|    1463.842||            ||                     |
|dihe| 14.092 164.332  0.003|    4524.148||            ||                     |
|repu|  4.214   5.200  0.325|   17584.032||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.109:  5883/ 5883|  0.00- 13.69:  7976/ 7976| 0.32- 0.81:     1/    1 |
|0.109-0.218:    19/   19| 13.69- 27.38:    41/   41| 0.81- 1.30:     3/    3 |
|0.218-0.327:     3/    3| 27.38- 41.07:     8/    8| 1.30- 1.79:    15/   15 |
|0.327-0.436:     1/    1| 41.07- 54.75:     1/    1| 1.79- 2.27:    50/   50 |
|0.436-0.545:     0/    0| 54.75- 68.44:     1/    1| 2.27- 2.76:  1660/ 1660 |
|0.545-0.654:     0/    0| 68.44- 82.13:     1/    1| 2.76- 3.25:  6487/ 6487 |
|0.654-0.763:     0/    0| 82.13- 95.82:     0/    0| 3.25- 3.74:  9153/ 9153 |
|0.763-0.872:     0/    0| 95.82-109.51:     1/    1| 3.74- 4.22: 12308/12308 |
|0.872-0.981:     2/    2|109.51-123.20:     3/    3| 4.22- 4.71: 16857/16857 |
|0.981-1.090:     2/    2|123.20-136.88:     2/    2| 4.71- 5.20: 20672/20672 |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00097 | norm of gradient =     0.00041 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  31.880   96.840    63.420            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       31.880 -   38.376:      25      |
|     38.376 -   44.872:     203      |       38.376 -   44.872:     203      |
|     44.872 -   51.368:     499      |       44.872 -   51.368:     499      |
|     51.368 -   57.864:    1161      |       51.368 -   57.864:    1161      |
|     57.864 -   64.360:    1263      |       57.864 -   64.360:    1263      |
|     64.360 -   70.856:    1162      |       64.360 -   70.856:    1162      |
|     70.856 -   77.352:     963      |       70.856 -   77.352:     963      |
|     77.352 -   83.848:     395      |       77.352 -   83.848:     395      |
|     83.848 -   90.344:     110      |       83.848 -   90.344:     110      |
|     90.344 -   96.840:      43      |       90.344 -   96.840:      43      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|

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

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


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

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 63.7 %           grid_step                = 0.751 A | 
| number of grid points = (135, 135, 144)                                     |
|-----------------------------------------------------------------------------|

|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.325085 r_work= 0.4343     |
| B(11,22,33,12,13,23)=   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 0.000                                      |
| mean alpha:  0.0863  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.35 b_sol=  80.00 target_w =            0.121760 r_work= 0.3082     |
| B(11,22,33,12,13,23)=  16.4222  16.4222  -3.6102   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 9.745                                      |
| mean alpha:  0.1122  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.35 b_sol=  80.00 target_w =            0.121760 r_work= 0.3082     |
| B(11,22,33,12,13,23)=  16.4222  16.4222  -3.6102   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 9.745                                      |
| mean alpha:  0.1122  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.120007 r_work= 0.3097     |
| B(11,22,33,12,13,23)=  20.1108  20.1108  -0.1894   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 13.344                                     |
| mean alpha:  0.1193  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.120007 r_work= 0.3097     |
| B(11,22,33,12,13,23)=  20.0975  20.0975  -0.2019   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 13.331                                     |
| mean alpha:  0.1193  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            3.965873 r_work= 0.3097     |
| B(11,22,33,12,13,23)=  20.0975  20.0975  -0.2019   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 13.331                                     |
| mean alpha:  0.8040  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|

         ----------after bulk solvent correction and scaling----------         

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.3097  scale (work) =  1.0000  ksol=  0.37  bsol=  80.00 |
| r-factor (free) = 0.3476  scale (free) =  0.9617                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=   20.097 B12=    0.000 B13=   -0.000 |target name=                 ml |
|                B22=   20.097 B23=    0.000 |target (work) =  3.964615E+00   |
|                              B33=   -0.202 |target (free) =  3.982157E+00   |
| (B11+B22+B33)/3 =   13.331                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 46.3560 -  8.1383 0.99    963  128 0.2485 0.3171  4.9557E+00  4.9725E+00|
|  2:  8.1383 -  6.4652 1.00    943  134 0.2901 0.3056  4.5775E+00  4.6056E+00|
|  3:  6.4652 -  5.6496 1.00    913  146 0.2940 0.3809  4.3752E+00  4.4182E+00|
|  4:  5.6496 -  5.1338 1.00    919  145 0.3011 0.3830  4.3014E+00  4.4089E+00|
|  5:  5.1338 -  4.7662 1.00    934  125 0.2843 0.2963  4.3075E+00  4.3221E+00|
|  6:  4.7662 -  4.4854 1.00    901  167 0.2796 0.2930  4.3452E+00  4.4542E+00|
|  7:  4.4854 -  4.2610 1.00    916  142 0.2817 0.3361  4.2714E+00  4.3676E+00|
|  8:  4.2610 -  4.0756 1.00    927  123 0.3048 0.2956  4.1888E+00  4.1930E+00|
|  9:  4.0756 -  3.9188 1.00    901  136 0.2992 0.3449  4.0868E+00  4.0233E+00|
| 10:  3.9188 -  3.7836 1.00    899  166 0.3203 0.3351  3.9601E+00  4.0055E+00|
| 11:  3.7836 -  3.6654 1.00    908  154 0.3325 0.3798  3.8933E+00  4.0366E+00|
| 12:  3.6654 -  3.5606 1.00    914  144 0.3412 0.3678  3.8533E+00  3.8347E+00|
| 13:  3.5606 -  3.4669 0.99    882  151 0.3598 0.3607  3.7856E+00  3.8049E+00|
| 14:  3.4669 -  3.3824 0.99    891  150 0.3649 0.3785  3.7036E+00  3.6308E+00|
| 15:  3.3824 -  3.3055 0.99    889  155 0.3618 0.3591  3.6038E+00  3.6544E+00|
| 16:  3.3055 -  3.2352 0.99    883  166 0.3727 0.3848  3.5135E+00  3.5765E+00|
| 17:  3.2352 -  3.1705 0.98    891  125 0.3910 0.4404  3.4357E+00  3.4590E+00|
| 18:  3.1705 -  3.1106 0.98    881  172 0.4047 0.4223  3.3925E+00  3.3653E+00|
| 19:  3.1106 -  3.0551 0.97    891  110 0.4121 0.4307  3.2809E+00  3.3254E+00|
| 20:  3.0551 -  3.0033 0.91    805  119 0.4098 0.4278  3.2017E+00  3.1997E+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: 46.3560 -  8.1383   963   128 0.792  27.301  31.055   0.916    3756.712 |
|  2:  8.1383 -  6.4652   943   134 0.692  36.948  36.241   0.823    2476.272 |
|  3:  6.4652 -  5.6496   913   146 0.679  38.159  38.948   0.762    1684.290 |
|  4:  5.6496 -  5.1338   919   145 0.694  36.867  37.654   0.762    1366.539 |
|  5:  5.1338 -  4.7662   934   125 0.742  33.122  31.881   0.814    1227.436 |
|  6:  4.7662 -  4.4854   901   167 0.798  28.892  24.724   0.864    1142.863 |
|  7:  4.4854 -  4.2610   916   142 0.782  29.458  30.447   0.881    1017.887 |
|  8:  4.2610 -  4.0756   927   123 0.745  32.822  33.015   0.863     877.943 |
|  9:  4.0756 -  3.9188   901   136 0.734  33.229  38.007   0.841     733.544 |
| 10:  3.9188 -  3.7836   899   166 0.695  37.432  36.020   0.829     665.222 |
| 11:  3.7836 -  3.6654   908   154 0.666  39.621  38.709   0.803     603.507 |
| 12:  3.6654 -  3.5606   914   144 0.660  40.172  39.084   0.804     520.932 |
| 13:  3.5606 -  3.4669   882   151 0.670  39.417  37.867   0.808     412.628 |
| 14:  3.4669 -  3.3824   891   150 0.668  39.379  40.461   0.831     336.971 |
| 15:  3.3824 -  3.3055   889   155 0.664  40.137  38.000   0.831     300.270 |
| 16:  3.3055 -  3.2352   883   166 0.620  43.602  41.959   0.800     278.792 |
| 17:  3.2352 -  3.1705   891   125 0.562  47.957  47.792   0.752     256.187 |
| 18:  3.1705 -  3.1106   881   172 0.530  50.135  51.734   0.697     223.075 |
| 19:  3.1106 -  3.0551   891   110 0.536  49.875  50.944   0.699     194.918 |
| 20:  3.0551 -  3.0033   805   119 0.539  49.810  49.114   0.707     158.238 |
|alpha:            min =       0.6816 max =       0.9238 mean =       0.8056  |
|beta:             min =     154.7119 max =    3862.7367 mean =     927.9768  |
|figures of merit: min =       0.0010 max =       1.0000 mean =       0.6751  |
|phase err.(work): min =       0.0000 max =      89.9143 mean =      38.5564  |
|phase err.(test): min =       0.0000 max =      89.6476 mean =      38.5502  |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00097 | norm of gradient =     0.00041 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  31.880   96.840    63.420            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       31.880 -   38.376:      25      |
|     38.376 -   44.872:     203      |       38.376 -   44.872:     203      |
|     44.872 -   51.368:     499      |       44.872 -   51.368:     499      |
|     51.368 -   57.864:    1161      |       51.368 -   57.864:    1161      |
|     57.864 -   64.360:    1263      |       57.864 -   64.360:    1263      |
|     64.360 -   70.856:    1162      |       64.360 -   70.856:    1162      |
|     70.856 -   77.352:     963      |       70.856 -   77.352:     963      |
|     77.352 -   83.848:     395      |       77.352 -   83.848:     395      |
|     83.848 -   90.344:     110      |       83.848 -   90.344:     110      |
|     90.344 -   96.840:      43      |       90.344 -   96.840:      43      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 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 =            1.300787 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.017416 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.044 (deg)            |
| angle between Xray and ADP gradient vectors:        91.473 (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 =            1.363509 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.017416 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.098 (deg)            |
| angle between Xray and ADP gradient vectors:        91.473 (deg)            |
| Number of Xray gradient terms excluded =      48 from total =    5776       |
|-----------------------------------------------------------------------------|

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

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3097      final r-factor (work) = 0.2929          |
| start r-factor (free) = 0.3476      final r-factor (free) = 0.3458          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc  * Echem                                |
| 3.475413 = 0.681754 * 3.964614 + 1.0 * 0.772520                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc  * Echem                                |
| 2.885123 = 0.681754 * 3.914773 + 1.0 * 0.216208                             |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   30   |
|-----------------------------------------------------------------------------|

| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.008   0.123  0.000|    1615.113||            ||  mean   max    min  |
|angl|  1.115  69.148  0.000|    5905.392||            ||                     |
|chir|  0.067   1.504  0.000|     265.590||   18187.692||  0.198  2.772  0.007|
|plan|  0.004   0.074  0.000|     395.895||            ||                     |
|dihe| 15.333 159.067  0.009|    4881.200||            ||                     |
|repu|  4.235   5.476  1.326|    5124.502||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.109:  5883/ 5907|  0.00- 13.69:  7976/ 8015| 0.32- 0.81:     1/    0 |
|0.109-0.218:    19/    3| 13.69- 27.38:    41/   18| 0.81- 1.30:     3/    0 |
|0.218-0.327:     3/    0| 27.38- 41.07:     8/    0| 1.30- 1.79:    15/    1 |
|0.327-0.436:     1/    0| 41.07- 54.75:     1/    0| 1.79- 2.27:    50/    9 |
|0.436-0.545:     0/    0| 54.75- 68.44:     1/    0| 2.27- 2.76:  1660/ 1340 |
|0.545-0.654:     0/    0| 68.44- 82.13:     1/    1| 2.76- 3.25:  6487/ 6197 |
|0.654-0.763:     0/    0| 82.13- 95.82:     0/    0| 3.25- 3.74:  9153/ 8876 |
|0.763-0.872:     0/    0| 95.82-109.51:     1/    0| 3.74- 4.22: 12308/12026 |
|0.872-0.981:     2/    0|109.51-123.20:     3/    0| 4.22- 4.71: 16857/16770 |
|0.981-1.090:     2/    0|123.20-136.88:     2/    0| 4.71- 5.20: 20672/20058 |
|-----------------------------------------------------------------------------|

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


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


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00093 | norm of gradient =     0.00038 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  31.880   96.840    63.420            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       31.880 -   38.376:      25      |
|     38.376 -   44.872:     203      |       38.376 -   44.872:     203      |
|     44.872 -   51.368:     499      |       44.872 -   51.368:     499      |
|     51.368 -   57.864:    1161      |       51.368 -   57.864:    1161      |
|     57.864 -   64.360:    1263      |       57.864 -   64.360:    1263      |
|     64.360 -   70.856:    1162      |       64.360 -   70.856:    1162      |
|     70.856 -   77.352:     963      |       70.856 -   77.352:     963      |
|     77.352 -   83.848:     395      |       77.352 -   83.848:     395      |
|     83.848 -   90.344:     110      |       83.848 -   90.344:     110      |
|     90.344 -   96.840:      43      |       90.344 -   96.840:      43      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2929      final r-factor (work) = 0.2871          |
| start r-factor (free) = 0.3458      final r-factor (free) = 0.3455          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.069053 = 0.017416 * 3.911475 + 1.0 * 0.000929                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.068900 = 0.017416 * 3.897248 + 1.0 * 0.001024                             |
|-----------------------------------------------------------------------------|
| number of iterations =    3    |    number of function evaluations =    4   |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


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


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

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 63.2 %           grid_step                = 0.751 A | 
| number of grid points = (135, 135, 144)                                     |
|-----------------------------------------------------------------------------|

|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.105198 r_work= 0.2845     |
| B(11,22,33,12,13,23)=  20.0975  20.0975  -0.2019   0.0000  -0.0000   0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 13.331                                     |
| mean alpha:  0.1201  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.104401 r_work= 0.2850     |
| B(11,22,33,12,13,23)=  24.0929  24.0929   5.6769   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.954                                     |
| mean alpha:  0.1297  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.104401 r_work= 0.2850     |
| B(11,22,33,12,13,23)=  24.0929  24.0929   5.6769   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.954                                     |
| mean alpha:  0.1297  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.104376 r_work= 0.2848     |
| B(11,22,33,12,13,23)=  23.8394  23.8394   5.4459   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.708                                     |
| mean alpha:  0.1292  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.104376 r_work= 0.2848     |
| B(11,22,33,12,13,23)=  23.8378  23.8378   5.4445   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.707                                     |
| mean alpha:  0.1292  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            3.895005 r_work= 0.2848     |
| B(11,22,33,12,13,23)=  23.8378  23.8378   5.4445   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.707                                     |
| mean alpha:  0.8296  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|

         ----------after bulk solvent correction and scaling----------         

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.2848  scale (work) =  1.0000  ksol=  0.37  bsol=  80.00 |
| r-factor (free) = 0.3431  scale (free) =  0.9602                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=   23.838 B12=    0.000 B13=    0.000 |target name=                 ml |
|                B22=   23.838 B23=   -0.000 |target (work) =  3.894912E+00   |
|                              B33=    5.444 |target (free) =  3.966526E+00   |
| (B11+B22+B33)/3 =   17.707                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 46.3560 -  8.1383 0.99    963  128 0.2441 0.3283  4.9473E+00  4.9771E+00|
|  2:  8.1383 -  6.4652 1.00    943  134 0.2827 0.3061  4.5503E+00  4.6005E+00|
|  3:  6.4652 -  5.6496 1.00    913  146 0.2801 0.3521  4.3257E+00  4.3859E+00|
|  4:  5.6496 -  5.1338 1.00    919  145 0.2779 0.3676  4.2432E+00  4.3964E+00|
|  5:  5.1338 -  4.7662 1.00    934  125 0.2577 0.2907  4.2385E+00  4.3012E+00|
|  6:  4.7662 -  4.4854 1.00    901  167 0.2447 0.2886  4.2655E+00  4.4425E+00|
|  7:  4.4854 -  4.2610 1.00    916  142 0.2504 0.3353  4.1951E+00  4.3545E+00|
|  8:  4.2610 -  4.0756 1.00    927  123 0.2699 0.2709  4.1082E+00  4.1560E+00|
|  9:  4.0756 -  3.9188 1.00    901  136 0.2700 0.3463  4.0168E+00  4.0256E+00|
| 10:  3.9188 -  3.7836 1.00    899  166 0.2904 0.3433  3.8929E+00  3.9965E+00|
| 11:  3.7836 -  3.6654 1.00    908  154 0.3037 0.3596  3.8349E+00  4.0091E+00|
| 12:  3.6654 -  3.5606 1.00    914  144 0.3105 0.3577  3.7797E+00  3.7919E+00|
| 13:  3.5606 -  3.4669 0.99    882  151 0.3147 0.3528  3.6869E+00  3.7887E+00|
| 14:  3.4669 -  3.3824 0.99    891  150 0.3094 0.3583  3.5885E+00  3.6143E+00|
| 15:  3.3824 -  3.3055 0.99    889  155 0.3091 0.3527  3.5060E+00  3.6271E+00|
| 16:  3.3055 -  3.2352 0.99    883  166 0.3194 0.3962  3.4328E+00  3.5777E+00|
| 17:  3.2352 -  3.1705 0.98    891  125 0.3423 0.4362  3.3650E+00  3.4488E+00|
| 18:  3.1705 -  3.1106 0.98    881  172 0.3566 0.4264  3.3200E+00  3.3529E+00|
| 19:  3.1106 -  3.0551 0.97    891  110 0.3655 0.4453  3.2217E+00  3.3229E+00|
| 20:  3.0551 -  3.0033 0.91    805  119 0.3511 0.3944  3.1098E+00  3.1757E+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: 46.3560 -  8.1383   963   128 0.785  27.899  32.050   0.929    3904.673 |
|  2:  8.1383 -  6.4652   943   134 0.691  37.060  35.239   0.834    2426.124 |
|  3:  6.4652 -  5.6496   913   146 0.700  36.442  36.373   0.768    1557.243 |
|  4:  5.6496 -  5.1338   919   145 0.719  34.791  35.515   0.761    1258.479 |
|  5:  5.1338 -  4.7662   934   125 0.761  31.499  30.064   0.809    1147.258 |
|  6:  4.7662 -  4.4854   901   167 0.812  27.522  23.876   0.859    1084.098 |
|  7:  4.4854 -  4.2610   916   142 0.795  28.113  30.297   0.881     972.653 |
|  8:  4.2610 -  4.0756   927   123 0.755  31.968  31.659   0.868     845.012 |
|  9:  4.0756 -  3.9188   901   136 0.743  32.360  37.714   0.847     710.733 |
| 10:  3.9188 -  3.7836   899   166 0.706  36.474  34.833   0.839     630.074 |
| 11:  3.7836 -  3.6654   908   154 0.694  37.431  35.441   0.833     549.660 |
| 12:  3.6654 -  3.5606   914   144 0.693  37.275  36.656   0.845     464.215 |
| 13:  3.5606 -  3.4669   882   151 0.704  36.748  34.073   0.852     373.513 |
| 14:  3.4669 -  3.3824   891   150 0.695  36.961  38.669   0.872     314.450 |
| 15:  3.3824 -  3.3055   889   155 0.672  39.209  38.010   0.874     288.280 |
| 16:  3.3055 -  3.2352   883   166 0.626  42.958  42.073   0.843     271.118 |
| 17:  3.2352 -  3.1705   891   125 0.572  46.933  47.782   0.790     249.556 |
| 18:  3.1705 -  3.1106   881   172 0.547  48.706  50.292   0.741     215.479 |
| 19:  3.1106 -  3.0551   891   110 0.565  47.394  50.020   0.765     181.945 |
| 20:  3.0551 -  3.0033   805   119 0.612  44.007  42.904   0.815     134.448 |
|alpha:            min =       0.7287 max =       0.9366 mean =       0.8317  |
|beta:             min =     129.8656 max =    4027.6517 mean =     895.2345  |
|figures of merit: min =       0.0025 max =       1.0000 mean =       0.6937  |
|phase err.(work): min =       0.0000 max =      89.6365 mean =      36.9606  |
|phase err.(test): min =       0.0000 max =      89.7768 mean =      37.0629  |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 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 =            1.395967 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.019913 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.578 (deg)            |
| angle between Xray and ADP gradient vectors:       103.924 (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 =            1.476809 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.019913 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.855 (deg)            |
| angle between Xray and ADP gradient vectors:       103.924 (deg)            |
| Number of Xray gradient terms excluded =      53 from total =    5771       |
|-----------------------------------------------------------------------------|

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

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2848      final r-factor (work) = 0.2780          |
| start r-factor (free) = 0.3431      final r-factor (free) = 0.3461          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc  * Echem                                |
| 3.092744 = 0.738404 * 3.894911 + 1.0 * 0.216723                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc  * Echem                                |
| 3.048888 = 0.738404 * 3.874005 + 1.0 * 0.188305                             |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   39   |
|-----------------------------------------------------------------------------|

| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.007   0.091  0.000|    1188.048||            ||  mean   max    min  |
|angl|  1.048  56.633  0.000|    4838.536||            ||                     |
|chir|  0.065   0.895  0.000|     197.458||   15747.608||  0.300  3.066  0.008|
|plan|  0.004   0.064  0.000|     288.725||            ||                     |
|dihe| 15.439 159.435  0.001|    4774.690||            ||                     |
|repu|  4.243   5.424  1.644|    4460.151||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.109:  5883/ 5910|  0.00- 13.69:  7976/ 8026| 0.32- 0.81:     1/    0 |
|0.109-0.218:    19/    0| 13.69- 27.38:    41/    6| 0.81- 1.30:     3/    0 |
|0.218-0.327:     3/    0| 27.38- 41.07:     8/    1| 1.30- 1.79:    15/    1 |
|0.327-0.436:     1/    0| 41.07- 54.75:     1/    0| 1.79- 2.27:    50/    6 |
|0.436-0.545:     0/    0| 54.75- 68.44:     1/    1| 2.27- 2.76:  1660/ 1277 |
|0.545-0.654:     0/    0| 68.44- 82.13:     1/    0| 2.76- 3.25:  6487/ 6077 |
|0.654-0.763:     0/    0| 82.13- 95.82:     0/    0| 3.25- 3.74:  9153/ 8673 |
|0.763-0.872:     0/    0| 95.82-109.51:     1/    0| 3.74- 4.22: 12308/11968 |
|0.872-0.981:     2/    0|109.51-123.20:     3/    0| 4.22- 4.71: 16857/16736 |
|0.981-1.090:     2/    0|123.20-136.88:     2/    0| 4.71- 5.20: 20672/19964 |
|-----------------------------------------------------------------------------|

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


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


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2780      final r-factor (work) = 0.2780          |
| start r-factor (free) = 0.3461      final r-factor (free) = 0.3461          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.078189 = 0.019912 * 3.875495 + 1.0 * 0.001018                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.078189 = 0.019912 * 3.875495 + 1.0 * 0.001018                             |
|-----------------------------------------------------------------------------|
| number of iterations =    1    |    number of function evaluations =    1   |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


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


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

|-mask parameters-------------------------------------------------------------|
| solvent radius        = 1.00 A           shrink truncation radius = 1.00 A  |
| solvent content       = 62.9 %           grid_step                = 0.751 A | 
| number of grid points = (135, 135, 144)                                     |
|-----------------------------------------------------------------------------|

|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.099626 r_work= 0.2766     |
| B(11,22,33,12,13,23)=  23.8378  23.8378   5.4445   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 17.707                                     |
| mean alpha:  0.1288  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.099564 r_work= 0.2772     |
| B(11,22,33,12,13,23)=  24.9868  24.9868   7.0957   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 19.023                                     |
| mean alpha:  0.1317  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.099564 r_work= 0.2772     |
| B(11,22,33,12,13,23)=  24.9868  24.9868   7.0957   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 19.023                                     |
| mean alpha:  0.1317  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.099532 r_work= 0.2768     |
| B(11,22,33,12,13,23)=  24.5578  24.5578   6.7061   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 18.607                                     |
| mean alpha:  0.1307  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            0.099532 r_work= 0.2768     |
| B(11,22,33,12,13,23)=  24.5502  24.5502   6.6992   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 18.600                                     |
| mean alpha:  0.1307  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ml-----------------------------------|
| k_sol= 0.37 b_sol=  80.00 target_w =            3.873851 r_work= 0.2768     |
| B(11,22,33,12,13,23)=  24.5502  24.5502   6.6992   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 18.600                                     |
| mean alpha:  0.8335  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|

         ----------after bulk solvent correction and scaling----------         

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.2768  scale (work) =  1.0000  ksol=  0.37  bsol=  80.00 |
| r-factor (free) = 0.3447  scale (free) =  0.9595                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=   24.550 B12=    0.000 B13=    0.000 |target name=                 ml |
|                B22=   24.550 B23=   -0.000 |target (work) =  3.873819E+00   |
|                              B33=    6.699 |target (free) =  3.963167E+00   |
| (B11+B22+B33)/3 =   18.600                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 46.3560 -  8.1383 0.99    963  128 0.2430 0.3379  4.9501E+00  4.9956E+00|
|  2:  8.1383 -  6.4652 1.00    943  134 0.2802 0.3123  4.5411E+00  4.6085E+00|
|  3:  6.4652 -  5.6496 1.00    913  146 0.2742 0.3417  4.3076E+00  4.3749E+00|
|  4:  5.6496 -  5.1338 1.00    919  145 0.2660 0.3642  4.2205E+00  4.3953E+00|
|  5:  5.1338 -  4.7662 1.00    934  125 0.2465 0.2816  4.2092E+00  4.2819E+00|
|  6:  4.7662 -  4.4854 1.00    901  167 0.2324 0.2874  4.2370E+00  4.4239E+00|
|  7:  4.4854 -  4.2610 1.00    916  142 0.2362 0.3383  4.1642E+00  4.3627E+00|
|  8:  4.2610 -  4.0756 1.00    927  123 0.2572 0.2795  4.0843E+00  4.1527E+00|
|  9:  4.0756 -  3.9188 1.00    901  136 0.2635 0.3569  4.0009E+00  4.0415E+00|
| 10:  3.9188 -  3.7836 1.00    899  166 0.2832 0.3468  3.8764E+00  4.0027E+00|
| 11:  3.7836 -  3.6654 1.00    908  154 0.2932 0.3531  3.8133E+00  4.0035E+00|
| 12:  3.6654 -  3.5606 1.00    914  144 0.2964 0.3508  3.7548E+00  3.7741E+00|
| 13:  3.5606 -  3.4669 0.99    882  151 0.3007 0.3590  3.6585E+00  3.7842E+00|
| 14:  3.4669 -  3.3824 0.99    891  150 0.2930 0.3572  3.5544E+00  3.5940E+00|
| 15:  3.3824 -  3.3055 0.99    889  155 0.2978 0.3529  3.4846E+00  3.6149E+00|
| 16:  3.3055 -  3.2352 0.99    883  166 0.3139 0.3903  3.4140E+00  3.5716E+00|
| 17:  3.2352 -  3.1705 0.98    891  125 0.3326 0.4313  3.3524E+00  3.4453E+00|
| 18:  3.1705 -  3.1106 0.98    881  172 0.3426 0.4449  3.3036E+00  3.3611E+00|
| 19:  3.1106 -  3.0551 0.97    891  110 0.3527 0.4436  3.2058E+00  3.3125E+00|
| 20:  3.0551 -  3.0033 0.91    805  119 0.3131 0.4051  3.0710E+00  3.1800E+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: 46.3560 -  8.1383   963   128 0.779  28.471  32.514   0.932    4078.037 |
|  2:  8.1383 -  6.4652   943   134 0.691  37.159  34.799   0.836    2437.357 |
|  3:  6.4652 -  5.6496   913   146 0.708  35.773  35.467   0.769    1505.916 |
|  4:  5.6496 -  5.1338   919   145 0.729  33.922  34.410   0.761    1212.058 |
|  5:  5.1338 -  4.7662   934   125 0.771  30.666  28.731   0.809    1106.736 |
|  6:  4.7662 -  4.4854   901   167 0.817  26.956  23.947   0.855    1063.834 |
|  7:  4.4854 -  4.2610   916   142 0.792  28.331  30.707   0.875     978.778 |
|  8:  4.2610 -  4.0756   927   123 0.749  32.436  31.846   0.860     862.055 |
|  9:  4.0756 -  3.9188   901   136 0.735  32.938  38.676   0.844     728.154 |
| 10:  3.9188 -  3.7836   899   166 0.704  36.597  34.902   0.840     633.685 |
| 11:  3.7836 -  3.6654   908   154 0.696  37.270  35.200   0.845     544.933 |
| 12:  3.6654 -  3.5606   914   144 0.704  36.258  36.649   0.864     452.813 |
| 13:  3.5606 -  3.4669   882   151 0.712  35.967  33.732   0.868     361.801 |
| 14:  3.4669 -  3.3824   891   150 0.705  36.100  38.033   0.887     304.309 |
| 15:  3.3824 -  3.3055   889   155 0.677  38.760  37.675   0.889     281.275 |
| 16:  3.3055 -  3.2352   883   166 0.629  42.738  41.378   0.858     267.734 |
| 17:  3.2352 -  3.1705   891   125 0.570  47.051  48.603   0.796     248.771 |
| 18:  3.1705 -  3.1106   881   172 0.543  48.980  50.771   0.739     216.938 |
| 19:  3.1106 -  3.0551   891   110 0.555  48.141  50.404   0.762     184.572 |
| 20:  3.0551 -  3.0033   805   119 0.603  44.667  44.138   0.817     138.303 |
|alpha:            min =       0.7255 max =       0.9399 mean =       0.8356  |
|beta:             min =     133.8376 max =    4214.9230 mean =     896.9348  |
|figures of merit: min =       0.0015 max =       1.0000 mean =       0.6949  |
|phase err.(work): min =       0.0000 max =      89.8885 mean =      36.8294  |
|phase err.(test): min =       0.0000 max =      89.4195 mean =      36.9923  |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00102 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 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 =            1.186765 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.020314 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.835 (deg)            |
| angle between Xray and ADP gradient vectors:       102.650 (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 =            1.256647 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.020314 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   90.285 (deg)            |
| angle between Xray and ADP gradient vectors:       102.650 (deg)            |
| Number of Xray gradient terms excluded =      53 from total =    5771       |
|-----------------------------------------------------------------------------|

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

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2768      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3447      final r-factor (free) = 0.3460          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc  * Echem                                |
| 2.622768 = 0.628323 * 3.873819 + 1.0 * 0.188756                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc  * Echem                                |
| 2.589482 = 0.628323 * 3.868036 + 1.0 * 0.159104                             |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   31   |
|-----------------------------------------------------------------------------|

| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.006   0.077  0.000|     956.465||            ||  mean   max    min  |
|angl|  0.940  48.919  0.000|    3610.179||            ||                     |
|chir|  0.060   0.691  0.000|     160.881||   13226.349||  0.371  2.836  0.010|
|plan|  0.003   0.044  0.000|     194.145||            ||                     |
|dihe| 15.241 153.967  0.008|    4701.171||            ||                     |
|repu|  4.245   5.552  1.603|    3603.506||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.109:  5883/ 5910|  0.00- 13.69:  7976/ 8030| 0.32- 0.81:     1/    0 |
|0.109-0.218:    19/    0| 13.69- 27.38:    41/    3| 0.81- 1.30:     3/    0 |
|0.218-0.327:     3/    0| 27.38- 41.07:     8/    0| 1.30- 1.79:    15/    1 |
|0.327-0.436:     1/    0| 41.07- 54.75:     1/    1| 1.79- 2.27:    50/    4 |
|0.436-0.545:     0/    0| 54.75- 68.44:     1/    0| 2.27- 2.76:  1660/ 1205 |
|0.545-0.654:     0/    0| 68.44- 82.13:     1/    0| 2.76- 3.25:  6487/ 6038 |
|0.654-0.763:     0/    0| 82.13- 95.82:     0/    0| 3.25- 3.74:  9153/ 8534 |
|0.763-0.872:     0/    0| 95.82-109.51:     1/    0| 3.74- 4.22: 12308/11954 |
|0.872-0.981:     2/    0|109.51-123.20:     3/    0| 4.22- 4.71: 16857/16634 |
|0.981-1.090:     2/    0|123.20-136.88:     2/    0| 4.71- 5.20: 20672/20011 |
|-----------------------------------------------------------------------------|

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


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


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00101 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2776      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3460      final r-factor (free) = 0.3460          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.079577 = 0.020313 * 3.867498 + 1.0 * 0.001013                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.079577 = 0.020313 * 3.867497 + 1.0 * 0.001013                             |
|-----------------------------------------------------------------------------|
| number of iterations =    1    |    number of function evaluations =    1   |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00101 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  77.122 | target =      0.00101 | norm of gradient =     0.00043 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  31.880   96.840    63.420          |  29.669   98.617    62.742            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     31.880 -   38.376:      25      |       29.669 -   36.564:      30      |
|     38.376 -   44.872:     203      |       36.564 -   43.459:     163      |
|     44.872 -   51.368:     499      |       43.459 -   50.354:     572      |
|     51.368 -   57.864:    1161      |       50.354 -   57.248:    1155      |
|     57.864 -   64.360:    1263      |       57.248 -   64.143:    1309      |
|     64.360 -   70.856:    1162      |       64.143 -   71.038:    1180      |
|     70.856 -   77.352:     963      |       71.038 -   77.933:     933      |
|     77.352 -   83.848:     395      |       77.933 -   84.828:     347      |
|     83.848 -   90.344:     110      |       84.828 -   91.723:     103      |
|     90.344 -   96.840:      43      |       91.723 -   98.617:      32      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 5824 total               |
|-----------------------------------------------------------------------------|


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

************************************************************************
Refinement target            :  ml
Number of atoms              :    5824
Number of geometry restraints:   83130
Unit cell volume             :     1073494.450
Space group number           :   78
Number of symmetries         :    4
Wilson B-factor              :     77.122
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    :  0.4343 0.3850   4.034525e+00   4.010795e+00   1.118320e-01
   1_bss:  0.3097 0.3476   3.964615e+00   3.982157e+00   6.336642e-02
   1_xyz:  0.2929 0.3458   3.911475e+00   3.972771e+00   5.249212e-02
   1_adp:  0.2871 0.3455   3.896615e+00   3.970236e+00   5.117023e-02
   2_bss:  0.2848 0.3431   3.894912e+00   3.966526e+00   5.071103e-02
   2_xyz:  0.2780 0.3461   3.875495e+00   3.965156e+00   4.633766e-02
   2_adp:  0.2780 0.3461   3.875495e+00   3.965156e+00   4.633763e-02
   3_bss:  0.2768 0.3447   3.873819e+00   3.963167e+00   4.697053e-02
   3_xyz:  0.2776 0.3460   3.867498e+00   3.962358e+00   4.593232e-02
   3_adp:  0.2776 0.3460   3.867498e+00   3.962358e+00   4.593203e-02
------------------------------------------------------------------------
 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    :    4.0272e-01   9.6369e-03   0.500   1.000   90.001   91.238
   1_bss:    4.0272e-01   9.6369e-03   0.500   1.000   90.001   91.238
   1_xyz:    6.8175e-01   1.7416e-02   0.500   1.000   90.098   91.473
   1_adp:    6.8175e-01   1.7416e-02   0.500   1.000   90.098   91.473
   2_bss:    6.8175e-01   1.7416e-02   0.500   1.000   90.098   91.473
   2_xyz:    7.3840e-01   1.9913e-02   0.500   1.000   89.855  103.924
   2_adp:    7.3840e-01   1.9913e-02   0.500   1.000   89.855  103.924
   3_bss:    7.3840e-01   1.9913e-02   0.500   1.000   89.855  103.924
   3_xyz:    6.2832e-01   2.0314e-02   0.500   1.000   90.285  102.650
   3_adp:    6.2832e-01   2.0314e-02   0.500   1.000   90.285  102.650
------------------------------------------------------------------------
 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:  0.375  80.000  20.097  20.097  -0.202   0.000  -0.000   0.000
   1_xyz:  0.375  80.000  20.097  20.097  -0.202   0.000  -0.000   0.000
   1_adp:  0.375  80.000  20.097  20.097  -0.202   0.000  -0.000   0.000
   2_bss:  0.373  80.000  23.838  23.838   5.444   0.000   0.000  -0.000
   2_xyz:  0.373  80.000  23.838  23.838   5.444   0.000   0.000  -0.000
   2_adp:  0.373  80.000  23.838  23.838   5.444   0.000   0.000  -0.000
   3_bss:  0.369  80.000  24.550  24.550   6.699   0.000   0.000  -0.000
   3_xyz:  0.369  80.000  24.550  24.550   6.699   0.000   0.000  -0.000
   3_adp:  0.369  80.000  24.550  24.550   6.699   0.000   0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.034 0.6449  1.1362     1126.394
   1_bss:  38.556 0.6751  0.8056      927.977
   1_xyz:  37.614 0.6860  0.8024      920.827
   1_adp:  37.321 0.6895  0.8003      917.713
   2_bss:  36.975 0.6937  0.8317      895.235
   2_xyz:  37.094 0.6920  0.8243      919.549
   2_adp:  37.094 0.6920  0.8243      919.549
   3_bss:  36.852 0.6949  0.8356      896.935
   3_xyz:  36.699 0.6967  0.8371      901.555
   3_adp:  36.699 0.6967  0.8371      901.558
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target     wc
   0    :   1.439  0.009  0.082 14.092  0.005  4.214   6.5847e+04   1.00
   1_bss:   1.439  0.009  0.082 14.092  0.005  4.214   6.5847e+04   1.00
   1_xyz:   1.115  0.008  0.067 15.333  0.004  4.235   1.8188e+04   1.00
   1_adp:   1.115  0.008  0.067 15.333  0.004  4.235   1.8188e+04   1.00
   2_bss:   1.115  0.008  0.067 15.333  0.004  4.235   1.8188e+04   1.00
   2_xyz:   1.048  0.007  0.065 15.439  0.004  4.243   1.5748e+04   1.00
   2_adp:   1.048  0.007  0.065 15.439  0.004  4.243   1.5748e+04   1.00
   3_bss:   1.048  0.007  0.065 15.439  0.004  4.243   1.5748e+04   1.00
   3_xyz:   0.940  0.006  0.060 15.241  0.003  4.245   1.3226e+04   1.00
   3_adp:   0.940  0.006  0.060 15.241  0.003  4.245   1.3226e+04   1.00
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    : 136.884  1.090  0.614164.332  0.190  0.325   2.6467e-01
   1_bss: 136.884  1.090  0.614164.332  0.190  0.325   2.6467e-01
   1_xyz:  69.148  0.123  1.504159.067  0.074  1.326   6.7829e-02
   1_adp:  69.148  0.123  1.504159.067  0.074  1.326   6.7829e-02
   2_bss:  69.148  0.123  1.504159.067  0.074  1.326   6.7829e-02
   2_xyz:  56.633  0.091  0.895159.435  0.064  1.644   4.2173e-02
   2_adp:  56.633  0.091  0.895159.435  0.064  1.644   4.2173e-02
   3_bss:  56.633  0.091  0.895159.435  0.064  1.644   4.2173e-02
   3_xyz:  48.919  0.077  0.691153.967  0.044  1.603   4.0884e-02
   3_adp:  48.919  0.077  0.691153.967  0.044  1.603   4.0884e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  96.84  31.88  63.42  96.84  32.85  63.47  75.62  31.88  56.69
   1_bss:  96.84  31.88  63.42  96.84  32.85  63.47  75.62  31.88  56.69
   1_xyz:  96.84  31.88  63.42  96.84  32.85  63.47  75.62  31.88  56.69
   1_adp:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   2_bss:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   2_xyz:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   2_adp:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   3_bss:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   3_xyz:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
   3_adp:  98.62  29.67  62.74  98.62  29.67  62.80  75.03  30.81  55.50
------------------------------------------------------------------------
 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:    2.772    0.007    0.198
   1_adp:    2.772    0.007    0.198
   2_bss:    2.772    0.007    0.198
   2_xyz:    3.066    0.008    0.300
   2_adp:    3.066    0.008    0.300
   3_bss:    3.066    0.008    0.300
   3_xyz:    2.836    0.010    0.371
   3_adp:    2.836    0.010    0.371
------------------------------------------------------------------------
 stage         k1_w     k1_t     k3_w     k3_t scale_ml
   0    :    1.0000   1.2427   1.2291   1.3946   1.0000
   1_bss:    1.0000   0.9617   1.0651   1.0463   1.0000
   1_xyz:    1.0000   0.9578   1.0589   1.0416   1.0000
   1_adp:    1.0000   0.9575   1.0571   1.0410   1.0000
   2_bss:    1.0000   0.9602   1.0562   1.0433   1.0000
   2_xyz:    1.0000   0.9566   1.0538   1.0405   1.0000
   2_adp:    1.0000   0.9566   1.0538   1.0405   1.0000
   3_bss:    1.0000   0.9595   1.0535   1.0423   1.0000
   3_xyz:    1.0000   0.9617   1.0540   1.0445   1.0000
   3_adp:    1.0000   0.9617   1.0540   1.0445   1.0000
------------------------------------------------------------------------
 stage      adp_target      wu
   0    :   9.7139e-04   1.000
   1_bss:   9.7139e-04   1.000
   1_xyz:   9.2972e-04   1.000
   1_adp:   1.0247e-03   1.000
   2_bss:   1.0247e-03   1.000
   2_xyz:   1.0185e-03   1.000
   2_adp:   1.0185e-03   1.000
   3_bss:   1.0185e-03   1.000
   3_xyz:   1.0139e-03   1.000
   3_adp:   1.0139e-03   1.000
------------------------------------------------------------------------

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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq_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/bastard/1rfq_refine_001.mtz

Writing 2m*Fobs-D*Fmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq_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/bastard/1rfq_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Notes/Poster/poster_1/poster/tmp/bastard/1rfq_refine_002.def

# Date 2006-07-10 Time 23:14:43 PDT -0700
Final R-work = 0.2776, R-free = 0.3460
Time per interpreted Python bytecode instruction: 6.002 micro seconds
Total CPU time: 8.90 minutes