# Date 2006-07-27 Time 21:48:20 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: (76.855, 76.855, 76.855, 90, 90, 90)
  Space group: I 4 3 2 (No. 211)

/net/cci-filer1/vol1/home/phzwart/Banu/Betty/phaser/refine/Betty_a.1.pdb
  Monomer Library directory:
    "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/ext_ref_files/mon_lib"
  Total number of atoms: 123
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 123
      Number of chains: 1
        Number of residues, atoms: 6, 123
          Unexpected atoms: {'  T,C7': 1}
          Classifications: {'DNA': 6}
          Link IDs: {'p': 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
  Number of atoms with unknown nonbonded energy type symbols: 1
    " C7    T A   6 "
  Time building chain proxies: 0.23, per 1000 atoms: 1.87

F-obs:
  ../Betty_a.1.mtz:FP,SIGFP

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

Experimental phases:
  ../Betty_a.1.mtz:HLA,HLB,HLC,HLD

Writing MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/phaser/refine/Betty_a.1_refine_data.mtz

  Number of scatterers: 123
  At special positions: 0
  Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
  Space group: I 4 3 2 (No. 211)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number   Weight
     P       6     15.00
     O      36      8.00
     N      23      7.00
     C      58      6.00
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.06 seconds
  Histogram of bond lengths:
        1.21 -     1.29: 8
        1.29 -     1.37: 28
        1.37 -     1.45: 37
        1.45 -     1.53: 46
        1.53 -     1.61: 17
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " C5    G A   5 " - " C4    G A   5 " 1.377  1.473 -0.096 2.50e+03 2.28e+01
  " C5    G A   4 " - " C4    G A   4 " 1.377  1.472 -0.095 2.50e+03 2.25e+01
  " N9    G A   5 " - " C4    G A   5 " 1.377  1.288  0.089 2.50e+03 1.97e+01
  " N9    G A   4 " - " C4    G A   4 " 1.377  1.289  0.088 2.50e+03 1.93e+01
  " N1    T A   6 " - " C2    T A   6 " 1.379  1.333  0.046 2.50e+03 5.22e+00
  ... (remaining 131 not shown)
  Histogram of nonbonded interaction distances:
        0.17 -     1.18: 3
        1.18 -     2.18: 34
        2.18 -     3.19: 184
        3.19 -     4.19: 656
        4.19 -     5.20: 985
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " N6    A A   7 " - " N1    C A   9 "  0.172 3.100 z+1/2,-y-1/2,x-1/2
  " C6    A A   7 " - " C2    C A   9 "  0.471 3.400 z+1/2,-y-1/2,x-1/2
  " C5    A A   7 " - " C2    C A   9 "  1.035 3.400 z+1/2,-y-1/2,x-1/2
  " C5    A A   7 " - " N3    C A   9 "  1.182 3.250 z+1/2,-y-1/2,x-1/2
  " C6    A A   7 " - " O2    C A   9 "  1.195 3.220 z+1/2,-y-1/2,x-1/2
  ... (remaining 1857 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.43 -    11.60: 6
       11.60 -    22.76: 7
       22.76 -    33.93: 11
       33.93 -    45.09: 12
       45.09 -    56.26: 21
  Dihedral angle restraints sorted by residual:
  " C3*   C A   8 "
  " O3*   C A   8 "
  " P     C A   9 "
  " O5*   C A   9 "
      ideal   model   delta periodicty    weight residual
     260.00 -156.26   56.26     3       1.11e-03 3.52e+00
  " C3*   G A   4 "
  " O3*   G A   4 "
  " P     G A   5 "
  " O5*   G A   5 "
      ideal   model   delta periodicty    weight residual
     260.00 -156.25   56.25     3       1.11e-03 3.52e+00
  " C3*   A A   7 "
  " O3*   A A   7 "
  " P     C A   8 "
  " O5*   C A   8 "
      ideal   model   delta periodicty    weight residual
     260.00 -156.25   56.25     3       1.11e-03 3.52e+00
  ... (remaining 54 not shown)


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

Miller array info: ../Betty_a.1.mtz:FP,SIGFP
Observation type: xray.amplitude
Type of data: double, size=5100
Type of sigmas: double, size=5100
Number of Miller indices: 5100
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 4 3 2 (No. 211)
Systematic absences: 0
Centric reflections: 1015
Resolution range: 38.4275 1.61737
Completeness in resolution range: 0.97254
Completeness with d_max=infinity: 0.972355

Number of F-obs in resolution range:                   5100
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  38.4275
                             d_min =   1.6174


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

Miller array info: R-free-flags
Observation type: None
Type of data: bool, size=5100
Type of sigmas: None
Number of Miller indices: 5100
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 4 3 2 (No. 211)
Systematic absences: 0
Centric reflections: 1015
Resolution range: 38.4275 1.61737
Completeness in resolution range: 0.97254
Completeness with d_max=infinity: 0.972355

Test flag value: True

Number of work/free reflections by resolution:
                                      work free  %free
  bin  1: 38.4383 -  3.4837 [592/594]  533   59  10.0%
  bin  2:  3.4837 -  2.7654 [533/533]  479   54  10.1%
  bin  3:  2.7654 -  2.4159 [525/530]  473   52   9.9%
  bin  4:  2.4159 -  2.1950 [513/517]  462   51   9.9%
  bin  5:  2.1950 -  2.0377 [515/523]  463   52  10.1%
  bin  6:  2.0377 -  1.9176 [506/516]  455   51  10.1%
  bin  7:  1.9176 -  1.8215 [487/503]  439   48   9.9%
  bin  8:  1.8215 -  1.7423 [484/505]  436   48   9.9%
  bin  9:  1.7423 -  1.6752 [490/506]  440   50  10.2%
  bin 10:  1.6752 -  1.6174 [455/517]  410   45   9.9%
                              overall 4590  510  10.0%


============================= Experimental phases =============================

Miller array info: ../Betty_a.1.mtz:HLA,HLB,HLC,HLD
Observation type: None
Type of data: hendrickson_lattman, size=5100
Type of sigmas: None
Number of Miller indices: 5100
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 4 3 2 (No. 211)
Systematic absences: 0
Centric reflections: 1015
Resolution range: 38.4275 1.61737
Completeness in resolution range: 0.97254
Completeness with d_max=infinity: 0.972355

Average figures of merit by resolution:
  bin  1: 38.4383 -  3.4837 [592/594]  0.276
  bin  2:  3.4837 -  2.7654 [533/533]  0.244
  bin  3:  2.7654 -  2.4159 [525/530]  0.190
  bin  4:  2.4159 -  2.1950 [513/517]  0.171
  bin  5:  2.1950 -  2.0377 [515/523]  0.147
  bin  6:  2.0377 -  1.9176 [506/516]  0.130
  bin  7:  1.9176 -  1.8215 [487/503]  0.118
  bin  8:  1.8215 -  1.7423 [484/505]  0.097
  bin  9:  1.7423 -  1.6752 [490/506]  0.100
  bin 10:  1.6752 -  1.6174 [455/517]  0.072
                              overall  0.159
  Note: Figures of merit are determined by integration of
        Hendrickson-Lattman coefficients.

Number and fraction of available experimental phases by resolution:
  bin  1: 38.4383 -  3.4837 [592/594] 592 1.0000
  bin  2:  3.4837 -  2.7654 [533/533] 533 1.0000
  bin  3:  2.7654 -  2.4159 [525/530] 525 1.0000
  bin  4:  2.4159 -  2.1950 [513/517] 513 1.0000
  bin  5:  2.1950 -  2.0377 [515/523] 515 1.0000
  bin  6:  2.0377 -  1.9176 [506/516] 506 1.0000
  bin  7:  1.9176 -  1.8215 [487/503] 487 1.0000
  bin  8:  1.8215 -  1.7423 [484/505] 484 1.0000
  bin  9:  1.7423 -  1.6752 [490/506] 490 1.0000
  bin 10:  1.6752 -  1.6174 [455/517] 455 1.0000


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

Number of scattering types: 4
  Type Number   Weight   Gaussians
   P       6     14.95       2
   O      36      7.97       2
   N      23      6.97       2
   C      58      5.97       2

*******************************************************************************
Automatic adjustment:
  refinement.main.target=mlhl

  To disable this automatic adjustment define:
    refinement.main.use_experimental_phases=False
*******************************************************************************


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

No NCS restraint groups specified.

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/phaser/refine/Betty_a.1_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/phaser/refine/Betty_a.1_refine_001.geo

Complete set of effective parameters:
#phil __ON__
refinement.crystal_symmetry {
  unit_cell = 76.855 76.855 76.855 90 90 90
  space_group = "I 4 3 2"
}
refinement.input {
  pdb {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Banu/Betty/phaser/refine/Betty_a.1.pdb"
  }
  xray_data {
    file_name = "../Betty_a.1.mtz"
    labels = "FP,SIGFP"
  }
  r_free_flags {
    file_name = None
    label = "R-free-flags"
    test_flag_value = True
    disable_suitability_test = False
  }
  experimental_phases {
    file_name = "../Betty_a.1.mtz"
    labels = "HLA,HLB,HLC,HLD"
  }
  monomers {
    file_name = None
  }
}
refinement.output {
  prefix = "Betty_a.1_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 = True
  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 = True
  r_free_flags_fraction = 0.1
  r_free_flags_max_free = 2000
  remove_test_set_memory = None
  use_form_factor_weights = False
  refine_site = True
  number_of_macro_cycles_for_uiso_site_refinement = 1
  tan_u_iso = False
  sf_algorithm = *fft direct
  use_convergence_test = False
  target = ml *mlhl ls 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 = 120
  keep_test_ref_in_bin = True
  number_of_macromolecule_atoms_absent = 225
  n_atoms_included = 0
  bf_atoms_absent = 15
  final_error = 0
  absent_atom_type = "O"
  method = *est calc
  verbose = -1
  interpolation = True
  fix_scale_for_calc_option = None
  number_of_waters_absent = 613
}
refinement.mask {
  solvent_radius = 1
  shrink_truncation_radius = 1
  grid_step_factor = 4
  verbose = 1
}
refinement.cartesian_dynamics {
  temperature = 300
  number_of_steps = 200
  time_step = 0.0005
  n_print = 100
  verbose = -1
}
refinement.simulated_annealing {
  start_temperature = 5000
  final_temperature = 300
  cool_rate = 100
  number_of_steps = 25
  time_step = 0.0005
  n_print = 100
  update_grads_shift = 0.3
  refine_sites = True
  refine_adp = False
  max_number_of_iterations = 25
  mode = every_macro_cycle *second_and_before_last
  verbose = -1
}
refinement.target_weights {
  wxc_scale = 0.5
  wxu_scale = 1
  wc = 1
  wu = 1
  fix_wxc = None
  fix_wxu = None
  allow_automatic_adjustment = False
  delta_r_free_r_work = 6
  wxc_scale_drop = 3
  wxu_scale_drop = 3
  max_number_of_macro_cycles = 12
  optimize_wxc = False
  optimization_criterion = *r_free gradient_angle
  optimize_wxu = False
  shake_sites = True
  shake_adp = 10
  regularize_ncycles = 50
  gradient_filtering = True
  gradient_filtering_method = *cns new
  rmsd_cutoff_for_gradient_filtering = 3
  verbose = 1
}
refinement.dbe {
  b_iso_cutoff = 10
  occupancy_cutoff = 0.8
  resolution = 0.7
}
refinement.ls_target_names {
  target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \
                ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \
                ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \
                ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \
                lsm_k1ask3_fixed
}
#phil __OFF__


============================ mlhl refinement start ============================


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

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.6984  scale (work) =  1.0000  ksol=  0.00  bsol=   0.00 |
| r-factor (free) = 0.6048  scale (free) =  1.7719                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    0.000 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    0.000 B23=    0.000 |target (work) =  6.058560E-01   |
|                              B33=    0.000 |target (free) =  5.752140E-01   |
| (B11+B22+B33)/3 =    0.000                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 38.4383 -  2.5672 1.00   1250  139 0.7396 0.6142  8.5004E-01  6.7890E-01|
|  2:  2.5672 -  2.0377 0.99   1160  129 0.5652 0.5416  1.7976E-01  1.8088E-01|
|  3:  2.0377 -  1.7801 0.97   1114  124 0.5483 0.6079  5.4900E-01  5.6585E-01|
|  4:  1.7801 -  1.6174 0.93   1066  118 0.5643 0.6307  8.4261E-01  8.9401E-01|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 38.4383 -  2.5672  1250   139 0.326  64.495  61.892   1.281    5031.501 |
|  2:  2.5672 -  2.0377  1160   129 0.072  84.644  83.630   0.828    1892.160 |
|  3:  2.0377 -  1.7801  1114   124 0.138  79.509  80.182   0.550     240.395 |
|  4:  1.7801 -  1.6174  1066   118 0.148  78.808  78.837   0.446      76.205 |
|alpha:            min =       0.4463 max =       1.2814 mean =       0.7953  |
|beta:             min =      76.2052 max =    5031.5014 mean =    1924.6246  |
|figures of merit: min =       0.0000 max =       1.0000 mean =       0.1750  |
|phase err.(work): min =       0.0000 max =      89.9993 mean =      76.5552  |
|phase err.(test): min =       0.0007 max =      89.8755 mean =      75.7580  |
|-----------------------------------------------------------------------------|

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

Wilson B =     25.497

             ----------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 =            0.895976 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.056037 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   94.086 (deg)            |
| angle between Xray and ADP gradient vectors:        92.084 (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 =            1.033465 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.056037 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   94.182 (deg)            |
| angle between Xray and ADP gradient vectors:        92.084 (deg)            |
| Number of Xray gradient terms excluded =       3 from total =     120       |
|-----------------------------------------------------------------------------|

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


| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.015   0.096  0.000|     161.093||            ||  mean   max    min  |
|angl|  2.253  10.595  0.000|     235.383||            ||                     |
|chir|  0.161   0.259  0.073|      18.784||    7330.176||  0.000  0.000  0.000|
|plan|  0.035   0.037  0.033|     185.735||            ||                     |
|dihe| 34.748  56.256  0.433|      91.174||            ||                     |
|repu|  4.116   5.199  0.172|    6638.008||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   58|  0.00-  1.06:    72/   72| 0.17- 0.67:     2/    2 |
|0.010-0.019:    46/   46|  1.06-  2.12:    54/   54| 0.67- 1.18:     1/    1 |
|0.019-0.029:    21/   21|  2.12-  3.18:    43/   43| 1.18- 1.68:    15/   15 |
|0.029-0.038:     6/    6|  3.18-  4.24:     2/    2| 1.68- 2.18:    19/   19 |
|0.038-0.048:     1/    1|  4.24-  5.30:    13/   13| 2.18- 2.69:    59/   59 |
|0.048-0.057:     0/    0|  5.30-  6.36:    11/   11| 2.69- 3.19:   125/  125 |
|0.057-0.067:     0/    0|  6.36-  7.42:     2/    2| 3.19- 3.69:   293/  293 |
|0.067-0.076:     0/    0|  7.42-  8.48:     4/    4| 3.69- 4.19:   363/  363 |
|0.076-0.086:     0/    0|  8.48-  9.54:     0/    0| 4.19- 4.70:   497/  497 |
|0.086-0.096:     4/    4|  9.54- 10.59:     6/    6| 4.70- 5.20:   488/  488 |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00000 | norm of gradient =     0.00000 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  20.000   20.000    20.000            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       20.000 -   20.000:     123      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 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       = 84.2 %           grid_step                = 0.404 A | 
| number of grid points = (192, 192, 192)                                     |
|-----------------------------------------------------------------------------|

|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.00 b_sol=   0.00 target_w =            0.689946 r_work= 0.6984     |
| 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:  0.0463  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.55 b_sol=  65.00 target_w =            0.411963 r_work= 0.5759     |
| B(11,22,33,12,13,23)=   7.5319   7.5319   7.5319   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.532                                      |
| mean alpha:  0.0796  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.55 b_sol=  65.00 target_w =            0.411828 r_work= 0.5746     |
| B(11,22,33,12,13,23)=   8.5379   8.5379   8.5379   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.538                                      |
| mean alpha:  0.0837  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.54 b_sol=  65.00 target_w =            0.411597 r_work= 0.5745     |
| B(11,22,33,12,13,23)=   8.2735   8.2735   8.2735   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.274                                      |
| mean alpha:  0.0825  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.54 b_sol=  65.00 target_w =            0.411597 r_work= 0.5745     |
| B(11,22,33,12,13,23)=   8.2735   8.2735   8.2735   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.274                                      |
| mean alpha:  0.0825  number of alpha <= 0.0:      0                         |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.5745  scale (work) =  1.0000  ksol=  0.54  bsol=  65.00 |
| r-factor (free) = 0.5797  scale (free) =  0.9773                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    8.274 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    8.274 B23=   -0.000 |target (work) =  8.392189E-01   |
|                              B33=    8.274 |target (free) =  8.289501E-01   |
| (B11+B22+B33)/3 =    8.274                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 38.4383 -  2.5672 1.00   1250  139 0.5783 0.5748  8.3666E-01  7.0614E-01|
|  2:  2.5672 -  2.0377 0.99   1160  129 0.5635 0.5392  7.9673E-01  8.2062E-01|
|  3:  2.0377 -  1.7801 0.97   1114  124 0.5483 0.6067  8.8045E-01  9.1046E-01|
|  4:  1.7801 -  1.6174 0.93   1066  118 0.5662 0.6343  8.4538E-01  8.9707E-01|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 38.4383 -  2.5672  1250   139 0.378  60.487  57.604   0.696    4644.041 |
|  2:  2.5672 -  2.0377  1160   129 0.250  71.245  68.463   0.404     473.298 |
|  3:  2.0377 -  1.7801  1114   124 0.217  73.521  74.392   0.332     147.955 |
|  4:  1.7801 -  1.6174  1066   118 0.159  77.966  78.021   0.327      75.704 |
|alpha:            min =       0.3271 max =       0.6960 mean =       0.4481  |
|beta:             min =      75.7038 max =    4644.0410 mean =    1437.9324  |
|figures of merit: min =       0.0001 max =       1.0000 mean =       0.2558  |
|phase err.(work): min =       0.0000 max =      89.9895 mean =      70.4284  |
|phase err.(test): min =       0.0000 max =      89.7856 mean =      69.1563  |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00000 | norm of gradient =     0.00000 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  20.000   20.000    20.000            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       20.000 -   20.000:     123      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 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 =            1.535249 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.052590 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   93.535 (deg)            |
| angle between Xray and ADP gradient vectors:        96.210 (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 =            1.733920 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.052590 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   93.667 (deg)            |
| angle between Xray and ADP gradient vectors:        96.210 (deg)            |
| Number of Xray gradient terms excluded =       3 from total =     120       |
|-----------------------------------------------------------------------------|

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

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5745      final r-factor (work) = 0.5836          |
| start r-factor (free) = 0.5797      final r-factor (free) = 0.5658          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc  * Echem                                |
| 3.925726 = 0.866960 * 0.839218 + 1.0 * 3.198156                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc  * Echem                                |
| 0.911884 = 0.866960 * 0.863110 + 1.0 * 0.163602                             |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   27   |
|-----------------------------------------------------------------------------|

| ----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.005   0.028  0.000|      16.410||            ||  mean   max    min  |
|angl|  1.201  10.129  0.000|      76.439||            ||                     |
|chir|  0.061   0.208  0.003|       3.898||     362.052||  0.380  2.089  0.006|
|plan|  0.005   0.009  0.003|       4.788||            ||                     |
|dihe| 33.447  59.752  0.674|      88.097||            ||                     |
|repu|  4.212   5.693  1.623|     172.421||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/  108|  0.00-  1.06:    72/  125| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   21|  1.06-  2.12:    54/   46| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/    5|  2.12-  3.18:    43/   19| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/    0|  3.18-  4.24:     2/   10| 1.68- 2.18:    19/    2 |
|0.038-0.048:     1/    0|  4.24-  5.30:    13/    4| 2.18- 2.69:    59/   39 |
|0.048-0.057:     0/    0|  5.30-  6.36:    11/    1| 2.69- 3.19:   125/  157 |
|0.057-0.067:     0/    0|  6.36-  7.42:     2/    0| 3.19- 3.69:   293/  272 |
|0.067-0.076:     0/    0|  7.42-  8.48:     4/    1| 3.69- 4.19:   363/  314 |
|0.076-0.086:     0/    0|  8.48-  9.54:     0/    0| 4.19- 4.70:   497/  438 |
|0.086-0.096:     4/    0|  9.54- 10.59:     6/    1| 4.70- 5.20:   488/  474 |
|-----------------------------------------------------------------------------|

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


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


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00000 | norm of gradient =     0.00000 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  20.000   20.000    20.000            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       20.000 -   20.000:     123      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
|     20.000 -   20.000:       0      |       20.000 -   20.000:       0      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 total                |
|-----------------------------------------------------------------------------|

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5836      final r-factor (work) = 0.5826          |
| start r-factor (free) = 0.5658      final r-factor (free) = 0.5656          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wu  * Eadp                                 |
| 0.034855 = 0.052590 * 0.662775 + 1.0 * 0.0                                  |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wu  * Eadp                                 |
| 0.034831 = 0.052590 * 0.661971 + 1.0 * 1.773307                             |
|-----------------------------------------------------------------------------|
| number of iterations =    2    |    number of function evaluations =    4   |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00002 | norm of gradient =     0.00088 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  18.520   21.273    19.869            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       18.520 -   18.795:       2      |
|     20.000 -   20.000:       0      |       18.795 -   19.070:       0      |
|     20.000 -   20.000:       0      |       19.070 -   19.346:       5      |
|     20.000 -   20.000:       0      |       19.346 -   19.621:      10      |
|     20.000 -   20.000:       0      |       19.621 -   19.896:      53      |
|     20.000 -   20.000:       0      |       19.896 -   20.172:      38      |
|     20.000 -   20.000:       0      |       20.172 -   20.447:      12      |
|     20.000 -   20.000:       0      |       20.447 -   20.722:       2      |
|     20.000 -   20.000:       0      |       20.722 -   20.998:       0      |
|     20.000 -   20.000:       0      |       20.998 -   21.273:       1      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 total                |
|-----------------------------------------------------------------------------|


|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00002 | norm of gradient =     0.00088 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  18.520   21.273    19.869            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       18.520 -   18.795:       2      |
|     20.000 -   20.000:       0      |       18.795 -   19.070:       0      |
|     20.000 -   20.000:       0      |       19.070 -   19.346:       5      |
|     20.000 -   20.000:       0      |       19.346 -   19.621:      10      |
|     20.000 -   20.000:       0      |       19.621 -   19.896:      53      |
|     20.000 -   20.000:       0      |       19.896 -   20.172:      38      |
|     20.000 -   20.000:       0      |       20.172 -   20.447:      12      |
|     20.000 -   20.000:       0      |       20.447 -   20.722:       2      |
|     20.000 -   20.000:       0      |       20.722 -   20.998:       0      |
|     20.000 -   20.000:       0      |       20.998 -   21.273:       1      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 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       = 84.6 %           grid_step                = 0.404 A | 
| number of grid points = (192, 192, 192)                                     |
|-----------------------------------------------------------------------------|

|-macro_cycle= 0 (start) target= ls_wunit_k1----------------------------------|
| k_sol= 0.54 b_sol=  65.00 target_w =            0.432535 r_work= 0.5867     |
| B(11,22,33,12,13,23)=   8.2735   8.2735   8.2735   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 8.274                                      |
| mean alpha:  0.0655  number of alpha <= 0.0:   1066                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: k & b: grid search; T= ls_wunit_k1--------------------------|
| k_sol= 0.55 b_sol=  80.00 target_w =            0.431550 r_work= 0.5871     |
| B(11,22,33,12,13,23)=   7.4821   7.4821   7.4821   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.482                                      |
| mean alpha:  0.0629  number of alpha <= 0.0:   1066                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 2: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.55 b_sol=  80.00 target_w =            0.431550 r_work= 0.5871     |
| B(11,22,33,12,13,23)=   7.4821   7.4821   7.4821   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.482                                      |
| mean alpha:  0.0629  number of alpha <= 0.0:   1066                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: k_sol & b_sol min.; T= ls_wunit_k1--------------------------|
| k_sol= 0.56 b_sol=  80.00 target_w =            0.431313 r_work= 0.5865     |
| B(11,22,33,12,13,23)=   7.9146   7.9146   7.9146   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.915                                      |
| mean alpha:  0.0640  number of alpha <= 0.0:   1066                         |
|-----------------------------------------------------------------------------|
|-macro_cycle= 3: anisotropic scale; T= ls_wunit_k1---------------------------|
| k_sol= 0.56 b_sol=  80.00 target_w =            0.431313 r_work= 0.5864     |
| B(11,22,33,12,13,23)=   7.9275   7.9275   7.9275   0.0000   0.0000  -0.0000 |
| trace(B) = (B11 + B22 + B33)/3 = 7.928                                      |
| mean alpha:  0.0640  number of alpha <= 0.0:   1066                         |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| r-factor (work) = 0.5864  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5547  scale (free) =  0.9998                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.647372E-01   |
|                              B33=    7.928 |target (free) =  6.314542E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 38.4383 -  2.5672 1.00   1250  139 0.5901 0.5497  8.7636E-01  7.2327E-01|
|  2:  2.5672 -  2.0377 0.99   1160  129 0.5634 0.4984  8.5626E-01  8.6956E-01|
|  3:  2.0377 -  1.7801 0.97   1114  124 0.5566 0.6056  8.6394E-01  8.8172E-01|
|  4:  1.7801 -  1.6174 0.93   1066  118 0.5653 0.6448  0.0000E+00  0.0000E+00|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error     Alpha        Beta |
|  #        range        work  test        work      test                     |
|  1: 38.4383 -  2.5672  1250   139 0.386  59.829  58.023   0.738    4574.070 |
|  2:  2.5672 -  2.0377  1160   129 0.317  65.966  64.318   0.474     446.369 |
|  3:  2.0377 -  1.7801  1114   124 0.105  82.037  82.810   0.160     158.874 |
|  4:  1.7801 -  1.6174  1066   118 0.000  90.000  90.000   0.000      79.292 |
|alpha:            min =       0.0000 max =       0.7385 mean =       0.3600  |
|beta:             min =      79.2916 max =    4574.0705 mean =    1415.5533  |
|figures of merit: min =       0.0000 max =       1.0000 mean =       0.2105  |
|phase err.(work): min =       0.0002 max =      90.0000 mean =      73.7770  |
|phase err.(test): min =       0.0000 max =      90.0000 mean =      73.0405  |
| *** f_model warning: there are some alpha <= 0.0 ***                        |
|                      number of alpha <= 0.0:   1184                         |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
| Wilson B =  25.497 | target =      0.00002 | norm of gradient =     0.00088 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  20.000   20.000    20.000          |  18.520   21.273    19.869            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     20.000 -   20.000:     123      |       18.520 -   18.795:       2      |
|     20.000 -   20.000:       0      |       18.795 -   19.070:       0      |
|     20.000 -   20.000:       0      |       19.070 -   19.346:       5      |
|     20.000 -   20.000:       0      |       19.346 -   19.621:      10      |
|     20.000 -   20.000:       0      |       19.621 -   19.896:      53      |
|     20.000 -   20.000:       0      |       19.896 -   20.172:      38      |
|     20.000 -   20.000:       0      |       20.172 -   20.447:      12      |
|     20.000 -   20.000:       0      |       20.447 -   20.722:       2      |
|     20.000 -   20.000:       0      |       20.722 -   20.998:       0      |
|     20.000 -   20.000:       0      |       20.998 -   21.273:       1      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 123 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 =            1.279474 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.060747 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   88.386 (deg)            |
| angle between Xray and ADP gradient vectors:        94.996 (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 =            1.487950 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.060747 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   87.643 (deg)            |
| angle between Xray and ADP gradient vectors:        94.996 (deg)            |
| Number of Xray gradient terms excluded =       3 from total =     120       |
|-----------------------------------------------------------------------------|

======================== simulated annealing refinement =======================


       ----------lbfgs minimization: before simulated annealing----------      

| lbfgs minimization----------------------------------------------------------|
| start r-factor (work) = 0.5864      final r-factor (work) = 0.5850          |
| start r-factor (free) = 0.5547      final r-factor (free) = 0.5430          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc  * Echem                                |
| 0.668862 = 0.743974 * 0.664737 + 1.0 * 0.174315                             |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc  * Echem                                |
| 0.614635 = 0.743974 * 0.667570 + 1.0 * 0.117979                             |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   28   |
|-----------------------------------------------------------------------------|

============================= simulated annealing =============================


|-2:SA temperatrure = 5000.0--------------------------------------------------|
| r-factor (work) = 0.5843  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5443  scale (free) =  0.9810                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.780827E-01   |
|                              B33=    7.928 |target (free) =  8.565733E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 5000.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.031   0.148  0.000|     443.798||            ||  mean   max    min  |
|angl|  3.772  15.228  0.057|     516.879||            ||                     |
|chir|  0.174   0.498  0.017|      26.944||    1457.391||  0.526  1.999  0.107|
|plan|  0.040   0.056  0.028|     262.585||            ||                     |
|dihe| 31.570  56.847  0.170|      76.575||            ||                     |
|repu|  4.169   5.750  1.400|     130.610||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   29|  0.00-  1.06:    72/   36| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   24|  1.06-  2.12:    54/   34| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   21|  2.12-  3.18:    43/   36| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   17|  3.18-  4.24:     2/   28| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   14|  4.24-  5.30:    13/   20| 2.18- 2.69:    59/   39 |
|0.048-0.057:     0/   11|  5.30-  6.36:    11/   16| 2.69- 3.19:   125/  144 |
|0.057-0.067:     0/    8|  6.36-  7.42:     2/   12| 3.19- 3.69:   293/  257 |
|0.067-0.076:     0/    4|  7.42-  8.48:     4/   10| 3.69- 4.19:   363/  326 |
|0.076-0.086:     0/    3|  8.48-  9.54:     0/    4| 4.19- 4.70:   497/  412 |
|0.086-0.096:     4/    0|  9.54- 10.59:     6/    5| 4.70- 5.20:   488/  398 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4900.0--------------------------------------------------|
| r-factor (work) = 0.5833  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5503  scale (free) =  0.9933                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.770249E-01   |
|                              B33=    7.928 |target (free) =  8.585484E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4900.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.031   0.146  0.000|     497.218||            ||  mean   max    min  |
|angl|  3.300  11.797  0.094|     397.773||            ||                     |
|chir|  0.142   0.350  0.000|      18.673||    1305.652||  0.511  2.003  0.062|
|plan|  0.034   0.045  0.024|     188.175||            ||                     |
|dihe| 32.721  59.765  1.115|      81.262||            ||                     |
|repu|  4.172   5.710  1.419|     122.551||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   27|  0.00-  1.06:    72/   42| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   28|  1.06-  2.12:    54/   43| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   21|  2.12-  3.18:    43/   27| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   19|  3.18-  4.24:     2/   36| 1.68- 2.18:    19/    0 |
|0.038-0.048:     1/   10|  4.24-  5.30:    13/   16| 2.18- 2.69:    59/   43 |
|0.048-0.057:     0/   13|  5.30-  6.36:    11/   16| 2.69- 3.19:   125/  139 |
|0.057-0.067:     0/    2|  6.36-  7.42:     2/   11| 3.19- 3.69:   293/  259 |
|0.067-0.076:     0/    8|  7.42-  8.48:     4/    8| 3.69- 4.19:   363/  314 |
|0.076-0.086:     0/    3|  8.48-  9.54:     0/    2| 4.19- 4.70:   497/  421 |
|0.086-0.096:     4/    0|  9.54- 10.59:     6/    3| 4.70- 5.20:   488/  408 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4800.0--------------------------------------------------|
| r-factor (work) = 0.5841  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5392  scale (free) =  0.9873                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.827369E-01   |
|                              B33=    7.928 |target (free) =  6.477109E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4800.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.036   0.167  0.000|     710.992||            ||  mean   max    min  |
|angl|  3.304  13.364  0.013|     423.665||            ||                     |
|chir|  0.203   0.581  0.007|      39.698||    1585.883||  0.514  1.971  0.057|
|plan|  0.037   0.056  0.024|     231.613||            ||                     |
|dihe| 31.033  58.544  0.463|      75.158||            ||                     |
|repu|  4.171   5.700  1.410|     104.758||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   33|  0.00-  1.06:    72/   47| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   26|  1.06-  2.12:    54/   44| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   13|  2.12-  3.18:    43/   23| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   15|  3.18-  4.24:     2/   29| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/    6|  4.24-  5.30:    13/   20| 2.18- 2.69:    59/   38 |
|0.048-0.057:     0/   13|  5.30-  6.36:    11/   16| 2.69- 3.19:   125/  144 |
|0.057-0.067:     0/    8|  6.36-  7.42:     2/   10| 3.19- 3.69:   293/  259 |
|0.067-0.076:     0/    7|  7.42-  8.48:     4/    7| 3.69- 4.19:   363/  317 |
|0.076-0.086:     0/    3|  8.48-  9.54:     0/    3| 4.19- 4.70:   497/  425 |
|0.086-0.096:     4/    5|  9.54- 10.59:     6/    3| 4.70- 5.20:   488/  399 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4700.0--------------------------------------------------|
| r-factor (work) = 0.5838  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5479  scale (free) =  0.9912                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.737365E-01   |
|                              B33=    7.928 |target (free) =  8.551952E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4700.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.035   0.194  0.000|     649.946||            ||  mean   max    min  |
|angl|  3.422  15.321  0.023|     451.970||            ||                     |
|chir|  0.184   0.506  0.012|      33.430||    1514.591||  0.508  1.981  0.017|
|plan|  0.033   0.053  0.020|     188.630||            ||                     |
|dihe| 32.492  59.341  0.552|      80.931||            ||                     |
|repu|  4.171   5.671  1.403|     109.684||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   26|  0.00-  1.06:    72/   42| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   23|  1.06-  2.12:    54/   44| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   20|  2.12-  3.18:    43/   32| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   17|  3.18-  4.24:     2/   23| 1.68- 2.18:    19/    0 |
|0.038-0.048:     1/   13|  4.24-  5.30:    13/   21| 2.18- 2.69:    59/   37 |
|0.048-0.057:     0/   14|  5.30-  6.36:    11/   20| 2.69- 3.19:   125/  142 |
|0.057-0.067:     0/    3|  6.36-  7.42:     2/    7| 3.19- 3.69:   293/  265 |
|0.067-0.076:     0/    6|  7.42-  8.48:     4/    5| 3.69- 4.19:   363/  316 |
|0.076-0.086:     0/    2|  8.48-  9.54:     0/    4| 4.19- 4.70:   497/  423 |
|0.086-0.096:     4/    5|  9.54- 10.59:     6/    2| 4.70- 5.20:   488/  399 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4600.0--------------------------------------------------|
| r-factor (work) = 0.5840  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5374  scale (free) =  0.9893                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.859459E-01   |
|                              B33=    7.928 |target (free) =  6.505362E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4600.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.037   0.206  0.000|     862.068||            ||  mean   max    min  |
|angl|  3.480  14.753  0.005|     484.418||            ||                     |
|chir|  0.237   0.686  0.021|      55.210||    1756.031||  0.513  1.938  0.054|
|plan|  0.031   0.057  0.018|     178.753||            ||                     |
|dihe| 31.263  59.478  0.281|      76.500||            ||                     |
|repu|  4.173   5.756  1.398|      99.082||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   38|  0.00-  1.06:    72/   47| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   19|  1.06-  2.12:    54/   40| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   19|  2.12-  3.18:    43/   29| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/    9|  3.18-  4.24:     2/   29| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   16|  4.24-  5.30:    13/   19| 2.18- 2.69:    59/   39 |
|0.048-0.057:     0/    8|  5.30-  6.36:    11/   12| 2.69- 3.19:   125/  139 |
|0.057-0.067:     0/    7|  6.36-  7.42:     2/    8| 3.19- 3.69:   293/  266 |
|0.067-0.076:     0/    4|  7.42-  8.48:     4/   10| 3.69- 4.19:   363/  303 |
|0.076-0.086:     0/    2|  8.48-  9.54:     0/    5| 4.19- 4.70:   497/  433 |
|0.086-0.096:     4/    1|  9.54- 10.59:     6/    1| 4.70- 5.20:   488/  406 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4500.0--------------------------------------------------|
| r-factor (work) = 0.5838  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5470  scale (free) =  0.9898                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.736323E-01   |
|                              B33=    7.928 |target (free) =  8.554541E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4500.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.037   0.218  0.000|     741.808||            ||  mean   max    min  |
|angl|  3.567  18.328  0.001|     530.763||            ||                     |
|chir|  0.211   0.654  0.030|      42.636||    1640.117||  0.508  1.939  0.017|
|plan|  0.027   0.051  0.014|     138.895||            ||                     |
|dihe| 32.435  59.607  0.326|      81.193||            ||                     |
|repu|  4.172   5.630  1.400|     104.823||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   24|  0.00-  1.06:    72/   48| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   22|  1.06-  2.12:    54/   44| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   19|  2.12-  3.18:    43/   26| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   25|  3.18-  4.24:     2/   21| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   10|  4.24-  5.30:    13/   17| 2.18- 2.69:    59/   34 |
|0.048-0.057:     0/   10|  5.30-  6.36:    11/   14| 2.69- 3.19:   125/  138 |
|0.057-0.067:     0/    5|  6.36-  7.42:     2/   12| 3.19- 3.69:   293/  268 |
|0.067-0.076:     0/    8|  7.42-  8.48:     4/   12| 3.69- 4.19:   363/  316 |
|0.076-0.086:     0/    1|  8.48-  9.54:     0/    3| 4.19- 4.70:   497/  419 |
|0.086-0.096:     4/    2|  9.54- 10.59:     6/    2| 4.70- 5.20:   488/  409 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4400.0--------------------------------------------------|
| r-factor (work) = 0.5838  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5359  scale (free) =  0.9919                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.868931E-01   |
|                              B33=    7.928 |target (free) =  6.516373E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4400.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.037   0.230  0.000|     936.526||            ||  mean   max    min  |
|angl|  3.632  15.826  0.043|     533.973||            ||                     |
|chir|  0.259   0.788  0.001|      71.073||    1836.342||  0.512  1.916  0.064|
|plan|  0.024   0.051  0.012|     121.314||            ||                     |
|dihe| 31.555  59.465  0.363|      77.757||            ||                     |
|repu|  4.175   5.802  1.390|      95.699||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   37|  0.00-  1.06:    72/   42| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   21|  1.06-  2.12:    54/   37| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   19|  2.12-  3.18:    43/   41| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   13|  3.18-  4.24:     2/   18| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   13|  4.24-  5.30:    13/   25| 2.18- 2.69:    59/   39 |
|0.048-0.057:     0/    7|  5.30-  6.36:    11/    8| 2.69- 3.19:   125/  134 |
|0.057-0.067:     0/    7|  6.36-  7.42:     2/   12| 3.19- 3.69:   293/  270 |
|0.067-0.076:     0/    3|  7.42-  8.48:     4/    6| 3.69- 4.19:   363/  292 |
|0.076-0.086:     0/    1|  8.48-  9.54:     0/    8| 4.19- 4.70:   497/  443 |
|0.086-0.096:     4/    1|  9.54- 10.59:     6/    2| 4.70- 5.20:   488/  408 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4300.0--------------------------------------------------|
| r-factor (work) = 0.5834  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5463  scale (free) =  0.9872                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.733334E-01   |
|                              B33=    7.928 |target (free) =  8.559772E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4300.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.038   0.227  0.000|     791.236||            ||  mean   max    min  |
|angl|  3.698  19.905  0.024|     583.553||            ||                     |
|chir|  0.224   0.738  0.032|      47.500||    1694.298||  0.507  1.965  0.037|
|plan|  0.021   0.043  0.010|      89.229||            ||                     |
|dihe| 32.271  59.467  0.349|      81.078||            ||                     |
|repu|  4.173   5.602  1.397|     101.703||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   24|  0.00-  1.06:    72/   44| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   24|  1.06-  2.12:    54/   48| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   21|  2.12-  3.18:    43/   26| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   15|  3.18-  4.24:     2/   20| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   13|  4.24-  5.30:    13/   11| 2.18- 2.69:    59/   33 |
|0.048-0.057:     0/   11|  5.30-  6.36:    11/   16| 2.69- 3.19:   125/  138 |
|0.057-0.067:     0/    9|  6.36-  7.42:     2/   15| 3.19- 3.69:   293/  273 |
|0.067-0.076:     0/    4|  7.42-  8.48:     4/   10| 3.69- 4.19:   363/  308 |
|0.076-0.086:     0/    1|  8.48-  9.54:     0/    6| 4.19- 4.70:   497/  422 |
|0.086-0.096:     4/    2|  9.54- 10.59:     6/    2| 4.70- 5.20:   488/  407 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4200.0--------------------------------------------------|
| r-factor (work) = 0.5835  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5341  scale (free) =  0.9924                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.870604E-01   |
|                              B33=    7.928 |target (free) =  6.522180E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4200.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.037   0.254  0.000|     968.383||            ||  mean   max    min  |
|angl|  3.729  16.769  0.039|     563.046||            ||                     |
|chir|  0.271   0.843  0.004|      80.597||    1860.499||  0.512  1.935  0.075|
|plan|  0.019   0.041  0.008|      76.517||            ||                     |
|dihe| 31.785  57.994  1.433|      78.712||            ||                     |
|repu|  4.176   5.838  1.385|      93.244||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   36|  0.00-  1.06:    72/   43| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   30|  1.06-  2.12:    54/   38| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   15|  2.12-  3.18:    43/   31| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   12|  3.18-  4.24:     2/   30| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   13|  4.24-  5.30:    13/   17| 2.18- 2.69:    59/   40 |
|0.048-0.057:     0/    9|  5.30-  6.36:    11/   13| 2.69- 3.19:   125/  130 |
|0.057-0.067:     0/    3|  6.36-  7.42:     2/    9| 3.19- 3.69:   293/  273 |
|0.067-0.076:     0/    4|  7.42-  8.48:     4/    9| 3.69- 4.19:   363/  292 |
|0.076-0.086:     0/    1|  8.48-  9.54:     0/    7| 4.19- 4.70:   497/  445 |
|0.086-0.096:     4/    1|  9.54- 10.59:     6/    2| 4.70- 5.20:   488/  406 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4100.0--------------------------------------------------|
| r-factor (work) = 0.5829  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5442  scale (free) =  0.9881                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.730451E-01   |
|                              B33=    7.928 |target (free) =  8.562386E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4100.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.038   0.228  0.001|     817.469||            ||  mean   max    min  |
|angl|  3.779  20.694  0.008|     611.735||            ||                     |
|chir|  0.229   0.784  0.037|      50.083||    1713.070||  0.507  1.988  0.024|
|plan|  0.016   0.034  0.007|      53.897||            ||                     |
|dihe| 32.032  59.629  0.250|      80.612||            ||                     |
|repu|  4.175   5.577  1.393|      99.274||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   30|  0.00-  1.06:    72/   46| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   19|  1.06-  2.12:    54/   43| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   23|  2.12-  3.18:    43/   26| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   13|  3.18-  4.24:     2/   24| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   15|  4.24-  5.30:    13/   10| 2.18- 2.69:    59/   34 |
|0.048-0.057:     0/    7|  5.30-  6.36:    11/   13| 2.69- 3.19:   125/  133 |
|0.057-0.067:     0/    6|  6.36-  7.42:     2/   17| 3.19- 3.69:   293/  281 |
|0.067-0.076:     0/    9|  7.42-  8.48:     4/   11| 3.69- 4.19:   363/  299 |
|0.076-0.086:     0/    1|  8.48-  9.54:     0/    4| 4.19- 4.70:   497/  429 |
|0.086-0.096:     4/    2|  9.54- 10.59:     6/    5| 4.70- 5.20:   488/  400 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 4000.0--------------------------------------------------|
| r-factor (work) = 0.5833  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5326  scale (free) =  0.9944                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  6.863587E-01   |
|                              B33=    7.928 |target (free) =  6.518731E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 4000.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.036   0.268  0.000|     976.353||            ||  mean   max    min  |
|angl|  3.824  18.218  0.003|     590.843||            ||                     |
|chir|  0.278   0.882  0.016|      86.754||    1872.096||  0.512  1.959  0.083|
|plan|  0.015   0.032  0.006|      47.275||            ||                     |
|dihe| 31.954  56.314  1.280|      79.408||            ||                     |
|repu|  4.178   5.868  1.382|      91.464||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   32|  0.00-  1.06:    72/   39| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   33|  1.06-  2.12:    54/   33| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   17|  2.12-  3.18:    43/   40| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   15|  3.18-  4.24:     2/   26| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   11|  4.24-  5.30:    13/   16| 2.18- 2.69:    59/   40 |
|0.048-0.057:     0/    6|  5.30-  6.36:    11/   18| 2.69- 3.19:   125/  129 |
|0.057-0.067:     0/    6|  6.36-  7.42:     2/   11| 3.19- 3.69:   293/  273 |
|0.067-0.076:     0/    2|  7.42-  8.48:     4/    6| 3.69- 4.19:   363/  291 |
|0.076-0.086:     0/    2|  8.48-  9.54:     0/    7| 4.19- 4.70:   497/  446 |
|0.086-0.096:     4/    0|  9.54- 10.59:     6/    3| 4.70- 5.20:   488/  403 |
|-----------------------------------------------------------------------------|

|-2:SA temperatrure = 3900.0--------------------------------------------------|
| r-factor (work) = 0.5823  scale (work) =  1.0000  ksol=  0.56  bsol=  80.00 |
| r-factor (free) = 0.5428  scale (free) =  0.9868                            |
| anisotropic scale matrix (Cartesian basis):|xray targets:                   |
|  B11=    7.928 B12=    0.000 B13=    0.000 |target name=               mlhl |
|                B22=    7.928 B23=   -0.000 |target (work) =  8.727883E-01   |
|                              B33=    7.928 |target (free) =  8.564556E-01   |
| (B11+B22+B33)/3 =    7.928                 |                                |
|-----------------------------------------------------------------------------|

| SA temperatrure = 3900.0----------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.038   0.225  0.001|     821.214||            ||  mean   max    min  |
|angl|  3.808  21.043  0.057|     624.781||            ||                     |
|chir|  0.231   0.812  0.043|      51.623||    1707.507||  0.506  2.009  0.025|
|plan|  0.013   0.025  0.006|      32.001||            ||                     |
|dihe| 31.852  58.549  0.153|      80.236||            ||                     |
|repu|  4.176   5.606  1.389|      97.653||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.010:    58/   33|  0.00-  1.06:    72/   42| 0.17- 0.67:     2/    0 |
|0.010-0.019:    46/   22|  1.06-  2.12:    54/   51| 0.67- 1.18:     1/    0 |
|0.019-0.029:    21/   19|  2.12-  3.18:    43/   17| 1.18- 1.68:    15/    1 |
|0.029-0.038:     6/   14|  3.18-  4.24:     2/   29| 1.68- 2.18:    19/    1 |
|0.038-0.048:     1/   12|  4.24-  5.30:    13/   11| 2.18- 2.69:    59/   33 |
|0.048-0.057:     0/    5|  5.30-  6.36:    11/   15| 2.69- 3.19:   125/  135 |
|0.057-0.067:     0/    7|  6.36-  7.42:     2/   14| 3.19- 3.69:   293/  279 |
|0.067-0.076:     0/    9|  7.42-  8.48:     4/   11| 3.69- 4.19:   363/  297 |
|0.076-0.086:     0/    3|  8.48-  9.54:     0/    4| 4.19- 4.70:   497/  434 |
|0.086-0.096:     4/    1|  9.54- 10.59:     6/    5| 4.70- 5.20:   488/  393 |
|-----------------------------------------------------------------------------|

Traceback (most recent call last):
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/phenix/phenix/command_line/refine.py", line 5, in ?
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/phenix/phenix/refinement/command_line.py", line 52, in run
    refine_object.run()
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/phenix/phenix/refinement/driver.py", line 1057, in run
    log      = log)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/phenix/phenix/refinement/strategies.py", line 442, in refinement_machine
    out                        = log)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/simulated_annealing.py", line 72, in manager
    out                        = out)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/simulated_annealing.py", line 121, in run_simulated_annealing
    reset_velocities            = reset_velocities)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/cartesian_dynamics.py", line 66, in __init__
    self()
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/cartesian_dynamics.py", line 112, in __call__
    self.verlet_leapfrog_integration(verbose = self.verbose)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/cartesian_dynamics.py", line 263, in verlet_leapfrog_integration
    residuals = self.residuals()
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/cartesian_dynamics.py", line 148, in residuals
    self.xray_gradient = self.xray_grads()
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/dynamics/cartesian_dynamics.py", line 164, in xray_grads
    beta  = beta_w)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/mmtbx/mmtbx/f_model.py", line 577, in gradient_wrt_atomic_parameters
    algorithm          = self.sf_algorithm)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/cctbx/cctbx/xray/structure_factors/gradients.py", line 36, in __call__
    n_parameters=n_parameters)
  File "/net/sharptail/scratch1/phzwart/phenix/phenix-1.24.1b/cctbx/cctbx/xray/structure_factors/gradients_fft.py", line 39, in __init__
    gradient_map = manager.rfft().backward(coeff_map.complex_map())
KeyboardInterrupt