# Date 2006-07-20 Time 09:24:43 PDT -0700
#phil __OFF__

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

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
  Space group: I 41 3 2 (No. 214)

/net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_001.pdb
  Monomer Library directory:
    "/net/sharptail/scratch1/phzwart/Sources/mon_lib"
  Total number of atoms: 110
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 110
      Number of chains: 1
        Number of residues, atoms: 110, 110
          Classifications: {'water': 110}
          Link IDs: {None: 109}
  Time building chain proxies: 0.14, per 1000 atoms: 1.27

I-obs:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz:I-obs,SIGI-obs

R-free flags:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz:R-free-flags

  Number of scatterers: 110
  At special positions: 16
  Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
  Space group: I 41 3 2 (No. 214)
  Number of sites at special positions: 16
    Minimum distance between symmetrically equivalent sites: 0.5
    Label               Mult   Shift    Fractional coordinates
    " O   WAT     9 "    24    0.000 (  0.1978   0.0522   0.1250) original
                      site sym 2     (  0.1978   0.0522   0.1250) exact
                                      1/2*x-1/2*y+1/8,-1/2*x+1/2*y+1/8,1/8
    " O   WAT    24 "    24    0.000 (  0.4183   0.3750  -0.3317) original
                      site sym 2     (  0.4183   0.3750  -0.3317) exact
                                      1/2*x+1/2*z+3/8,3/8,1/2*x+1/2*z-3/8
    " O   WAT    28 "    16    0.000 (  0.2814   0.2186  -0.2186) original
                      site sym 3     (  0.2814   0.2186  -0.2186) exact
                                      1/3*x-1/3*y+1/3*z+1/3,-1/3*x+1/3*y-1/3*z+1/6,1/3*x-1/3*y+1/3*z-1/6
    " O   WAT    31 "    12    0.000 (  0.6250  -0.0000   0.2500) original
                      site sym 222   (  0.6250   0.0000   0.2500) exact
                                              5/8,0,1/4
    " O   WAT    34 "    24    0.000 (  0.3896  -0.1250   0.3604) original
                      site sym 2     (  0.3896  -0.1250   0.3604) exact
                                      1/2*x-1/2*z+3/8,-1/8,-1/2*x+1/2*z+3/8
    " O   WAT    37 "    24    0.000 (  0.2152   0.1250  -0.0348) original
                      site sym 2     (  0.2152   0.1250  -0.0348) exact
                                      1/2*x+1/2*z+1/8,1/8,1/2*x+1/2*z-1/8
    " O   WAT    42 "    24    0.001 (  0.4611   0.3750  -0.2889) original
                      site sym 2     (  0.4611   0.3750  -0.2889) exact
                                      1/2*x+1/2*z+3/8,3/8,1/2*x+1/2*z-3/8
    " O   WAT    65 "    24    0.001 (  0.6250   0.1092   0.1408) original
                      site sym 2     (  0.6250   0.1092   0.1408) exact
                                      5/8,1/2*y-1/2*z+1/8,-1/2*y+1/2*z+1/8
    " O   WAT    75 "    24    0.000 (  0.5629  -0.0000   0.2500) original
                      site sym 2     (  0.5629   0.0000   0.2500) exact
                                               x,0,1/4
    " O   WAT    78 "     8    0.000 (  0.6250  -0.1250   0.1250) original
                      site sym 32    (  0.6250  -0.1250   0.1250) exact
                                             5/8,-1/8,1/8
    " O   WAT    79 "    16    0.000 (  0.4946   0.0054  -0.0054) original
                      site sym 3     (  0.4946   0.0054  -0.0054) exact
                                      1/3*x-1/3*y+1/3*z+1/3,-1/3*x+1/3*y-1/3*z+1/6,1/3*x-1/3*y+1/3*z-1/6
    " O   WAT    80 "    24    0.000 (  0.5831  -0.1250   0.1669) original
                      site sym 2     (  0.5831  -0.1250   0.1669) exact
                                      1/2*x-1/2*z+3/8,-1/8,-1/2*x+1/2*z+3/8
    " O   WAT    81 "    24    0.000 (  0.5218  -0.1250   0.2282) original
                      site sym 2     (  0.5218  -0.1250   0.2282) exact
                                      1/2*x-1/2*z+3/8,-1/8,-1/2*x+1/2*z+3/8
    " O   WAT    93 "    24    0.000 (  0.1489   0.1250  -0.1011) original
                      site sym 2     (  0.1489   0.1250  -0.1011) exact
                                      1/2*x+1/2*z+1/8,1/8,1/2*x+1/2*z-1/8
    " O   WAT   105 "    24    0.000 (  0.6250  -0.0431   0.2069) original
                      site sym 2     (  0.6250  -0.0431   0.2069) exact
                                      5/8,1/2*y+1/2*z-1/8,1/2*y+1/2*z+1/8
    " O   WAT   106 "     8    0.000 (  0.3750   0.1250  -0.1250) original
                      site sym 32    (  0.3750   0.1250  -0.1250) exact
                                             3/8,1/8,-1/8
  Number of scattering types: 1
    Type Number    sf(0)
     O     110      8.00
    sf(0) = scattering factor at diffraction angle 0.
  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.05 seconds
  Histogram of nonbonded interaction distances:
        3.32 -     3.54: 31
        3.54 -     3.75: 19
        3.75 -     3.97: 28
        3.97 -     4.18: 47
        4.18 -     4.40: 74
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   WAT    22 " - " O   WAT    71 "  3.320 3.400
  " O   WAT    21 " - " O   WAT    51 "  3.340 3.400
  " O   WAT    84 " - " O   WAT    92 "  3.354 3.400
  " O   WAT     4 " - " O   WAT    56 "  3.357 3.400 y+1/4,x-1/4,-z-1/4
  " O   WAT    45 " - " O   WAT    69 "  3.359 3.400 x-1/4,z+1/4,-y+1/4
  ... (remaining 194 not shown)

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 55,939,072
Resident set size:   45,375,488
Stack size:              98,304
u+s,u,s: 3.12 2.93 0.19 micro-seconds/tick: 0.618
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

Miller array info: /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz:I-obs,SIGI-obs
Observation type: xray.intensity
Type of data: double, size=5224
Type of sigmas: double, size=5224
Number of Miller indices: 5224
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 41 3 2 (No. 214)
Systematic absences: 0
Centric reflections: 1055
Resolution range: 31.3759 1.61737
Completeness in resolution range: 0.998471
Completeness with d_max=infinity: 0.99828

X-ray intensities converted to amplitudes for use in refinement.

Number of F-obs in resolution range:                   5224
Number of F-obs <= 0:                                  136
Refinement resolution range: d_max =  31.3759
                             d_min =   1.6174

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,664,064
Resident set size:   46,698,496
Stack size:              98,304
u+s,u,s: 3.82 3.62 0.20 micro-seconds/tick: 0.754
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

Miller array info: /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz:R-free-flags
Observation type: None
Type of data: int, size=5224
Type of sigmas: None
Number of Miller indices: 5224
Anomalous flag: False
Unit cell: (76.855, 76.855, 76.855, 90, 90, 90)
Space group: I 41 3 2 (No. 214)
Systematic absences: 0
Centric reflections: 1055
Resolution range: 31.3759 1.61737
Completeness in resolution range: 0.998471
Completeness with d_max=infinity: 0.99828

Test flag value: 1

Number of work/free reflections by resolution:
                                      work free  %free
  bin  1: 31.3818 -  3.4831 [586/588]  527   59  10.1%
  bin  2:  3.4831 -  2.7652 [532/532]  479   53  10.0%
  bin  3:  2.7652 -  2.4158 [524/529]  471   53  10.1%
  bin  4:  2.4158 -  2.1950 [523/527]  471   52   9.9%
  bin  5:  2.1950 -  2.0377 [504/512]  453   51  10.1%
  bin  6:  2.0377 -  1.9175 [505/515]  453   52  10.3%
  bin  7:  1.9175 -  1.8215 [486/502]  439   47   9.7%
  bin  8:  1.8215 -  1.7422 [484/505]  436   48   9.9%
  bin  9:  1.7422 -  1.6752 [490/506]  440   50  10.2%
  bin 10:  1.6752 -  1.6174 [454/516]  414   40   8.8%
                              overall 4583  505   9.9%

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,664,064
Resident set size:   46,743,552
Stack size:              98,304
u+s,u,s: 3.89 3.69 0.20 micro-seconds/tick: 0.767
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

Number of scattering types: 1
  Type Number    sf(0)   Gaussians
   O     110      7.97       2
  sf(0) = scattering factor at diffraction angle 0.

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,664,064
Resident set size:   46,747,648
Stack size:              98,304
u+s,u,s: 3.89 3.69 0.20 micro-seconds/tick: 0.767
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

No NCS restraint groups specified.

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,696,832
Resident set size:   46,759,936
Stack size:              98,304
u+s,u,s: 3.89 3.69 0.20 micro-seconds/tick: 0.767
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

================================= Output files ================================

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_002.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_002.geo

CPU time processing inputs: 3.94

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,696,832
Resident set size:   46,956,544
Stack size:              98,304
u+s,u,s: 3.94 3.74 0.20 micro-seconds/tick: 0.764
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

#phil __ON__
refinement.crystal_symmetry {
  unit_cell = 76.855 76.855 76.855 90 90 90
  space_group = "I 41 3 2"
}
refinement.input {
  pdb {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_001.pdb"
  }
  neutron_data {
    file_name = None
    labels = None
  }
  neutron_r_free_flags {
    file_name = None
    label = None
    test_flag_value = None
    disable_suitability_test = False
  }
  xray_data {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz"
    labels = "I-obs,SIGI-obs"
  }
  r_free_flags {
    file_name = "/net/cci-filer1/vol1/home/phzwart/Banu/Betty/refine/hyss_refine_data.mtz"
    label = "R-free-flags"
    test_flag_value = 1
    disable_suitability_test = False
  }
  experimental_phases {
    file_name = None
    labels = None
  }
  monomers {
    file_name = None
  }
  symmetry_safety_check = *error warning
}
refinement.output {
  prefix = "hyss_refine"
  serial = 2
  serial_format = "%03d"
  write_eff_file = True
  write_geo_file = True
  write_def_file = True
  write_refined_mtz_file = True
  write_refined_hkl_file = False
  write_maps = True
  write_map_coefficients = True
  refined_fmodel_data_labels {
    f_obs = "FOBS"
    f_model_amplitudes = "FMODEL"
    f_model_phases = "PHMODEL"
    figures_of_merit = "FOM"
    alpha = "D"
    cross_validation_flags = "CVFLAGS"
  }
}
refinement.electron_density_map {
  map_types = k*Fobs-n*Fmodel *2m*Fobs-D*Fmodel *m*Fobs-D*Fmodel
  map_format = *xplor
  map_coefficients_format = *mtz phs
  mtz_labels {
    map_type = "2m*Fobs-D*Fmodel"
    amplitudes = "2FOFCWT"
    phases = "PH2FOFCWT"
  }
  mtz_labels {
    map_type = "m*Fobs-D*Fmodel"
    amplitudes = "FOFCWT"
    phases = "PHFOFCWT"
  }
  mtz_labels {
    map_type = "k*Fobs-n*Fmodel"
    amplitudes = "oFOoFCWT"
    phases = "oPHFOoFCWT"
  }
  grid_resolution_factor = 0.3333333333
  region = *selection cell
  atom_selection = None
  atom_selection_buffer = 3
}
refinement.main {
  refine_adp_individual = True
  refine_adp_group = False
  refine_tls = False
  high_resolution = None
  low_resolution = None
  bulk_solvent_and_scale = True
  simulated_annealing = False
  fcalc_accuracy_check = False
  scale_adp = True
  ordered_solvent = True
  ls_bulk_solvent_and_scale_if_r_greater_then = 0.99
  put_water_after_macro_cycle_number = True
  number_of_macro_cycles = 3
  max_number_of_iterations = 25
  use_experimental_sigmas = False
  generate_neutron_r_free_flags = False
  generate_r_free_flags = False
  r_free_flags_fraction = 0.1
  r_free_flags_max_free = 2000
  remove_test_set_memory = None
  use_form_factor_weights = False
  refine_site = True
  number_of_macro_cycles_for_uiso_site_refinement = 1
  tan_u_iso = False
  sf_algorithm = *fft direct
  use_convergence_test = False
  target = *ml mlhl ls
  min_number_of_test_set_reflections_for_max_likelihood_target = 50
  max_number_of_resolution_bins = 30
  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 = 2772306
  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
  b_cart = "0" "0" "0" "0" "0" "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 = 1
  max_number_of_iterations = 25
  one_residue_one_group = True
  convergence_test = False
  selection = None
}
refinement.adp {
  convert_to_isotropic = True
  iso {
    max_number_of_iterations = 25
    automatic_randomization_if_all_equal = True
    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 = 1
  max_number_of_iterations = 15
  start_tls_value = None
  run_finite_differences_test = False
  eps = 1e-06
  write_out_as {
    tls_and_adp_local = True
    tls_zero_and_adp_total = False
  }
}
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 = 10000000
  max_iterations = 25
  convergence_test = False
  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 = 0.8
  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 = 100
  b_sol_min = 10
  k_sol_step = 0.05
  b_sol_step = 5
  number_of_macro_cycles = 2
  number_of_minimization_macro_cycles = 3
  number_of_cycles_for_anisotropic_scaling = 3
  fix_k_sol = None
  fix_b_sol = None
  fix_b_cart {
    u11 = None
    u22 = None
    u33 = None
    u12 = None
    u13 = None
    u23 = None
  }
  apply_back_trace_of_b_cart = False
  start_minimization_from_k_sol = 0.35
  start_minimization_from_b_sol = 46
  start_minimization_from_b_cart {
    u11 = 0
    u22 = 0
    u33 = 0
    u12 = 0
    u13 = 0
    u23 = 0
  }
  nu_fix_n_atoms = None
  nu_fix_b_atoms = None
  verbose = 1
}
refinement.fcalc_accuracy_check {
  nref_in_bin = 100
  r_lim = 1
  r_lim_high = 0.5
  scat_table = *wk1995 it1992
}
refinement.alpha_beta {
  test_ref_in_bin = 120
  keep_test_ref_in_bin = True
  number_of_macromolecule_atoms_absent = 225
  n_atoms_included = 0
  bf_atoms_absent = 15
  final_error = 0
  absent_atom_type = "O"
  method = *est calc
  verbose = -1
  interpolation = True
  fix_scale_for_calc_option = None
  number_of_waters_absent = 613
}
refinement.mask {
  solvent_radius = 1
  shrink_truncation_radius = 1
  grid_step_factor = 4
  verbose = 1
}
refinement.cartesian_dynamics {
  temperature = 300
  number_of_steps = 200
  time_step = 0.0005
  n_print = 100
  verbose = -1
}
refinement.simulated_annealing {
  start_temperature = 5000
  final_temperature = 300
  cool_rate = 100
  number_of_steps = 25
  time_step = 0.0005
  n_print = 100
  update_grads_shift = 0.3
  refine_sites = True
  refine_adp = False
  max_number_of_iterations = 25
  mode = every_macro_cycle *second_and_before_last
  verbose = -1
}
refinement.target_weights {
  wxc_scale = 0.5
  wxu_scale = 1
  wc = 1
  wu = 1
  fix_wxc = None
  fix_wxu = None
  allow_automatic_adjustment = False
  delta_r_free_r_work = 6
  wxc_scale_drop = 3
  wxu_scale_drop = 3
  max_number_of_macro_cycles = 12
  optimize_wxc = False
  optimization_criterion = *r_free gradient_angle
  optimize_wxu = False
  shake_sites = True
  shake_adp = 10
  regularize_ncycles = 50
  gradient_filtering = True
  gradient_filtering_method = *cns new
  rmsd_cutoff_for_gradient_filtering = 3
  verbose = 1
}
refinement.dbe {
  b_iso_cutoff = 10
  occupancy_cutoff = 0.8
  resolution = 0.7
}
refinement.ls_target_names {
  target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \
                ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \
                ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \
                ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \
                lsm_k1ask3_fixed
}
refinement.neutron {
  low_resolution = None
  high_resolution = None
}
#phil __OFF__

\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 56,696,832
Resident set size:   46,956,544
Stack size:              98,304
u+s,u,s: 3.98 3.78 0.20 micro-seconds/tick: 0.758
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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


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

|-----------------------------------------------------------------------------|
|                                                                             |
| all [31.4-1.62]  high resolution [6.0-1.62]  low resolution [31.4-6.00]     |
| r_work = 0.5064  r_work = 0.4997             r_work = 0.5432                |
| r_free = 0.6041  r_free = 0.5841             r_free = 0.7885                |
|                                                                             |
| scale (work) = 0.2233  scale (free) = 0.1880  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ml:  work = 3.884224E+00  free = 3.927172E+00                        |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 31.3818 -  2.5671 1.00   1243  139 0.4485 0.5913  5.0580E+00  5.1596E+00|
|  2:  2.5671 -  2.0377 0.99   1158  129 0.5334 0.5475  4.3037E+00  4.3134E+00|
|  3:  2.0377 -  1.7801 0.97   1113  123 0.4706 0.5531  3.1866E+00  3.1193E+00|
|  4:  1.7801 -  1.6174 0.94   1069  114 0.5008 0.5702  2.7914E+00  2.8591E+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: 31.3818 -  2.5671  1243   139 0.370  60.623  62.491   0.135    5031.889 |
|  2:  2.5671 -  2.0377  1158   129 0.110  81.780  80.556   0.092    1842.410 |
|  3:  2.0377 -  1.7801  1113   123 0.163  77.560  79.432   0.047     193.975 |
|  4:  1.7801 -  1.6174  1069   114 0.145  79.090  78.863   0.047      86.583 |
|alpha:            min =       0.0471 max =       0.1354 mean =       0.0825  |
|beta:             min =      86.5832 max =    5031.8895 mean =    1900.0460  |
|figures of merit: min =       0.0000 max =       1.0000 mean =       0.2014  |
|phase err.(work): min =       0.0000 max =      89.9985 mean =      74.3897  |
|phase err.(test): min =      13.5815 max =      89.9391 mean =      74.9277  |
|-----------------------------------------------------------------------------|

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

Wilson B = 25.613    

             ----------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 =            0.082150 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.769208 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   96.693 (deg)            |
| angle between Xray and ADP gradient vectors:       147.272 (deg)            |
|-----------------------------------------------------------------------------|

|-target weights and weight scales : after gradient filtering-----------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            0.082150 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.769208 | wxu_scale =          1.000 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   96.693 (deg)            |
| angle between Xray and ADP gradient vectors:       147.272 (deg)            |
| Number of Xray gradient terms excluded =       0 from total =     110       |
|-----------------------------------------------------------------------------|

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


|-----------------------------------------------------------------------------|
|Type| Deviation from ideal |   Targets  ||Target (sum)|| Deviation of start  |
|    |  mean     max    min |            ||            || model from current  |
|bond|  0.000   0.000  0.000|       0.000||            ||  mean   max    min  |
|angl|  0.000   0.000  0.000|       0.000||            ||                     |
|chir|  0.000   0.000  0.000|       0.000||       0.001||  0.000  0.000  0.000|
|plan|  0.000   0.000  0.000|       0.000||            ||                     |
|dihe|  0.000   0.000  0.000|       0.000||            ||                     |
|repu|  3.988   4.399  3.320|       0.001||            ||                     |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|                 Histograms for start / current models of                    |
|                        |                          |                         |
|        deviations from ideal values for           |                         |
|                        |                          |                         |
| bonds                  | angles                   | nonbonded contacts      |
|                        |                          |                         |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.32- 3.43:    20/   20 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.43- 3.54:    11/   11 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.54- 3.64:     7/    7 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.64- 3.75:    12/   12 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.75- 3.86:    13/   13 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.86- 3.97:    15/   15 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 3.97- 4.08:    27/   27 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 4.08- 4.18:    20/   20 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 4.18- 4.29:    29/   29 |
|0.000-0.000:     0/    0|  0.00-  0.00:     0/    0| 4.29- 4.40:    45/   45 |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Wilson B =  25.613 | target =      0.00014 | norm of gradient =     0.00159 |
|-----------------------------------------------------------------------------|
|            Reference model          |            Current model              |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                           Isotropic B-factors:                              |
|     min      max      mean          |     min      max      mean            |
|  21.940   32.500    25.365          |  21.940   32.500    25.365            |
| number of B < 0.5:     0            |  number of B < 0.5:     0             |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|     21.940 -   22.996:      12      |       21.940 -   22.996:      12      |
|     22.996 -   24.052:      17      |       22.996 -   24.052:      17      |
|     24.052 -   25.108:      23      |       24.052 -   25.108:      23      |
|     25.108 -   26.164:      20      |       25.108 -   26.164:      20      |
|     26.164 -   27.220:      23      |       26.164 -   27.220:      23      |
|     27.220 -   28.276:       8      |       27.220 -   28.276:       8      |
|     28.276 -   29.332:       4      |       28.276 -   29.332:       4      |
|     29.332 -   30.388:       1      |       29.332 -   30.388:       1      |
|     30.388 -   31.444:       1      |       30.388 -   31.444:       1      |
|     31.444 -   32.500:       1      |       31.444 -   32.500:       1      |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
| Number of anisotropically refinable ADP = 0 out of 110 total                |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 0.85   min = 0.85   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|
\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 58,892,288
Resident set size:   49,782,784
Stack size:              98,304
from_scatterers_fft:    5 calls, 1.99 s
gradients_fft:          4 calls, 2.78 s
u+s,u,s: 16.14 14.67 1.47 micro-seconds/tick: 2.922
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

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

|-macro cycle = 1-------------------------------------------------------------|
|                                                                             |
| all [31.4-1.62]  high resolution [6.0-1.62]  low resolution [31.4-6.00]     |
| r_work = 0.5064  r_work = 0.4997             r_work = 0.5432                |
| r_free = 0.6041  r_free = 0.5841             r_free = 0.7885                |
|                                                                             |
| scale (work) = 0.2233  scale (free) = 0.1880  ksol = 0.00  Bsol = 0.00      |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis):                         |
| (B11,B22,B33,B12,B13,B23)= (0.00,0.00,0.00,0.00,0.00,0.00)                  |
| (B11+B22+B33)/3 = 0.00                                                      |
|                                                                             |
| Target ml:  work = 3.884224E+00  free = 3.927172E+00                        |
|-----------------------------------------------------------------------------|
\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/
Virtual memory size: 58,892,288
Resident set size:   49,782,784
Stack size:              98,304
from_scatterers_fft:    5 calls, 1.99 s
gradients_fft:          4 calls, 2.78 s
u+s,u,s: 16.18 14.71 1.47 micro-seconds/tick: 2.919
/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\

================== ordered solvent: location/analysis/update ==================

Traceback (most recent call last):
  File "/net/sharptail/scratch1/phzwart/Sources/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/Sources/phenix/phenix/refinement/command_line.py", line 71, in run
    refine_object.run()
  File "/net/sharptail/scratch1/phzwart/Sources/phenix/phenix/refinement/driver.py", line 1235, in run
    log                     = log)
  File "/net/sharptail/scratch1/phzwart/Sources/phenix/phenix/refinement/strategies.py", line 398, in refinement_machine
    log               = log)
  File "/net/sharptail/scratch1/phzwart/Sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 56, in get_manager
    min_cross_distance          = params.peak_search.min_cross_distance)
  File "/net/sharptail/scratch1/phzwart/Sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 102, in __init__
    if(self.verbose > 0): self.show_current_state(header = "Start model:")
  File "/net/sharptail/scratch1/phzwart/Sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 169, in show_current_state
    st2 = (flex.max(b_solv),flex.max(b_prot))
RuntimeError: max() argument is an empty array