Starting phenix.aquaref
on Thu Jun 11 12:10:22 2026 by afonine
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found miller_array, 3njw.mtz
  Found model, iam2_001.pdb

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    engine=aimnet2

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    miller_array {
      file = "3njw.mtz"
    }
    default_miller_array = "3njw.mtz"
    model {
      file = "iam2_001.pdb"
    }
    default_model = "iam2_001.pdb"
  }
  quantum {
    engine_name = mopac fairchem *aimnet2 aimnet2-old torchani terachem \
                  turbomole pyscf orca gaussian xtb server
  }


Starting job
===============================================================================
Validate inputs:

  expansion/clustering require minimizer=lbfgs and gradient_only=True 

-------------------------------------------------------------------------------
Refinement start
****************
-------------------------------------------------------------------------------
Extracting fmodel
*****************
                   start: r(all,work,free)=0.1251 0.1251 0.1243 n_refl.: 10638
       re-set all scales: r(all,work,free)=0.1251 0.1251 0.1243 n_refl.: 10638
         remove outliers: r(all,work,free)=0.1251 0.1251 0.1243 n_refl.: 10635
bulk-solvent and scaling: r(all,work,free)=0.1102 0.1097 0.1140 n_refl.: 10635
         remove outliers: r(all,work,free)=0.1100 0.1096 0.1140 n_refl.: 10633
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
  8.943-4.242    99.02    90    11 0.1427   108.486   105.840 0.931 0.949 0.077
  4.237-3.403   100.00    90    10 0.0757   115.394   114.517 0.993 0.952 0.066
  3.400-2.732   100.00   159    17 0.1148    81.743    80.577 1.004 0.953 0.058
  2.728-2.190   100.00   313    35 0.1150    67.726    67.365 1.054 0.952 0.000
  2.188-1.756   100.00   585    64 0.1033    51.277    50.900 1.102 0.952 0.000
  1.756-1.409   100.00  1103   123 0.0898    33.445    33.472 1.125 0.951 0.000
  1.408-1.130   100.00  2106   235 0.0869    23.925    23.992 1.138 0.949 0.000
  1.130-0.907    99.89  4002   445 0.1304    13.365    13.364 1.153 0.946 0.000
  0.906-0.865    89.06  1121   124 0.2124     6.747     6.340 0.993 0.944 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0576   b_overall=0.0120  
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.1096 r_free=0.1140
-------------------------------------------------------------------------------
Setting refinement target
*************************
ml
auto_cust = True
max_atoms = 50000
debug_rss = False
debug = False
scattering_table = wk1995 it1992 *n_gaussian electron neutron
use_reduce = True
cluster {
  charge_cutoff = 8
  clustering = True
  charge_embedding = False
  two_buffers = False
  maxnum_residues_in_cluster = 15
  bcc_threshold = 9
  select_within_radius = 10
  clustering_method = gnc *bcc
  altloc_method = average *subtract
  save_clusters = True
  bond_with_altloc = True
  re_calculate_rmsd_tolerance = 0.5
}
restraints = cctbx *qm
expansion = False
quantum {
  engine_name = mopac fairchem *aimnet2 aimnet2-old torchani terachem \
                turbomole pyscf orca gaussian xtb server
  basis = Auto
  charge = None
  method = Auto
  memory = None
  nproc = 1
  server_url = "http://127.0.0.1:8000"
  qm_addon = gcp dftd3 gcp-d3
  qm_addon_method = None
}
refine {
  dry_run = False
  sf_algorithm = *direct fft
  refinement_target_name = *ml ls_wunit_k1
  mode = opt *refine gtest
  number_of_macro_cycles = 1
  number_of_weight_search_cycles = 50
  number_of_refine_cycles = 5
  number_of_micro_cycles = 50
  data_weight = None
  skip_weight_search = False
  adjust_restraints_weight_scale_value = 2
  max_iterations_weight = 50
  max_iterations_refine = 50
  use_ase_lbfgs = False
  line_search = True
  stpmax = 0.2
  gradient_only = True
  refine_sites = True
  refine_adp = False
  restraints_weight_scale = 1
  shake_sites = False
  use_convergence_test = True
  max_bond_rmsd = 0.03
  max_angle_rmsd = 1.7
  stop_one_found_first_good_weight = True
  max_r_work_r_free_gap = 5
  r_tolerance = 0.001
  rmsd_tolerance = 0.01
  opt_log = False
  pre_opt = False
  pre_opt_stpmax = 0.1
  pre_opt_iter = 10
  pre_opt_switch = 2
  pre_opt_gconv = 3000
  minimizer = *lbfgs lbfgsb
  shift_evaluation = max *mean
  exclude = None
}
parallel {
  method = *multiprocessing slurm pbs sge lsf threading
  nproc = 1
  qsub_command = None
}
output_file_name_prefix = None
output_folder_name = "pdb"
rst_file = None
dump_gradients = None
output {
  filename = None
  file_name = None
  prefix = None
  suffix = None
  serial = 0
  serial_format = "%03d"
  target_output_format = None *pdb mmcif
  overwrite = False
}

-------------------------------------------------------------------------------
Extracting model
****************
  Monomer Library directory:
    "/net/cci-gpu-00/raid1/scratch1/pavel/phenix-dev-6083/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 343
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 268
          Classifications: {'peptide': 19}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 75
          Classifications: {'water': 25}
          Link IDs: {None: 24}
  Residues with excluded nonbonded symmetry interactions: 21
    residue:
      pdb=" O   HOH A1003 " occ=0.98
      pdb=" H1  HOH A1003 " occ=0.00
      pdb=" H2  HOH A1003 " occ=0.00
    residue:
      pdb=" O   HOH A1004 " occ=0.93
      pdb=" H1  HOH A1004 " occ=0.00
      pdb=" H2  HOH A1004 " occ=0.00
    residue:
      pdb=" O   HOH A1006 " occ=0.52
      pdb=" H1  HOH A1006 " occ=0.00
      pdb=" H2  HOH A1006 " occ=0.00
    residue:
      pdb=" O   HOH A1007 " occ=0.92
      pdb=" H1  HOH A1007 " occ=0.00
      pdb=" H2  HOH A1007 " occ=0.00
    residue:
      pdb=" O   HOH A1008 " occ=0.93
      pdb=" H1  HOH A1008 " occ=0.00
      pdb=" H2  HOH A1008 " occ=0.00
    residue:
      pdb=" O   HOH A1009 " occ=0.51
      pdb=" H1  HOH A1009 " occ=0.00
      pdb=" H2  HOH A1009 " occ=0.00
    residue:
      pdb=" O   HOH A1010 " occ=0.99
      pdb=" H1  HOH A1010 " occ=0.00
      pdb=" H2  HOH A1010 " occ=0.00
    residue:
      pdb=" O   HOH A1011 " occ=0.99
      pdb=" H1  HOH A1011 " occ=0.00
      pdb=" H2  HOH A1011 " occ=0.00
    residue:
      pdb=" O   HOH A1012 " occ=0.41
      pdb=" H1  HOH A1012 " occ=0.00
      pdb=" H2  HOH A1012 " occ=0.00
    residue:
      pdb=" O   HOH A1013 " occ=0.57
      pdb=" H1  HOH A1013 " occ=0.00
      pdb=" H2  HOH A1013 " occ=0.00
    residue:
      pdb=" O   HOH A1016 " occ=0.47
      pdb=" H1  HOH A1016 " occ=0.00
      pdb=" H2  HOH A1016 " occ=0.00
    residue:
      pdb=" O   HOH A1017 " occ=0.81
      pdb=" H1  HOH A1017 " occ=0.00
      pdb=" H2  HOH A1017 " occ=0.00
    ... (remaining 9 not shown)
  Time building chain proxies: 0.11, per 1000 atoms: 0.32
  Number of scatterers: 343
  At special positions: 0
  Unit cell: (19.465, 21.432, 29.523, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O      49      8.00
     N      23      7.00
     C      95      6.00
     H     174      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  19 " distance=2.03
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ASP_CG-ANY_N
      " ASP A   9 " - " GLY A   1 "
  Time building additional restraints: 0.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  32

  Time building geometry restraints manager: 0.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.66 -     0.89: 61
        0.89 -     1.12: 113
        1.12 -     1.36: 45
        1.36 -     1.59: 106
        1.59 -     1.82: 2
  Bond restraints: 327
  Sorted by residual:
  bond pdb=" O   HOH A1014 "
       pdb=" H2  HOH A1014 "
    ideal  model  delta    sigma   weight residual
    0.980  0.655  0.325 2.00e-02 2.50e+03 2.64e+02
  bond pdb=" O   HOH A1018 "
       pdb=" H1  HOH A1018 "
    ideal  model  delta    sigma   weight residual
    0.980  0.739  0.241 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" CH2 TRP A  17 "
       pdb=" HH2 TRP A  17 "
    ideal  model  delta    sigma   weight residual
    1.080  0.893  0.187 2.00e-02 2.50e+03 8.76e+01
  bond pdb=" O   HOH A1017 "
       pdb=" H2  HOH A1017 "
    ideal  model  delta    sigma   weight residual
    0.980  0.807  0.173 2.00e-02 2.50e+03 7.51e+01
  bond pdb=" O   HOH A1004 "
       pdb=" H2  HOH A1004 "
    ideal  model  delta    sigma   weight residual
    0.980  0.808  0.172 2.00e-02 2.50e+03 7.41e+01
  ... (remaining 322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 290
        0.99 -     1.98: 157
        1.98 -     2.97: 47
        2.97 -     3.96: 18
        3.96 -     4.95: 15
  Bond angle restraints: 527
  Sorted by residual:
  angle pdb=" CA  ASP A   9 "
        pdb=" CB  ASP A   9 "
        pdb=" CG  ASP A   9 "
      ideal   model   delta    sigma   weight residual
     112.60  116.45   -3.85 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" C   PRO A   7 "
        pdb=" N   SER A   8 "
        pdb=" CA  SER A   8 "
      ideal   model   delta    sigma   weight residual
     121.70  126.65   -4.95 1.80e+00 3.09e-01 7.58e+00
  angle pdb=" CA  THR A  15 "
        pdb=" CB  THR A  15 "
        pdb=" OG1 THR A  15 "
      ideal   model   delta    sigma   weight residual
     109.60  105.54    4.06 1.50e+00 4.44e-01 7.32e+00
  angle pdb=" CA  THR A  15 "
        pdb=" CB  THR A  15 "
        pdb=" CG2 THR A  15 "
      ideal   model   delta    sigma   weight residual
     110.50  114.83   -4.33 1.70e+00 3.46e-01 6.48e+00
  angle pdb=" C   ASP A   9 "
        pdb=" CA  ASP A   9 "
        pdb=" CB  ASP A   9 "
      ideal   model   delta    sigma   weight residual
     110.10  114.51   -4.41 1.90e+00 2.77e-01 5.39e+00
  ... (remaining 522 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.05 -    10.97: 116
       10.97 -    21.89: 18
       21.89 -    32.81: 2
       32.81 -    43.73: 4
       43.73 -    54.65: 4
  Dihedral angle restraints: 144
    sinusoidal: 75
      harmonic: 69
  Sorted by residual:
  dihedral pdb=" C   ILE A  10 "
           pdb=" N   ILE A  10 "
           pdb=" CA  ILE A  10 "
           pdb=" CB  ILE A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.74    8.74     0      2.50e+00 1.60e-01 1.22e+01
  dihedral pdb=" CA  SER A   8 "
           pdb=" C   SER A   8 "
           pdb=" N   ASP A   9 "
           pdb=" CA  ASP A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.90   14.10     0      5.00e+00 4.00e-02 7.95e+00
  dihedral pdb=" C   ASP A   9 "
           pdb=" N   ASP A   9 "
           pdb=" CA  ASP A   9 "
           pdb=" CB  ASP A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.07    6.47     0      2.50e+00 1.60e-01 6.69e+00
  ... (remaining 141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.008 -    0.057: 9
       0.057 -    0.106: 4
       0.106 -    0.155: 2
       0.155 -    0.204: 3
       0.204 -    0.253: 1
  Chirality restraints: 19
  Sorted by residual:
  chirality pdb=" CA  ASP A   9 "
            pdb=" N   ASP A   9 "
            pdb=" C   ASP A   9 "
            pdb=" CB  ASP A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  PRO A   7 "
            pdb=" N   PRO A   7 "
            pdb=" C   PRO A   7 "
            pdb=" CB  PRO A   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.92   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ILE A  10 "
            pdb=" N   ILE A  10 "
            pdb=" C   ILE A  10 "
            pdb=" CB  ILE A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 16 not shown)

  Planarity restraints: 42
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  17 "    0.036 2.00e-02 2.50e+03   3.57e-02 5.11e+01
        pdb=" CG  TRP A  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  17 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  17 "   -0.063 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  17 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  17 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  17 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  17 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  17 "    0.020 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  17 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  17 "    0.009 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  17 "   -0.031 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  17 "   -0.060 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  17 "    0.007 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  17 "    0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A   4 "   -0.011 2.00e-02 2.50e+03   3.27e-02 4.27e+01
        pdb=" CG  TRP A   4 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A   4 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A   4 "   -0.079 2.00e-02 2.50e+03
        pdb=" NE1 TRP A   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A   4 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE3 TRP A   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A   4 "    0.022 2.00e-02 2.50e+03
        pdb=" CH2 TRP A   4 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 TRP A   4 "    0.075 2.00e-02 2.50e+03
        pdb=" HE1 TRP A   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" HE3 TRP A   4 "    0.007 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A   4 "    0.041 2.00e-02 2.50e+03
        pdb=" HH2 TRP A   4 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  13 "   -0.030 2.00e-02 2.50e+03   2.74e-02 3.00e+01
        pdb=" CG  TRP A  13 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  13 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  13 "    0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  13 "    0.047 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  13 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  13 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  13 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  13 "    0.016 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  13 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  13 "   -0.037 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  13 "    0.049 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  13 "    0.019 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  13 "   -0.014 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  13 "    0.025 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  13 "   -0.038 2.00e-02 2.50e+03
  ... (remaining 39 not shown)

  Histogram of nonbonded interaction distances:
        0.77 -     1.53: 16
        1.53 -     2.30: 186
        2.30 -     3.07: 1253
        3.07 -     3.83: 2249
        3.83 -     4.60: 3839
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 7543
  Sorted by model distance:
  nonbonded pdb=" O   HOH A1012 "
            pdb=" O   HOH A1112 "
     model   vdw
     0.768 2.800
  nonbonded pdb=" O   HOH A1006 "
            pdb=" O   HOH A1106 "
     model   vdw
     0.823 2.800
  nonbonded pdb=" O   HOH A1007 "
            pdb=" O   HOH A1016 "
     model   vdw
     1.321 2.800
  nonbonded pdb=" H1  HOH A1012 "
            pdb=" O   HOH A1112 "
     model   vdw
     1.433 2.400
  nonbonded pdb=" O   HOH A1009 "
            pdb=" H2  HOH A1118 "
     model   vdw
     1.445 2.400
  ... (remaining 7538 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

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


                ----------X-ray scattering dictionary----------                

Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   S       2     15.96       2
   O      49      7.97       2
   N      23      6.97       2
   C      95      5.97       2
   H     174      1.00       3
  sf(0) = scattering factor at diffraction angle 0.

The following settings have been auto-set to match refine.mode=refine
and quantum.engine_name=aimnet2:

  restraints                               qm
  cluster.clustering                       False
  refine.minimizer                         lbfgs
  refine.number_of_weight_search_cycles    10
  refine.number_of_refine_cycles           5
  expansion                                True
  use_reduce                               False
  cluster.select_within_radius             7
  refine.max_iterations_weight             100
  refine.max_bond_rmsd                     0.025
  refine.max_angle_rmsd                    2.5
  refine.stop_one_found_first_good_weight  False
  refine.gradient_only                     True

***
To disable auto-custing of parameters use auto_cust=False
***


Setting aimnet2 specific defaults:
  Default Aimnet2 model: aimnet2-qr
Found model file: /net/cci/afonine/.local/lib/python3.9/site-packages/aimnet2calc/assets/aimnet2-qr/aimnet2-qr_b97md4_qzvp_2.jpt
Restraints are from restraints.from_expansion
Found model file: /net/cci/afonine/.local/lib/python3.9/site-packages/aimnet2calc/assets/aimnet2-qr/aimnet2-qr_b97md4_qzvp_2.jpt
Optimize H with d.o.f.
  start: r_work=0.1096 r_free=0.1140
  Monomer Library directory:
    "/net/cci-gpu-00/raid1/scratch1/pavel/phenix-dev-6083/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 343
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 268
          Classifications: {'peptide': 19}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 75
          Classifications: {'water': 25}
          Link IDs: {None: 24}
  Residues with excluded nonbonded symmetry interactions: 21
    residue:
      pdb=" O   HOH A1003 " occ=0.98
      pdb=" H1  HOH A1003 " occ=0.00
      pdb=" H2  HOH A1003 " occ=0.00
    residue:
      pdb=" O   HOH A1004 " occ=0.93
      pdb=" H1  HOH A1004 " occ=0.00
      pdb=" H2  HOH A1004 " occ=0.00
    residue:
      pdb=" O   HOH A1006 " occ=0.52
      pdb=" H1  HOH A1006 " occ=0.00
      pdb=" H2  HOH A1006 " occ=0.00
    residue:
      pdb=" O   HOH A1007 " occ=0.92
      pdb=" H1  HOH A1007 " occ=0.00
      pdb=" H2  HOH A1007 " occ=0.00
    residue:
      pdb=" O   HOH A1008 " occ=0.93
      pdb=" H1  HOH A1008 " occ=0.00
      pdb=" H2  HOH A1008 " occ=0.00
    residue:
      pdb=" O   HOH A1009 " occ=0.51
      pdb=" H1  HOH A1009 " occ=0.00
      pdb=" H2  HOH A1009 " occ=0.00
    residue:
      pdb=" O   HOH A1010 " occ=0.99
      pdb=" H1  HOH A1010 " occ=0.00
      pdb=" H2  HOH A1010 " occ=0.00
    residue:
      pdb=" O   HOH A1011 " occ=0.99
      pdb=" H1  HOH A1011 " occ=0.00
      pdb=" H2  HOH A1011 " occ=0.00
    residue:
      pdb=" O   HOH A1012 " occ=0.41
      pdb=" H1  HOH A1012 " occ=0.00
      pdb=" H2  HOH A1012 " occ=0.00
    residue:
      pdb=" O   HOH A1013 " occ=0.57
      pdb=" H1  HOH A1013 " occ=0.00
      pdb=" H2  HOH A1013 " occ=0.00
    residue:
      pdb=" O   HOH A1016 " occ=0.47
      pdb=" H1  HOH A1016 " occ=0.00
      pdb=" H2  HOH A1016 " occ=0.00
    residue:
      pdb=" O   HOH A1017 " occ=0.81
      pdb=" H1  HOH A1017 " occ=0.00
      pdb=" H2  HOH A1017 " occ=0.00
    ... (remaining 9 not shown)
  Time building chain proxies: 0.11, per 1000 atoms: 0.32
  Number of scatterers: 343
  At special positions: 0
  Unit cell: (19.465, 21.432, 29.523, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O      49      8.00
     N      23      7.00
     C      95      6.00
     H     174      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  19 " distance=2.03
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ASP_CG-ANY_N
      " ASP A   9 " - " GLY A   1 "
  Time building additional restraints: 0.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  32

  Time building geometry restraints manager: 0.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.66 -     0.89: 61
        0.89 -     1.12: 113
        1.12 -     1.36: 45
        1.36 -     1.59: 106
        1.59 -     1.82: 2
  Bond restraints: 327
  Sorted by residual:
  bond pdb=" O   HOH A1014 "
       pdb=" H1  HOH A1014 "
    ideal  model  delta    sigma   weight residual
    0.850  1.070 -0.220 2.00e-02 2.50e+03 1.21e+02
  bond pdb=" O   HOH A1014 "
       pdb=" H2  HOH A1014 "
    ideal  model  delta    sigma   weight residual
    0.850  0.655  0.195 2.00e-02 2.50e+03 9.49e+01
  bond pdb=" O   HOH A1113 "
       pdb=" H2  HOH A1113 "
    ideal  model  delta    sigma   weight residual
    0.850  1.004 -0.154 2.00e-02 2.50e+03 5.92e+01
  bond pdb=" O   HOH A1020 "
       pdb=" H2  HOH A1020 "
    ideal  model  delta    sigma   weight residual
    0.850  0.982 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" O   HOH A1006 "
       pdb=" H2  HOH A1006 "
    ideal  model  delta    sigma   weight residual
    0.850  0.980 -0.130 2.00e-02 2.50e+03 4.22e+01
  ... (remaining 322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 290
        0.99 -     1.98: 157
        1.98 -     2.97: 47
        2.97 -     3.96: 18
        3.96 -     4.95: 15
  Bond angle restraints: 527
  Sorted by residual:
  angle pdb=" CA  ASP A   9 "
        pdb=" CB  ASP A   9 "
        pdb=" CG  ASP A   9 "
      ideal   model   delta    sigma   weight residual
     112.60  116.45   -3.85 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" C   PRO A   7 "
        pdb=" N   SER A   8 "
        pdb=" CA  SER A   8 "
      ideal   model   delta    sigma   weight residual
     121.70  126.65   -4.95 1.80e+00 3.09e-01 7.58e+00
  angle pdb=" CA  THR A  15 "
        pdb=" CB  THR A  15 "
        pdb=" OG1 THR A  15 "
      ideal   model   delta    sigma   weight residual
     109.60  105.54    4.06 1.50e+00 4.44e-01 7.32e+00
  angle pdb=" CA  THR A  15 "
        pdb=" CB  THR A  15 "
        pdb=" CG2 THR A  15 "
      ideal   model   delta    sigma   weight residual
     110.50  114.83   -4.33 1.70e+00 3.46e-01 6.48e+00
  angle pdb=" C   ASP A   9 "
        pdb=" CA  ASP A   9 "
        pdb=" CB  ASP A   9 "
      ideal   model   delta    sigma   weight residual
     110.10  114.51   -4.41 1.90e+00 2.77e-01 5.39e+00
  ... (remaining 522 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.05 -    10.97: 116
       10.97 -    21.89: 18
       21.89 -    32.81: 2
       32.81 -    43.73: 4
       43.73 -    54.65: 4
  Dihedral angle restraints: 144
    sinusoidal: 75
      harmonic: 69
  Sorted by residual:
  dihedral pdb=" C   ILE A  10 "
           pdb=" N   ILE A  10 "
           pdb=" CA  ILE A  10 "
           pdb=" CB  ILE A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.74    8.74     0      2.50e+00 1.60e-01 1.22e+01
  dihedral pdb=" CA  SER A   8 "
           pdb=" C   SER A   8 "
           pdb=" N   ASP A   9 "
           pdb=" CA  ASP A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.90   14.10     0      5.00e+00 4.00e-02 7.95e+00
  dihedral pdb=" C   ASP A   9 "
           pdb=" N   ASP A   9 "
           pdb=" CA  ASP A   9 "
           pdb=" CB  ASP A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.07    6.47     0      2.50e+00 1.60e-01 6.69e+00
  ... (remaining 141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.008 -    0.057: 9
       0.057 -    0.106: 4
       0.106 -    0.155: 2
       0.155 -    0.204: 3
       0.204 -    0.253: 1
  Chirality restraints: 19
  Sorted by residual:
  chirality pdb=" CA  ASP A   9 "
            pdb=" N   ASP A   9 "
            pdb=" C   ASP A   9 "
            pdb=" CB  ASP A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  PRO A   7 "
            pdb=" N   PRO A   7 "
            pdb=" C   PRO A   7 "
            pdb=" CB  PRO A   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.92   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ILE A  10 "
            pdb=" N   ILE A  10 "
            pdb=" C   ILE A  10 "
            pdb=" CB  ILE A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 16 not shown)

  Planarity restraints: 42
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  17 "    0.036 2.00e-02 2.50e+03   3.57e-02 5.11e+01
        pdb=" CG  TRP A  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  17 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  17 "   -0.063 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  17 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  17 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  17 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  17 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  17 "    0.020 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  17 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  17 "    0.009 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  17 "   -0.031 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  17 "   -0.060 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  17 "    0.007 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  17 "    0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A   4 "   -0.011 2.00e-02 2.50e+03   3.27e-02 4.27e+01
        pdb=" CG  TRP A   4 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A   4 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A   4 "   -0.079 2.00e-02 2.50e+03
        pdb=" NE1 TRP A   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A   4 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE3 TRP A   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A   4 "    0.022 2.00e-02 2.50e+03
        pdb=" CH2 TRP A   4 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 TRP A   4 "    0.075 2.00e-02 2.50e+03
        pdb=" HE1 TRP A   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" HE3 TRP A   4 "    0.007 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A   4 "    0.041 2.00e-02 2.50e+03
        pdb=" HH2 TRP A   4 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  13 "   -0.030 2.00e-02 2.50e+03   2.74e-02 3.00e+01
        pdb=" CG  TRP A  13 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  13 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  13 "    0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  13 "    0.047 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  13 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  13 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  13 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  13 "    0.016 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  13 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  13 "   -0.037 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  13 "    0.049 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  13 "    0.019 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  13 "   -0.014 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  13 "    0.025 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  13 "   -0.038 2.00e-02 2.50e+03
  ... (remaining 39 not shown)

  Histogram of nonbonded interaction distances:
        0.77 -     1.53: 16
        1.53 -     2.30: 186
        2.30 -     3.07: 1253
        3.07 -     3.83: 2249
        3.83 -     4.60: 3839
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 7543
  Sorted by model distance:
  nonbonded pdb=" O   HOH A1012 "
            pdb=" O   HOH A1112 "
     model   vdw
     0.768 2.800
  nonbonded pdb=" O   HOH A1006 "
            pdb=" O   HOH A1106 "
     model   vdw
     0.823 2.800
  nonbonded pdb=" O   HOH A1007 "
            pdb=" O   HOH A1016 "
     model   vdw
     1.321 2.800
  nonbonded pdb=" H1  HOH A1012 "
            pdb=" O   HOH A1112 "
     model   vdw
     1.433 2.450
  nonbonded pdb=" O   HOH A1009 "
            pdb=" H2  HOH A1118 "
     model   vdw
     1.445 2.450
  ... (remaining 7538 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  final: r_work=0.1007 r_free=0.1053
Start:
   Rw: 0.1007 Rf: 0.1053 Rf-Rw: 0.0045 bond: 0.012 angle: 1.76 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.26 cb: 0.00 shift start/prev: 0.047 0.047 
Optimal weight search:
Data weight (initial): 2115.3107393024
0: Rw: 0.1002 Rf: 0.1058 Rf-Rw: 0.0056 bond: 0.016 angle: 1.92 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.40 cb: 0.00 shift start/prev: 0.100 0.070 rws:  1.000 n_fev: 54
0: Rw: 0.1002 Rf: 0.1058 Rf-Rw: 0.0056 bond: 0.016 angle: 1.92 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.40 cb: 0.00 shift start/prev: 0.100 0.070 rws:  0.667 n_fev: 0 (NEXT)
1: Rw: 0.1004 Rf: 0.1049 Rf-Rw: 0.0044 bond: 0.018 angle: 1.91 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.34 cb: 0.00 shift start/prev: 0.067 0.042 rws:  0.667 n_fev: 32
1: Rw: 0.1004 Rf: 0.1049 Rf-Rw: 0.0044 bond: 0.018 angle: 1.91 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.34 cb: 0.00 shift start/prev: 0.067 0.042 rws:  0.444 n_fev: 0 (NEXT)
2: Rw: 0.1002 Rf: 0.1050 Rf-Rw: 0.0048 bond: 0.020 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.39 cb: 0.00 shift start/prev: 0.065 0.006 rws:  0.444 n_fev: 37
2: Rw: 0.1002 Rf: 0.1050 Rf-Rw: 0.0048 bond: 0.020 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.39 cb: 0.00 shift start/prev: 0.065 0.006 rws:  0.296 n_fev: 0 (NEXT)
3: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0055 bond: 0.018 angle: 1.98 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.081 0.025 rws:  0.296 n_fev: 70
3: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0055 bond: 0.018 angle: 1.98 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.081 0.025 rws:  0.198 n_fev: 0 (NEXT)
4: Rw: 0.0997 Rf: 0.1048 Rf-Rw: 0.0051 bond: 0.017 angle: 1.92 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.38 cb: 0.00 shift start/prev: 0.051 0.043 rws:  0.198 n_fev: 29
4: Rw: 0.0997 Rf: 0.1048 Rf-Rw: 0.0051 bond: 0.017 angle: 1.92 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.38 cb: 0.00 shift start/prev: 0.051 0.043 rws:  0.132 n_fev: 0 (NEXT)
5: Rw: 0.0994 Rf: 0.1043 Rf-Rw: 0.0049 bond: 0.019 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.057 0.012 rws:  0.132 n_fev: 49
5: Rw: 0.0994 Rf: 0.1043 Rf-Rw: 0.0049 bond: 0.019 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.057 0.012 rws:  0.088 n_fev: 0 (NEXT)
6: Rw: 0.0994 Rf: 0.1041 Rf-Rw: 0.0048 bond: 0.018 angle: 1.96 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.005 rws:  0.088 n_fev: 56
6: Rw: 0.0994 Rf: 0.1041 Rf-Rw: 0.0048 bond: 0.018 angle: 1.96 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.005 rws:  0.059 n_fev: 0 (NEXT)
7: Rw: 0.0993 Rf: 0.1044 Rf-Rw: 0.0050 bond: 0.018 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.053 0.005 rws:  0.059 n_fev: 51
7: Rw: 0.0993 Rf: 0.1044 Rf-Rw: 0.0050 bond: 0.018 angle: 1.99 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.053 0.005 rws:  0.039 n_fev: 0 (NEXT)
8: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0053 bond: 0.017 angle: 1.94 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.050 0.006 rws:  0.039 n_fev: 25
8: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0053 bond: 0.017 angle: 1.94 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.050 0.006 rws:  0.026 n_fev: 0 (NEXT)
9: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0054 bond: 0.017 angle: 1.94 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.050 0.000 rws:  0.026 n_fev: 26
9: Rw: 0.0996 Rf: 0.1050 Rf-Rw: 0.0054 bond: 0.017 angle: 1.94 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.42 cb: 0.00 shift start/prev: 0.050 0.000 rws:  0.017 n_fev: 0 (NEXT)
Bond rmsd stalled. Stopping weight search.
Best Rfree from above: 0.1041
Best restraints scale: 0.088
Best Rwork, Rfree (at refinement start): 0.0994 0.1041
At refinement start
 Rw: 0.0994 Rf: 0.1041 Rf-Rw: 0.0048 bond: 0.018 angle: 1.96 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.011 
Refinement:
0: Rw: 0.0992 Rf: 0.1041 Rf-Rw: 0.0049 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.001 rws:  0.088 n_fev: 22
1: Rw: 0.0993 Rf: 0.1042 Rf-Rw: 0.0050 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.40 cb: 0.00 shift start/prev: 0.055 0.001 rws:  0.088 n_fev: 26
2: Rw: 0.0992 Rf: 0.1042 Rf-Rw: 0.0049 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.001 rws:  0.088 n_fev: 23
3: Rw: 0.0993 Rf: 0.1042 Rf-Rw: 0.0050 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.001 rws:  0.088 n_fev: 24
4: Rw: 0.0992 Rf: 0.1042 Rf-Rw: 0.0049 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.001 rws:  0.088 n_fev: 25
At refinement end:
 Rw: 0.0992 Rf: 0.1042 Rf-Rw: 0.0049 bond: 0.018 angle: 1.97 clash: 3.7 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.41 cb: 0.00 shift start/prev: 0.055 0.001 
Best Rwork, Rfree (after refinement): 0.0992 0.1042
See iam2_001_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 35629.21 seconds
wall clock time: 11 minutes 39.81 seconds (699.81 seconds total)
