Starting qr.refine
on Mon May 20 18:33:03 2024 by afonine
===============================================================================

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

  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2etc.pdb

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

  Adding command-line PHIL:
  -------------------------
    mode=opt
    restraints=qm
    engine=aimnet2
    clustering=false
    minimizer=lbfgs
    gradient_only=true
    use_reduce=False
    select_within_radius=7
    number_of_micro_cycles=3
    max_iterations_refine=100

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2etc.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2etc.pdb"
  }
  use_reduce = False
  cluster {
    clustering = false
    select_within_radius = 7
  }
  quantum {
    engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \
                  gaussian xtb server
  }
  refine {
    mode = *opt refine gtest
    number_of_micro_cycles = 3
    max_iterations_refine = 100
    gradient_only = true
  }


Starting job
===============================================================================
Validate inputs:
-------------------------------------------------------------------------------
Refinement start
****************
max_atoms = 50000
debug_rss = False
debug = False
scattering_table = wk1995 it1992 *n_gaussian electron neutron
use_reduce = False
cluster {
  charge_cutoff = 8
  clustering = False
  charge_embedding = False
  two_buffers = False
  maxnum_residues_in_cluster = 15
  bcc_threshold = 9
  select_within_radius = 7
  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 *aimnet2 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 = 3
  data_weight = None
  skip_weight_search = False
  adjust_restraints_weight_scale_value = 2
  max_iterations_weight = 50
  max_iterations_refine = 100
  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
}
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
****************

  Symmetric amino acids flipped
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib"
  Total number of atoms: 7817
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 3938
          Classifications: {'peptide': 252}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240}
    Chain: "B"
      Number of atoms: 3879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 3879
          Inner-chain residues flagged as termini: ['pdbres="LYS B 201 "', 'pdbres="GLY B 204 "']
          Classifications: {'peptide': 248}
          Modifications used: {'COO': 2, 'NH3': 2}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 235}
          Chain breaks: 1
  Time building chain proxies: 0.92, per 1000 atoms: 0.12
  Number of scatterers: 7817
  At special positions: 0
  Unit cell: (39.514, 95.862, 164.504, 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      26     16.00
     O     742      8.00
     N     678      7.00
     C    2473      6.00
     H    3898      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 195 " - pdb=" SG  CYS B 206 " 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  - 3.50
        Amino acid           : False - 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
  Time building additional restraints: 1.51
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  936

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        0.98 -     1.14: 3886
        1.14 -     1.31: 685
        1.31 -     1.48: 1541
        1.48 -     1.65: 1745
        1.65 -     1.81: 36
  Bond restraints: 7893
  Sorted by residual:
  bond pdb=" CB  PRO A  72 "
       pdb=" CG  PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.492  1.551 -0.059 5.00e-02 4.00e+02 1.40e+00
  bond pdb=" C   GLU B 211 "
       pdb=" N   LEU B 212 "
    ideal  model  delta    sigma   weight residual
    1.329  1.344 -0.015 1.40e-02 5.10e+03 1.17e+00
  bond pdb=" CA  GLU B  71 "
       pdb=" C   GLU B  71 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.10e-02 2.27e+03 6.93e-01
  bond pdb=" N   GLY B 117 "
       pdb=" CA  GLY B 117 "
    ideal  model  delta    sigma   weight residual
    1.451  1.439  0.012 1.60e-02 3.91e+03 5.22e-01
  bond pdb=" C   MET B 137 "
       pdb=" O   MET B 137 "
    ideal  model  delta    sigma   weight residual
    1.231  1.245 -0.014 2.00e-02 2.50e+03 4.86e-01
  ... (remaining 7888 not shown)

  Histogram of bond angle deviations from ideal:
      100.41 -   107.13: 195
      107.13 -   113.84: 9477
      113.84 -   120.56: 2543
      120.56 -   127.27: 2027
      127.27 -   133.99: 47
  Bond angle restraints: 14289
  Sorted by residual:
  angle pdb=" C   SER A 115 "
        pdb=" N   THR A 116 "
        pdb=" CA  THR A 116 "
      ideal   model   delta    sigma   weight residual
     121.70  127.70   -6.00 1.80e+00 3.09e-01 1.11e+01
  angle pdb=" CA  MET B 137 "
        pdb=" C   MET B 137 "
        pdb=" N   PRO B 138 "
      ideal   model   delta    sigma   weight residual
     116.90  121.35   -4.45 1.50e+00 4.44e-01 8.82e+00
  angle pdb=" CA  MET A 137 "
        pdb=" C   MET A 137 "
        pdb=" N   PRO A 138 "
      ideal   model   delta    sigma   weight residual
     116.90  120.79   -3.89 1.50e+00 4.44e-01 6.74e+00
  angle pdb=" C   ASP B 258 "
        pdb=" N   ASN B 259 "
        pdb=" CA  ASN B 259 "
      ideal   model   delta    sigma   weight residual
     121.70  125.91   -4.21 1.80e+00 3.09e-01 5.48e+00
  angle pdb=" CA  GLU B  71 "
        pdb=" C   GLU B  71 "
        pdb=" N   PRO B  72 "
      ideal   model   delta    sigma   weight residual
     116.90  120.34   -3.44 1.50e+00 4.44e-01 5.26e+00
  ... (remaining 14284 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 3406
       17.71 -    35.42: 204
       35.42 -    53.12: 70
       53.12 -    70.83: 24
       70.83 -    88.54: 6
  Dihedral angle restraints: 3710
    sinusoidal: 2042
      harmonic: 1668
  Sorted by residual:
  dihedral pdb=" CA  ALA A 257 "
           pdb=" C   ALA A 257 "
           pdb=" N   ASP A 258 "
           pdb=" CA  ASP A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.54   18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CB  ARG B 197 "
           pdb=" CG  ARG B 197 "
           pdb=" CD  ARG B 197 "
           pdb=" NE  ARG B 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.03  -58.03     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   LYS B 144 "
           pdb=" CA  LYS B 144 "
           pdb=" CB  LYS B 144 "
           pdb=" CG  LYS B 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.02  -53.98     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 3707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 350
       0.024 -    0.048: 158
       0.048 -    0.073: 67
       0.073 -    0.097: 33
       0.097 -    0.121: 6
  Chirality restraints: 614
  Sorted by residual:
  chirality pdb=" CA  PRO B 261 "
            pdb=" N   PRO B 261 "
            pdb=" C   PRO B 261 "
            pdb=" CB  PRO B 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  VAL A  88 "
            pdb=" N   VAL A  88 "
            pdb=" C   VAL A  88 "
            pdb=" CB  VAL A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.25e-01
  chirality pdb=" CA  PRO B  89 "
            pdb=" N   PRO B  89 "
            pdb=" C   PRO B  89 "
            pdb=" CB  PRO B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.11e-01
  ... (remaining 611 not shown)

  Planarity restraints: 1182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  71 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.80e+00
        pdb=" N   PRO A  72 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 137 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.76e+00
        pdb=" N   PRO A 138 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 138 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 138 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 137 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO B 138 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 138 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 138 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1179 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 711
        2.16 -     2.77: 14617
        2.77 -     3.38: 23226
        3.38 -     3.99: 31103
        3.99 -     4.60: 46120
  Nonbonded interactions: 115777
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B  97 "
            pdb=" H   GLU B  97 "
     model   vdw
     1.552 1.800
  nonbonded pdb=" H   ASP B 159 "
            pdb=" O   TYR B 162 "
     model   vdw
     1.562 1.800
  nonbonded pdb=" OD1 ASP B 258 "
            pdb=" HG  SER B 260 "
     model   vdw
     1.579 1.800
  nonbonded pdb=" OD1 ASP A 159 "
            pdb=" H   TYR A 162 "
     model   vdw
     1.583 1.800
  nonbonded pdb=" OD1 ASN B 133 "
            pdb=" H   CYS B 135 "
     model   vdw
     1.601 1.800
  ... (remaining 115772 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      26     15.96       2
   O     742      7.97       2
   N     678      6.97       2
   C    2473      5.97       2
   H    3898      1.00       3
  sf(0) = scattering factor at diffraction angle 0.
 Setting QM defaults
  Setting QM method to HF
  Setting QM basis to 6-31g

start:  bond: 0.004 angle: 0.98 clash: 2.2 rota: 4.86 rama: f: 94.53 o: 1.01 Z: -1.25 cb: 0.00 shift start/prev: 0.000 0.000 
LBFGS: function start/end, n_calls: -1294.364496 -1397.171914 101
cycle 0:   bond: 0.009 angle: 1.58 clash: 0.1 rota: 3.70 rama: f: 95.75 o: 0.40 Z: -1.87 cb: 0.85 shift start/prev: 0.204 0.204 
LBFGS: function start/end, n_calls: -1397.171914 -1402.977801 102
cycle 1:   bond: 0.009 angle: 1.55 clash: 0.4 rota: 3.47 rama: f: 95.95 o: 0.40 Z: -1.95 cb: 0.43 shift start/prev: 0.272 0.111 
LBFGS: function start/end, n_calls: -1402.977801 -1406.005094 102
cycle 2:   bond: 0.009 angle: 1.57 clash: 0.4 rota: 3.01 rama: f: 95.95 o: 0.40 Z: -2.04 cb: 0.64 shift start/prev: 0.318 0.079 
calculator(opt), total_time (target_and_gradients) 78.52548885345459
calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305
See 2etc_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 268.17 seconds
wall clock time: 4 minutes 35.00 seconds (275.00 seconds total)
/net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  if LooseVersion(np.__version__) < '1.9':
/net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  other = LooseVersion(other)