Starting qr.refine
on Mon May 20 18:28:09 2024 by afonine
===============================================================================

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

  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1m10.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/1m10.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1m10.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 PHE  603": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  130": "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: 7468
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 3250
          Classifications: {'peptide': 199}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 189}
    Chain: "B"
      Number of atoms: 4218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 4218
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 246}
  Time building chain proxies: 0.89, per 1000 atoms: 0.12
  Number of scatterers: 7468
  At special positions: 0
  Unit cell: (89.84, 89.84, 124.63, 90, 90, 120)
  Space group: P 61 (No. 169)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     O     682      8.00
     N     628      7.00
     C    2366      6.00
     H    3778      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 509 " - pdb=" SG  CYS A 695 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  17 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 209 " - pdb=" SG  CYS B 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 211 " - pdb=" SG  CYS B 264 " 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: 1.45
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  886

  Time building geometry restraints manager: 1.69 seconds

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

  Histogram of bond lengths:
        0.98 -     1.15: 3777
        1.15 -     1.31: 613
        1.31 -     1.48: 1435
        1.48 -     1.65: 1700
        1.65 -     1.82: 19
  Bond restraints: 7544
  Sorted by residual:
  bond pdb=" C   LYS B  19 "
       pdb=" N   ARG B  20 "
    ideal  model  delta    sigma   weight residual
    1.329  1.342 -0.013 1.40e-02 5.10e+03 8.49e-01
  bond pdb=" C   LEU B  92 "
       pdb=" N   PRO B  93 "
    ideal  model  delta    sigma   weight residual
    1.341  1.330  0.011 1.60e-02 3.91e+03 5.05e-01
  bond pdb=" C   ASN B 205 "
       pdb=" O   ASN B 205 "
    ideal  model  delta    sigma   weight residual
    1.231  1.245 -0.014 2.00e-02 2.50e+03 4.68e-01
  bond pdb=" C   LEU B 115 "
       pdb=" N   PRO B 116 "
    ideal  model  delta    sigma   weight residual
    1.341  1.330  0.011 1.60e-02 3.91e+03 4.64e-01
  bond pdb=" C   LEU B 139 "
       pdb=" N   PRO B 140 "
    ideal  model  delta    sigma   weight residual
    1.341  1.331  0.010 1.60e-02 3.91e+03 4.26e-01
  ... (remaining 7539 not shown)

  Histogram of bond angle deviations from ideal:
      100.73 -   107.40: 336
      107.40 -   114.06: 9315
      114.06 -   120.73: 2267
      120.73 -   127.40: 1775
      127.40 -   134.06: 43
  Bond angle restraints: 13736
  Sorted by residual:
  angle pdb=" C   ALA B  10 "
        pdb=" CA  ALA B  10 "
        pdb=" CB  ALA B  10 "
      ideal   model   delta    sigma   weight residual
     110.50  115.92   -5.42 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" CA  MET B  52 "
        pdb=" C   MET B  52 "
        pdb=" N   PRO B  53 "
      ideal   model   delta    sigma   weight residual
     116.90  121.55   -4.65 1.50e+00 4.44e-01 9.62e+00
  angle pdb=" CA  TYR A 508 "
        pdb=" CB  TYR A 508 "
        pdb=" CG  TYR A 508 "
      ideal   model   delta    sigma   weight residual
     113.90  118.76   -4.86 1.80e+00 3.09e-01 7.30e+00
  angle pdb=" CA  LEU B 115 "
        pdb=" C   LEU B 115 "
        pdb=" N   PRO B 116 "
      ideal   model   delta    sigma   weight residual
     116.90  120.10   -3.20 1.50e+00 4.44e-01 4.56e+00
  angle pdb=" CA  ALA B  10 "
        pdb=" C   ALA B  10 "
        pdb=" N   SER B  11 "
      ideal   model   delta    sigma   weight residual
     116.20  120.07   -3.87 2.00e+00 2.50e-01 3.74e+00
  ... (remaining 13731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 3220
       16.16 -    32.33: 225
       32.33 -    48.49: 71
       48.49 -    64.66: 22
       64.66 -    80.82: 3
  Dihedral angle restraints: 3541
    sinusoidal: 1982
      harmonic: 1559
  Sorted by residual:
  dihedral pdb=" CA  HIS A 559 "
           pdb=" C   HIS A 559 "
           pdb=" N   ASP A 560 "
           pdb=" CA  ASP A 560 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.49   17.51     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  PRO B  77 "
           pdb=" C   PRO B  77 "
           pdb=" N   VAL B  78 "
           pdb=" CA  VAL B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.85  -17.15     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ARG A 545 "
           pdb=" CB  ARG A 545 "
           pdb=" CG  ARG A 545 "
           pdb=" CD  ARG A 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.25   58.25     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 3538 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 357
       0.028 -    0.055: 162
       0.055 -    0.083: 35
       0.083 -    0.110: 24
       0.110 -    0.137: 18
  Chirality restraints: 596
  Sorted by residual:
  chirality pdb=" CA  VAL B 239 "
            pdb=" N   VAL B 239 "
            pdb=" C   VAL B 239 "
            pdb=" CB  VAL B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  ILE A 647 "
            pdb=" N   ILE A 647 "
            pdb=" C   ILE A 647 "
            pdb=" CB  ILE A 647 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  VAL A 556 "
            pdb=" N   VAL A 556 "
            pdb=" C   VAL A 556 "
            pdb=" CB  VAL A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 593 not shown)

  Planarity restraints: 1091
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  25 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.27e+00
        pdb=" N   PRO B  26 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B  26 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  26 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 140 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.49e+00
        pdb=" N   PRO B 141 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 141 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 141 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  26 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO B  27 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B  27 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  27 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1088 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 661
        2.16 -     2.77: 14384
        2.77 -     3.38: 21876
        3.38 -     3.99: 30213
        3.99 -     4.60: 44740
  Nonbonded interactions: 111874
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 550 "
            pdb="HH22 ARG A 611 "
     model   vdw
     1.554 1.800
  nonbonded pdb=" O   GLN B 127 "
            pdb=" H   GLU B 151 "
     model   vdw
     1.562 1.800
  nonbonded pdb=" OE1 GLN B 180 "
            pdb=" H   GLN B 180 "
     model   vdw
     1.563 1.800
  nonbonded pdb=" OE1 GLN A 548 "
            pdb=" HE  ARG A 571 "
     model   vdw
     1.572 1.800
  nonbonded pdb=" HG  SER B  39 "
            pdb=" OD1 ASP B  63 "
     model   vdw
     1.582 1.800
  ... (remaining 111869 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      14     15.96       2
   O     682      7.97       2
   N     628      6.97       2
   C    2366      5.97       2
   H    3778      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: 0.003 angle: 0.98 clash: 3.5 rota: 2.40 rama: f: 89.39 o: 1.73 Z: -3.48 cb: 0.00 shift start/prev: 0.000 0.000 
LBFGS: function start/end, n_calls: -1265.426625 -1365.309976 101
cycle 0:   bond: 0.009 angle: 1.56 clash: 0.1 rota: 0.96 rama: f: 94.81 o: 0.43 Z: -1.80 cb: 0.00 shift start/prev: 0.213 0.213 
LBFGS: function start/end, n_calls: -1365.309976 -1371.880475 102
cycle 1:   bond: 0.009 angle: 1.52 clash: 0.3 rota: 0.72 rama: f: 95.67 o: 0.43 Z: -1.68 cb: 0.00 shift start/prev: 0.277 0.107 
LBFGS: function start/end, n_calls: -1371.880475 -1375.127687 102
cycle 2:   bond: 0.009 angle: 1.54 clash: 0.1 rota: 0.72 rama: f: 95.89 o: 0.43 Z: -1.65 cb: 0.23 shift start/prev: 0.333 0.091 
calculator(opt), total_time (target_and_gradients) 79.94189214706421
calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305
See 1m10_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 284.11 seconds
wall clock time: 4 minutes 50.93 seconds (290.93 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)