Starting qr.refine
on Fri Jun 21 15:01:22 2024 by afonine
===============================================================================

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

  Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6DKZ.mtz
  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/6DKZ.pdb

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

  Adding command-line PHIL:
  -------------------------
    mode=refine
    restraints=qm
    engine=aimnet2
    clustering=false
    minimizer=lbfgs
    number_of_weight_search_cycles=10
    number_of_refine_cycles=5
    expansion=true
    use_reduce=False
    select_within_radius=7
    max_iterations_weight=100
    max_bond_rmsd=0.03
    max_angle_rmsd=3.0
    gradient_only=True

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    miller_array {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6DKZ.mtz"
    }
    default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6DKZ.mtz"
    model {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/6DKZ.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/6DKZ.pdb"
  }
  use_reduce = False
  cluster {
    clustering = false
    select_within_radius = 7
  }
  expansion = true
  quantum {
    engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \
                  gaussian xtb server
  }
  refine {
    number_of_weight_search_cycles = 10
    max_iterations_weight = 100
    gradient_only = True
    max_angle_rmsd = 3.0
  }


Starting job
===============================================================================
Validate inputs:
-------------------------------------------------------------------------------
Refinement start
****************
-------------------------------------------------------------------------------
Extracting fmodel
*****************
                   start: r(all,work,free)=0.1870 0.1868 0.1893 n_refl.: 5296
       re-set all scales: r(all,work,free)=0.1870 0.1868 0.1893 n_refl.: 5296
         remove outliers: r(all,work,free)=0.1870 0.1868 0.1893 n_refl.: 5296
bulk-solvent and scaling: r(all,work,free)=0.1732 0.1727 0.1772 n_refl.: 5296
         remove outliers: r(all,work,free)=0.1717 0.1712 0.1761 n_refl.: 5291
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 11.473-3.457    74.62    85    12 0.3373    49.076    45.422 0.927 1.004 0.165
  3.422-2.852    98.04    93     7 0.1509    57.186    56.275 0.975 1.006 0.000
  2.845-2.368    99.42   156    15 0.1629    47.703    46.741 0.998 1.005 0.000
  2.365-1.967    99.36   280    29 0.1933    40.954    39.923 1.030 1.006 0.000
  1.967-1.635    98.49   463    58 0.1885    28.963    28.550 1.026 1.005 0.000
  1.635-1.360    97.27   805    87 0.1694    22.011    21.731 1.032 1.006 0.000
  1.359-1.131    95.05  1385   151 0.1529    18.821    18.553 1.011 1.006 0.000
  1.130-0.990    90.64  1504   161 0.1476    14.304    14.338 0.989 1.011 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0286   b_overall=0.1044  
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.1712 r_free=0.1761
-------------------------------------------------------------------------------
Setting refinement target
*************************
ml
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 = True
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 = 10
  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 = 100
  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 = 3
  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
    None
  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: 126
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 120
          Classifications: {'peptide': 8}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'TRANS': 7}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 0.04, per 1000 atoms: 0.32
  Number of scatterers: 126
  At special positions: 0
  Unit cell: (14.061, 19.862, 18.632, 90, 91.699, 90)
  Space group: P 1 21/n 1 (No. 14)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O      11      8.00
     N       8      7.00
     C      37      6.00
     H      70      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=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
  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: 0.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  12

  Time building geometry restraints manager: 0.04 seconds

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

  Histogram of bond lengths:
        0.84 -     0.98: 70
        0.98 -     1.13: 0
        1.13 -     1.27: 8
        1.27 -     1.41: 7
        1.41 -     1.55: 38
  Bond restraints: 123
  Sorted by residual:
  bond pdb=" N   LEU A   4 "
       pdb=" H   LEU A   4 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.47e+01
  bond pdb=" N   LEU A   7 "
       pdb=" H   LEU A   7 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.46e+01
  bond pdb=" N   ILE A   3 "
       pdb=" H   ILE A   3 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.41e+01
  bond pdb=" N   ILE A   2 "
       pdb=" H   ILE A   2 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" N   GLY A   8 "
       pdb=" H   GLY A   8 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.39e+01
  ... (remaining 118 not shown)

  Histogram of bond angle deviations from ideal:
      103.84 -   108.10: 37
      108.10 -   112.36: 127
      112.36 -   116.62: 22
      116.62 -   120.88: 13
      120.88 -   125.14: 22
  Bond angle restraints: 221
  Sorted by residual:
  angle pdb=" C   LEU A   4 "
        pdb=" CA  LEU A   4 "
        pdb=" CB  LEU A   4 "
      ideal   model   delta    sigma   weight residual
     110.10  107.11    2.99 1.90e+00 2.77e-01 2.48e+00
  angle pdb=" C   LEU A   7 "
        pdb=" CA  LEU A   7 "
        pdb=" CB  LEU A   7 "
      ideal   model   delta    sigma   weight residual
     110.10  113.00   -2.90 1.90e+00 2.77e-01 2.33e+00
  angle pdb=" N   ILE A   6 "
        pdb=" CA  ILE A   6 "
        pdb=" C   ILE A   6 "
      ideal   model   delta    sigma   weight residual
     111.00  106.89    4.11 2.80e+00 1.28e-01 2.16e+00
  angle pdb=" N   ILE A   2 "
        pdb=" CA  ILE A   2 "
        pdb=" CB  ILE A   2 "
      ideal   model   delta    sigma   weight residual
     111.50  109.37    2.13 1.70e+00 3.46e-01 1.57e+00
  angle pdb=" N   LEU A   4 "
        pdb=" CA  LEU A   4 "
        pdb=" HA  LEU A   4 "
      ideal   model   delta    sigma   weight residual
     110.00  106.25    3.75 3.00e+00 1.11e-01 1.56e+00
  ... (remaining 216 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.12 -     7.40: 38
        7.40 -    14.68: 7
       14.68 -    21.96: 2
       21.96 -    29.23: 1
       29.23 -    36.51: 2
  Dihedral angle restraints: 50
    sinusoidal: 31
      harmonic: 19
  Sorted by residual:
  dihedral pdb=" N   ILE A   6 "
           pdb=" CA  ILE A   6 "
           pdb=" CB  ILE A   6 "
           pdb=" CG1 ILE A   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -151.98  -28.02     3      1.50e+01 4.44e-03 4.25e+00
  dihedral pdb=" C   LEU A   7 "
           pdb=" N   LEU A   7 "
           pdb=" CA  LEU A   7 "
           pdb=" CB  LEU A   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -127.68    5.08     0      2.50e+00 1.60e-01 4.13e+00
  dihedral pdb=" CA  LEU A   4 "
           pdb=" C   LEU A   4 "
           pdb=" N   GLY A   5 "
           pdb=" CA  GLY A   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -171.23   -8.77     0      5.00e+00 4.00e-02 3.08e+00
  ... (remaining 47 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 5
       0.038 -    0.075: 3
       0.075 -    0.113: 1
       0.113 -    0.150: 0
       0.150 -    0.188: 2
  Chirality restraints: 11
  Sorted by residual:
  chirality pdb=" CA  ILE A   6 "
            pdb=" N   ILE A   6 "
            pdb=" C   ILE A   6 "
            pdb=" CB  ILE A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.81e-01
  chirality pdb=" CA  LEU A   7 "
            pdb=" N   LEU A   7 "
            pdb=" C   LEU A   7 "
            pdb=" CB  LEU A   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CB  ILE A   6 "
            pdb=" CA  ILE A   6 "
            pdb=" CG1 ILE A   6 "
            pdb=" CG2 ILE A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.55    0.09 2.00e-01 2.50e+01 2.05e-01
  ... (remaining 8 not shown)

  Planarity restraints: 14
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A   4 "    0.005 2.00e-02 2.50e+03   9.79e-03 9.57e-01
        pdb=" C   LEU A   4 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   LEU A   4 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLY A   5 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A   7 "    0.002 2.00e-02 2.50e+03   4.27e-03 1.82e-01
        pdb=" C   LEU A   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O   LEU A   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N   GLY A   8 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A   1 "   -0.002 2.00e-02 2.50e+03   4.18e-03 1.75e-01
        pdb=" C   SER A   1 "    0.007 2.00e-02 2.50e+03
        pdb=" O   SER A   1 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   ILE A   2 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 11 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     1.98: 7
        1.98 -     2.59: 143
        2.59 -     3.19: 506
        3.19 -     3.80: 610
        3.80 -     4.40: 1043
  Nonbonded interactions: 2309
  Sorted by model distance:
  nonbonded pdb=" N   SER A   1 "
            pdb=" C   GLY A   8 "
     model   vdw
     1.377 3.250
  nonbonded pdb=" HG  SER A   1 "
            pdb=" O   HOH A 101 "
     model   vdw
     1.902 1.800
  nonbonded pdb=" H1  HOH A 101 "
            pdb=" O   GLY A   8 "
     model   vdw sym.op.
     1.912 1.800 -x+1,-y+2,-z+1
  nonbonded pdb=" O   GLY A   8 "
            pdb=" H1  HOH A 101 "
     model   vdw sym.op.
     1.912 1.800 -x+1,-y+2,-z+1
  nonbonded pdb=" H3  SER A   1 "
            pdb=" O   ILE A   6 "
     model   vdw
     1.962 1.800
  ... (remaining 2304 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: 4
  Type Number    sf(0)   Gaussians
   O      11      7.97       2
   N       8      6.97       2
   C      37      5.97       2
   H      70      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:
   Rw: 0.1712 Rf: 0.1761 Rf-Rw: 0.0049 bond: 0.006 angle: 1.33 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.50 cb: 0.00 shift start/prev: 0.000 0.000 
Optimal weight search:
Data weight (initial): 312.50466098430195
r_work: 0.17120 shift mean:   0.000 shift max:   0.000 1
r_work: 0.27964 shift mean:   0.070 shift max:   0.200 2
r_work: 0.27964 shift mean:   0.000 shift max:   0.000 3
r_work: 0.25022 shift mean:   0.011 shift max:   0.033 4
r_work: 0.21788 shift mean:   0.013 shift max:   0.046 5
r_work: 0.20217 shift mean:   0.007 shift max:   0.024 6
r_work: 0.19207 shift mean:   0.004 shift max:   0.015 7
r_work: 0.18439 shift mean:   0.003 shift max:   0.014 8
r_work: 0.17922 shift mean:   0.002 shift max:   0.012 9
r_work: 0.17571 shift mean:   0.002 shift max:   0.011 10
r_work: 0.17336 shift mean:   0.002 shift max:   0.010 11
r_work: 0.17169 shift mean:   0.002 shift max:   0.009 12
r_work: 0.17061 shift mean:   0.002 shift max:   0.008 13
r_work: 0.16978 shift mean:   0.002 shift max:   0.007 14
r_work: 0.16928 shift mean:   0.002 shift max:   0.006 15
r_work: 0.16897 shift mean:   0.002 shift max:   0.006 16
r_work: 0.16881 shift mean:   0.002 shift max:   0.005 17
r_work: 0.16871 shift mean:   0.003 shift max:   0.006 18
r_work: 0.16865 shift mean:   0.003 shift max:   0.006 19
r_work: 0.16867 shift mean:   0.004 shift max:   0.008 20
r_work: 0.16869 shift mean:   0.005 shift max:   0.011 21
r_work: 0.16873 shift mean:   0.005 shift max:   0.011 22
r_work: 0.16877 shift mean:   0.005 shift max:   0.010 23
r_work: 0.16873 shift mean:   0.004 shift max:   0.009 24
r_work: 0.16876 shift mean:   0.003 shift max:   0.006 25
r_work: 0.16880 shift mean:   0.003 shift max:   0.005 26
r_work: 0.16880 shift mean:   0.002 shift max:   0.004 27
r_work: 0.16886 shift mean:   0.002 shift max:   0.004 28
r_work: 0.16889 shift mean:   0.001 shift max:   0.003 29
r_work: 0.16892 shift mean:   0.001 shift max:   0.003 30
r_work: 0.16897 shift mean:   0.001 shift max:   0.002 31
r_work: 0.16896 shift mean:   0.001 shift max:   0.002 32
r_work: 0.16897 shift mean:   0.001 shift max:   0.002 33
r_work: 0.16900 shift mean:   0.001 shift max:   0.002 34
r_work: 0.16899 shift mean:   0.001 shift max:   0.002 35
r_work: 0.16899 shift mean:   0.001 shift max:   0.002 36
r_work: 0.16900 shift mean:   0.001 shift max:   0.003 37
r_work: 0.16901 shift mean:   0.001 shift max:   0.003 38
r_work: 0.16899 shift mean:   0.001 shift max:   0.005 39
r_work: 0.16900 shift mean:   0.001 shift max:   0.004 40
r_work: 0.16896 shift mean:   0.001 shift max:   0.005 41
r_work: 0.16894 shift mean:   0.001 shift max:   0.006 42
r_work: 0.16891 shift mean:   0.001 shift max:   0.006 43
r_work: 0.16888 shift mean:   0.002 shift max:   0.008 44
r_work: 0.16883 shift mean:   0.001 shift max:   0.006 45
r_work: 0.16883 shift mean:   0.002 shift max:   0.008 46
r_work: 0.16879 shift mean:   0.001 shift max:   0.007 47
r_work: 0.16872 shift mean:   0.002 shift max:   0.009 48
r_work: 0.16865 shift mean:   0.001 shift max:   0.007 49
r_work: 0.16863 shift mean:   0.001 shift max:   0.006 50
r_work: 0.16858 shift mean:   0.001 shift max:   0.007 51
r_work: 0.16854 shift mean:   0.001 shift max:   0.006 52
r_work: 0.16850 shift mean:   0.001 shift max:   0.006 53
r_work: 0.16846 shift mean:   0.001 shift max:   0.006 54
r_work: 0.16845 shift mean:   0.001 shift max:   0.005 55
r_work: 0.16842 shift mean:   0.001 shift max:   0.005 56
r_work: 0.16839 shift mean:   0.001 shift max:   0.004 57
r_work: 0.16839 shift mean:   0.001 shift max:   0.004 58
r_work: 0.16835 shift mean:   0.001 shift max:   0.004 59
r_work: 0.16836 shift mean:   0.001 shift max:   0.003 60
r_work: 0.16838 shift mean:   0.001 shift max:   0.003 61
r_work: 0.16834 shift mean:   0.001 shift max:   0.003 62
r_work: 0.16836 shift mean:   0.001 shift max:   0.002 63
r_work: 0.16836 shift mean:   0.000 shift max:   0.002 64
r_work: 0.16834 shift mean:   0.000 shift max:   0.002 65
r_work: 0.16836 shift mean:   0.000 shift max:   0.002 66
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 67
r_work: 0.16835 shift mean:   0.000 shift max:   0.002 68
r_work: 0.16837 shift mean:   0.000 shift max:   0.002 69
r_work: 0.16835 shift mean:   0.000 shift max:   0.001 70
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 71
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 72
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 73
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 74
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 75
r_work: 0.16842 shift mean:   0.000 shift max:   0.001 76
r_work: 0.16843 shift mean:   0.000 shift max:   0.001 77
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 78
r_work: 0.16844 shift mean:   0.000 shift max:   0.001 79
r_work: 0.16844 shift mean:   0.000 shift max:   0.001 80
r_work: 0.16846 shift mean:   0.000 shift max:   0.001 81
r_work: 0.16845 shift mean:   0.000 shift max:   0.001 82
r_work: 0.16847 shift mean:   0.000 shift max:   0.001 83
r_work: 0.16850 shift mean:   0.000 shift max:   0.001 84
r_work: 0.16851 shift mean:   0.000 shift max:   0.001 85
r_work: 0.16851 shift mean:   0.000 shift max:   0.001 86
r_work: 0.16851 shift mean:   0.000 shift max:   0.001 87
r_work: 0.16853 shift mean:   0.000 shift max:   0.001 88
r_work: 0.16853 shift mean:   0.000 shift max:   0.001 89
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 90
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 91
r_work: 0.16854 shift mean:   0.000 shift max:   0.001 92
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 93
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 94
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 95
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 96
r_work: 0.16854 shift mean:   0.000 shift max:   0.001 97
r_work: 0.16854 shift mean:   0.000 shift max:   0.001 98
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 99
r_work: 0.16854 shift mean:   0.000 shift max:   0.001 100
r_work: 0.16855 shift mean:   0.000 shift max:   0.001 101
r_work: 0.16854 shift mean:   0.000 shift max:   0.001 102
0: Rw: 0.1685 Rf: 0.1785 Rf-Rw: 0.0100 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.81 cb: 0.00 shift start/prev: 0.076 0.076 rws(prev):  1.000 rws:  1.000 n_fev: 102
Optimal weight found. Stopping weight search.
Best Rfree from above: 0.1685
Best restraints scale: 1.0
Best Rwork, Rfree (at refinement start): 0.1684 0.1774
At refinement start
 Rw: 0.1684 Rf: 0.1774 Rf-Rw: 0.0089 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.81 cb: 0.00 shift start/prev: 0.076 0.000 
Refinement:
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 1
r_work: 0.23215 shift mean:   0.029 shift max:   0.200 2
r_work: 0.17092 shift mean:   0.024 shift max:   0.169 3
r_work: 0.17014 shift mean:   0.001 shift max:   0.006 4
r_work: 0.16962 shift mean:   0.001 shift max:   0.005 5
r_work: 0.16926 shift mean:   0.001 shift max:   0.005 6
r_work: 0.16902 shift mean:   0.000 shift max:   0.003 7
r_work: 0.16884 shift mean:   0.000 shift max:   0.002 8
r_work: 0.16872 shift mean:   0.000 shift max:   0.002 9
r_work: 0.16861 shift mean:   0.000 shift max:   0.002 10
r_work: 0.16857 shift mean:   0.000 shift max:   0.001 11
r_work: 0.16856 shift mean:   0.000 shift max:   0.001 12
r_work: 0.16851 shift mean:   0.000 shift max:   0.001 13
r_work: 0.16849 shift mean:   0.000 shift max:   0.001 14
r_work: 0.16848 shift mean:   0.000 shift max:   0.000 15
r_work: 0.16845 shift mean:   0.000 shift max:   0.000 16
r_work: 0.16845 shift mean:   0.000 shift max:   0.000 17
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 18
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 19
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 20
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 21
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 22
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 23
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 24
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 25
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 26
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 27
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 28
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 29
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 30
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 31
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 32
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 33
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 34
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 35
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 36
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 37
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 38
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 39
r_work: 0.16842 shift mean:   0.000 shift max:   0.001 40
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 41
r_work: 0.16842 shift mean:   0.000 shift max:   0.002 42
r_work: 0.16843 shift mean:   0.000 shift max:   0.001 43
r_work: 0.16844 shift mean:   0.000 shift max:   0.002 44
r_work: 0.16843 shift mean:   0.000 shift max:   0.002 45
r_work: 0.16841 shift mean:   0.000 shift max:   0.003 46
r_work: 0.16842 shift mean:   0.000 shift max:   0.004 47
r_work: 0.16841 shift mean:   0.000 shift max:   0.004 48
r_work: 0.16839 shift mean:   0.000 shift max:   0.004 49
r_work: 0.16839 shift mean:   0.000 shift max:   0.005 50
r_work: 0.16837 shift mean:   0.000 shift max:   0.005 51
r_work: 0.16835 shift mean:   0.000 shift max:   0.005 52
0: Rw: 0.1683 Rf: 0.1775 Rf-Rw: 0.0092 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.83 cb: 0.00 shift start/prev: 0.077 0.004 n_fev: 52
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 1
r_work: 0.24587 shift mean:   0.031 shift max:   0.200 2
r_work: 0.16881 shift mean:   0.029 shift max:   0.186 3
r_work: 0.16866 shift mean:   0.000 shift max:   0.003 4
r_work: 0.16855 shift mean:   0.000 shift max:   0.003 5
r_work: 0.16846 shift mean:   0.000 shift max:   0.002 6
r_work: 0.16843 shift mean:   0.000 shift max:   0.001 7
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 8
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 9
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 10
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 11
r_work: 0.16835 shift mean:   0.000 shift max:   0.001 12
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 13
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 14
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 15
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 16
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 17
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 18
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 19
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 20
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 21
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 22
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 23
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 24
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 25
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 26
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 27
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 28
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 29
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 30
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 31
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 32
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 33
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 34
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 35
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 36
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 37
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 38
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 39
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 40
r_work: 0.16836 shift mean:   0.000 shift max:   0.002 41
r_work: 0.16837 shift mean:   0.000 shift max:   0.002 42
r_work: 0.16839 shift mean:   0.000 shift max:   0.002 43
r_work: 0.16839 shift mean:   0.000 shift max:   0.002 44
r_work: 0.16839 shift mean:   0.000 shift max:   0.002 45
r_work: 0.16839 shift mean:   0.000 shift max:   0.002 46
r_work: 0.16840 shift mean:   0.000 shift max:   0.002 47
r_work: 0.16838 shift mean:   0.000 shift max:   0.002 48
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 49
r_work: 0.16840 shift mean:   0.000 shift max:   0.002 50
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 51
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 52
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 53
1: Rw: 0.1684 Rf: 0.1777 Rf-Rw: 0.0093 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.82 cb: 0.00 shift start/prev: 0.078 0.003 n_fev: 53
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 1
r_work: 0.22656 shift mean:   0.031 shift max:   0.179 2
r_work: 0.16844 shift mean:   0.030 shift max:   0.174 3
r_work: 0.16843 shift mean:   0.000 shift max:   0.001 4
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 5
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 6
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 7
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 8
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 9
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 10
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 11
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 12
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 13
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 14
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 15
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 16
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 17
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 18
r_work: 0.16842 shift mean:   0.000 shift max:   0.000 19
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 20
r_work: 0.16843 shift mean:   0.000 shift max:   0.000 21
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 22
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 23
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 24
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 25
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 26
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 27
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 28
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 29
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 30
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 31
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 32
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 33
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 34
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 35
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 36
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 37
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 38
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 39
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 40
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 41
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 42
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 43
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 44
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 45
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 46
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 47
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 48
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 49
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 50
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 51
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 52
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 53
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 54
2: Rw: 0.1684 Rf: 0.1776 Rf-Rw: 0.0092 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.82 cb: 0.00 shift start/prev: 0.078 0.002 n_fev: 54
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 1
r_work: 0.21972 shift mean:   0.025 shift max:   0.129 2
r_work: 0.16838 shift mean:   0.024 shift max:   0.126 3
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 4
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 5
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 6
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 7
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 8
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 9
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 10
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 11
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 12
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 13
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 14
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 15
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 16
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 17
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 18
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 19
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 20
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 21
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 22
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 23
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 24
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 25
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 26
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 27
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 28
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 29
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 30
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 31
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 32
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 33
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 34
r_work: 0.16835 shift mean:   0.000 shift max:   0.000 35
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 36
r_work: 0.16836 shift mean:   0.000 shift max:   0.001 37
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 38
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 39
r_work: 0.16838 shift mean:   0.000 shift max:   0.001 40
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 41
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 42
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 43
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 44
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 45
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 46
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 47
r_work: 0.16841 shift mean:   0.000 shift max:   0.001 48
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 49
r_work: 0.16840 shift mean:   0.000 shift max:   0.001 50
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 51
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 52
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 53
3: Rw: 0.1684 Rf: 0.1776 Rf-Rw: 0.0092 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.83 cb: 0.00 shift start/prev: 0.079 0.001 n_fev: 53
r_work: 0.16841 shift mean:   0.000 shift max:   0.000 1
r_work: 0.21816 shift mean:   0.024 shift max:   0.149 2
r_work: 0.16838 shift mean:   0.023 shift max:   0.145 3
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 4
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 5
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 6
r_work: 0.16836 shift mean:   0.000 shift max:   0.000 7
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 8
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 9
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 10
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 11
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 12
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 13
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 14
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 15
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 16
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 17
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 18
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 19
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 20
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 21
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 22
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 23
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 24
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 25
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 26
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 27
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 28
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 29
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 30
r_work: 0.16840 shift mean:   0.000 shift max:   0.000 31
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 32
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 33
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 34
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 35
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 36
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 37
r_work: 0.16837 shift mean:   0.000 shift max:   0.001 38
r_work: 0.16839 shift mean:   0.000 shift max:   0.001 39
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 40
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 41
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 42
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 43
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 44
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 45
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 46
r_work: 0.16839 shift mean:   0.000 shift max:   0.000 47
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 48
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 49
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 50
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 51
r_work: 0.16838 shift mean:   0.000 shift max:   0.000 52
r_work: 0.16837 shift mean:   0.000 shift max:   0.000 53
4: Rw: 0.1684 Rf: 0.1777 Rf-Rw: 0.0093 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.83 cb: 0.00 shift start/prev: 0.079 0.001 n_fev: 53
At refinement end:
 Rw: 0.1684 Rf: 0.1777 Rf-Rw: 0.0093 bond: 0.013 angle: 1.59 clash: 0.0 rota: 0.00 rama: f: 83.33 o: 0.00 Z: -2.83 cb: 0.00 shift start/prev: 0.079 0.001 
Best Rwork, Rfree (after refinement): 0.1684 0.1777
See 6DKZ_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 88.02 seconds
wall clock time: 95.31 seconds
/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)