Starting qr.refine
on Tue May 21 00:47:18 2024 by afonine
===============================================================================

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

  Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/1w60/1w60.mtz
  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/qrefine_optimized/1w60.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=0.01
    max_angle_rmsd=1.7
    stop_one_found_first_good_weight=False
    gradient_only=True

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/qrefine_optimized/1w60.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/qrefine_optimized/1w60.pdb"
    miller_array {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/1w60/1w60.mtz"
    }
    default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/1w60/1w60.mtz"
  }
  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_bond_rmsd = 0.01
    stop_one_found_first_good_weight = False
  }


Starting job
===============================================================================
Validate inputs:
-------------------------------------------------------------------------------
Refinement start
****************
-------------------------------------------------------------------------------
Extracting fmodel
*****************
                   start: r(all,work,free)=0.3679 0.3661 0.3989 n_refl.: 9258
       re-set all scales: r(all,work,free)=0.3679 0.3661 0.3989 n_refl.: 9258
         remove outliers: r(all,work,free)=0.3678 0.3661 0.3989 n_refl.: 9255
bulk-solvent and scaling: r(all,work,free)=0.2666 0.2649 0.2989 n_refl.: 9255
         remove outliers: r(all,work,free)=0.2666 0.2649 0.2989 n_refl.: 9255
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 25.215-13.182   84.48    95     3 0.2363   720.927   693.799 2.048 1.047 0.390
 13.182-10.771   92.52    92     7 0.2034   728.577   690.547 1.723 1.047 0.363
 10.742-8.763    94.15   183    10 0.1837   646.556   622.269 1.605 1.040 0.358
  8.709-7.139    97.85   350    14 0.2107   566.962   550.877 1.578 1.034 0.357
  7.120-5.819    98.85   652    33 0.2594   394.630   369.309 1.402 1.021 0.334
  5.810-4.742    98.41  1191    49 0.2252   477.646   449.487 1.401 1.003 0.313
  4.737-3.861    98.48  2221   114 0.2504   429.398   404.944 1.471 0.975 0.260
  3.860-3.143    97.34  4027   214 0.3296   247.845   224.355 1.473 0.932 0.040

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.5339   b_overall=5.0511  
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.2649 r_free=0.2989
-------------------------------------------------------------------------------
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 = 0.01
  max_angle_rmsd = 1.7
  stop_one_found_first_good_weight = False
  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 ASP   41": "OD1" <-> "OD2"
    Residue "A PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   97": "OD1" <-> "OD2"
    Residue "A TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  169": "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: 7874
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 3937
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "B"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 3937
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
  Time building chain proxies: 0.92, per 1000 atoms: 0.12
  Number of scatterers: 7874
  At special positions: 0
  Unit cell: (82.892, 82.892, 70.859, 90, 90, 120)
  Space group: P 3 (No. 143)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O     786      8.00
     N     644      7.00
     C    2466      6.00
     H    3946      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: 1.49
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  968

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 3934
        1.13 -     1.30: 700
        1.30 -     1.47: 1462
        1.47 -     1.64: 1778
        1.64 -     1.81: 52
  Bond restraints: 7926
  Sorted by residual:
  bond pdb=" ND1 HIS A 153 "
       pdb=" CE1 HIS A 153 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.65e+00
  bond pdb=" ND1 HIS B 246 "
       pdb=" CE1 HIS B 246 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.47e+00
  bond pdb=" ND1 HIS B 153 "
       pdb=" CE1 HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.07e+00
  bond pdb=" ND1 HIS A  44 "
       pdb=" CE1 HIS A  44 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+00
  bond pdb=" ND1 HIS A 246 "
       pdb=" CE1 HIS A 246 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.49e+00
  ... (remaining 7921 not shown)

  Histogram of bond angle deviations from ideal:
       95.26 -   102.94: 52
      102.94 -   110.61: 7220
      110.61 -   118.28: 3968
      118.28 -   125.95: 3034
      125.95 -   133.62: 100
  Bond angle restraints: 14374
  Sorted by residual:
  angle pdb=" CA  ASN B  36 "
        pdb=" CB  ASN B  36 "
        pdb=" CG  ASN B  36 "
      ideal   model   delta    sigma   weight residual
     112.60  118.49   -5.89 1.00e+00 1.00e+00 3.47e+01
  angle pdb=" C   VAL B 195 "
        pdb=" CA  VAL B 195 "
        pdb=" CB  VAL B 195 "
      ideal   model   delta    sigma   weight residual
     111.40  122.56  -11.16 1.90e+00 2.77e-01 3.45e+01
  angle pdb=" CA  ASN A  36 "
        pdb=" CB  ASN A  36 "
        pdb=" CG  ASN A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  118.24   -5.64 1.00e+00 1.00e+00 3.18e+01
  angle pdb=" C   GLN B 108 "
        pdb=" N   GLU B 109 "
        pdb=" CA  GLU B 109 "
      ideal   model   delta    sigma   weight residual
     121.70  130.48   -8.78 1.80e+00 3.09e-01 2.38e+01
  angle pdb=" CD2 HIS B  44 "
        pdb=" NE2 HIS B  44 "
        pdb=" CE1 HIS B  44 "
      ideal   model   delta    sigma   weight residual
     109.00  104.81    4.19 1.00e+00 1.00e+00 1.76e+01
  ... (remaining 14369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3423
       17.47 -    34.93: 195
       34.93 -    52.39: 57
       52.39 -    69.85: 33
       69.85 -    87.31: 4
  Dihedral angle restraints: 3712
    sinusoidal: 2056
      harmonic: 1656
  Sorted by residual:
  dihedral pdb=" C   VAL B 195 "
           pdb=" N   VAL B 195 "
           pdb=" CA  VAL B 195 "
           pdb=" CB  VAL B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.82   13.82     0      2.50e+00 1.60e-01 3.05e+01
  dihedral pdb=" CA  LEU A  19 "
           pdb=" C   LEU A  19 "
           pdb=" N   LYS A  20 "
           pdb=" CA  LYS A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.88  -24.12     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ALA B 194 "
           pdb=" C   ALA B 194 "
           pdb=" N   VAL B 195 "
           pdb=" CA  VAL B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.22   22.78     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 396
       0.076 -    0.151: 178
       0.151 -    0.227: 39
       0.227 -    0.302: 17
       0.302 -    0.378: 6
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" CB  VAL B 195 "
            pdb=" CA  VAL B 195 "
            pdb=" CG1 VAL B 195 "
            pdb=" CG2 VAL B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.56e+00
  chirality pdb=" CA  VAL B 195 "
            pdb=" N   VAL B 195 "
            pdb=" C   VAL B 195 "
            pdb=" CB  VAL B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.12    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  LEU A 175 "
            pdb=" N   LEU A 175 "
            pdb=" C   LEU A 175 "
            pdb=" CB  LEU A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  ... (remaining 633 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  91 "    0.120 9.50e-02 1.11e+02   9.22e-02 1.57e+02
        pdb=" NE  ARG B  91 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  91 "    0.038 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  91 "    0.101 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  91 "    0.088 2.00e-02 2.50e+03
        pdb="HH11 ARG B  91 "   -0.140 2.00e-02 2.50e+03
        pdb="HH12 ARG B  91 "    0.070 2.00e-02 2.50e+03
        pdb="HH21 ARG B  91 "   -0.013 2.00e-02 2.50e+03
        pdb="HH22 ARG B  91 "   -0.133 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  61 "    0.366 9.50e-02 1.11e+02   1.46e-01 1.56e+02
        pdb=" NE  ARG A  61 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  61 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  61 "    0.119 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  61 "   -0.133 2.00e-02 2.50e+03
        pdb="HH11 ARG A  61 "   -0.093 2.00e-02 2.50e+03
        pdb="HH12 ARG A  61 "    0.049 2.00e-02 2.50e+03
        pdb="HH21 ARG A  61 "    0.110 2.00e-02 2.50e+03
        pdb="HH22 ARG A  61 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B   5 "    0.112 9.50e-02 1.11e+02   8.73e-02 1.41e+02
        pdb=" NE  ARG B   5 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG B   5 "   -0.042 2.00e-02 2.50e+03
        pdb=" NH1 ARG B   5 "   -0.075 2.00e-02 2.50e+03
        pdb=" NH2 ARG B   5 "   -0.096 2.00e-02 2.50e+03
        pdb="HH11 ARG B   5 "    0.140 2.00e-02 2.50e+03
        pdb="HH12 ARG B   5 "   -0.071 2.00e-02 2.50e+03
        pdb="HH21 ARG B   5 "    0.055 2.00e-02 2.50e+03
        pdb="HH22 ARG B   5 "    0.106 2.00e-02 2.50e+03
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        0.68 -     1.47: 9
        1.47 -     2.25: 1103
        2.25 -     3.03: 23022
        3.03 -     3.82: 35038
        3.82 -     4.60: 56848
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 116020
  Sorted by model distance:
  nonbonded pdb=" HD3 LYS A 190 "
            pdb=" CD2 LEU B 126 "
     model   vdw sym.op.
     0.682 2.870 -x+y+1,-x+1,z
  nonbonded pdb=" HD3 LYS A 190 "
            pdb="HD22 LEU B 126 "
     model   vdw sym.op.
     0.781 2.340 -x+y+1,-x+1,z
  nonbonded pdb=" HD3 LYS A 190 "
            pdb="HD23 LEU B 126 "
     model   vdw sym.op.
     1.048 2.340 -x+y+1,-x+1,z
  nonbonded pdb="HD11 LEU A 126 "
            pdb=" HB2 ASP B 189 "
     model   vdw sym.op.
     1.112 2.340 x-1,y-1,z-1
  nonbonded pdb=" CD  LYS A 190 "
            pdb="HD23 LEU B 126 "
     model   vdw sym.op.
     1.332 2.870 -x+y+1,-x+1,z
  ... (remaining 116015 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      32     15.96       2
   O     786      7.97       2
   N     644      6.97       2
   C    2466      5.97       2
   H    3946      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: 0.2649 Rf: 0.2989 Rf-Rw: 0.0339 bond: 0.009 angle: 1.63 clash: 0.4 rota: 2.47 rama: f: 96.25 o: 0.59 Z: -1.83 cb: 0.21 shift start/prev: 0.018 0.018 
Optimal weight search:
Data weight (initial): 176.14995822727568
r_work: 0.26493 shift mean:   0.000 shift max:   0.000 1
r_work: 0.26476 shift mean:   0.000 shift max:   0.200 2
r_work: 0.26472 shift mean:   0.000 shift max:   0.022 3
r_work: 0.26472 shift mean:   0.000 shift max:   0.000 4
r_work: 0.26450 shift mean:   0.000 shift max:   0.094 5
r_work: 0.26435 shift mean:   0.000 shift max:   0.041 6
r_work: 0.26412 shift mean:   0.000 shift max:   0.039 7
r_work: 0.26378 shift mean:   0.001 shift max:   0.040 8
r_work: 0.26378 shift mean:   0.000 shift max:   0.000 9
r_work: 0.26271 shift mean:   0.002 shift max:   0.151 10
r_work: 0.26221 shift mean:   0.001 shift max:   0.069 11
r_work: 0.26156 shift mean:   0.001 shift max:   0.078 12
r_work: 0.26087 shift mean:   0.001 shift max:   0.070 13
r_work: 0.26021 shift mean:   0.001 shift max:   0.060 14
r_work: 0.25941 shift mean:   0.002 shift max:   0.071 15
r_work: 0.25852 shift mean:   0.002 shift max:   0.076 16
r_work: 0.25757 shift mean:   0.002 shift max:   0.085 17
r_work: 0.25663 shift mean:   0.002 shift max:   0.090 18
r_work: 0.25561 shift mean:   0.002 shift max:   0.102 19
r_work: 0.25464 shift mean:   0.002 shift max:   0.096 20
r_work: 0.25374 shift mean:   0.002 shift max:   0.092 21
r_work: 0.25286 shift mean:   0.002 shift max:   0.090 22
r_work: 0.25202 shift mean:   0.002 shift max:   0.088 23
r_work: 0.25118 shift mean:   0.003 shift max:   0.089 24
r_work: 0.25040 shift mean:   0.003 shift max:   0.084 25
r_work: 0.24960 shift mean:   0.003 shift max:   0.080 26
r_work: 0.24885 shift mean:   0.003 shift max:   0.081 27
r_work: 0.24816 shift mean:   0.002 shift max:   0.069 28
r_work: 0.24746 shift mean:   0.003 shift max:   0.074 29
r_work: 0.24685 shift mean:   0.002 shift max:   0.068 30
r_work: 0.24619 shift mean:   0.003 shift max:   0.076 31
r_work: 0.24559 shift mean:   0.003 shift max:   0.070 32
r_work: 0.24495 shift mean:   0.003 shift max:   0.076 33
r_work: 0.24436 shift mean:   0.003 shift max:   0.068 34
r_work: 0.24377 shift mean:   0.003 shift max:   0.069 35
r_work: 0.24313 shift mean:   0.003 shift max:   0.073 36
r_work: 0.24257 shift mean:   0.003 shift max:   0.064 37
r_work: 0.24193 shift mean:   0.003 shift max:   0.072 38
r_work: 0.24143 shift mean:   0.003 shift max:   0.055 39
r_work: 0.24082 shift mean:   0.003 shift max:   0.065 40
r_work: 0.24037 shift mean:   0.002 shift max:   0.046 41
r_work: 0.23987 shift mean:   0.003 shift max:   0.049 42
r_work: 0.23938 shift mean:   0.003 shift max:   0.047 43
r_work: 0.23885 shift mean:   0.003 shift max:   0.046 44
r_work: 0.23835 shift mean:   0.003 shift max:   0.043 45
r_work: 0.23787 shift mean:   0.003 shift max:   0.038 46
r_work: 0.23736 shift mean:   0.003 shift max:   0.040 47
r_work: 0.23694 shift mean:   0.003 shift max:   0.030 48
r_work: 0.23643 shift mean:   0.003 shift max:   0.034 49
r_work: 0.23600 shift mean:   0.003 shift max:   0.028 50
r_work: 0.23560 shift mean:   0.003 shift max:   0.029 51
r_work: 0.23516 shift mean:   0.003 shift max:   0.036 52
r_work: 0.23483 shift mean:   0.002 shift max:   0.028 53
r_work: 0.23441 shift mean:   0.003 shift max:   0.036 54
r_work: 0.23406 shift mean:   0.003 shift max:   0.032 55
r_work: 0.23370 shift mean:   0.003 shift max:   0.036 56
r_work: 0.23333 shift mean:   0.003 shift max:   0.039 57
r_work: 0.23299 shift mean:   0.003 shift max:   0.036 58
r_work: 0.23259 shift mean:   0.003 shift max:   0.042 59
r_work: 0.23234 shift mean:   0.002 shift max:   0.029 60
r_work: 0.23203 shift mean:   0.003 shift max:   0.035 61
r_work: 0.23173 shift mean:   0.003 shift max:   0.033 62
r_work: 0.23147 shift mean:   0.002 shift max:   0.030 63
r_work: 0.23117 shift mean:   0.003 shift max:   0.036 64
r_work: 0.23096 shift mean:   0.002 shift max:   0.026 65
r_work: 0.23073 shift mean:   0.002 shift max:   0.030 66
r_work: 0.23051 shift mean:   0.002 shift max:   0.027 67
r_work: 0.23030 shift mean:   0.002 shift max:   0.026 68
r_work: 0.23010 shift mean:   0.002 shift max:   0.025 69
r_work: 0.22990 shift mean:   0.002 shift max:   0.026 70
r_work: 0.22972 shift mean:   0.002 shift max:   0.023 71
r_work: 0.22955 shift mean:   0.002 shift max:   0.024 72
r_work: 0.22938 shift mean:   0.002 shift max:   0.023 73
r_work: 0.22920 shift mean:   0.002 shift max:   0.022 74
r_work: 0.22905 shift mean:   0.002 shift max:   0.021 75
r_work: 0.22891 shift mean:   0.002 shift max:   0.021 76
r_work: 0.22878 shift mean:   0.002 shift max:   0.019 77
r_work: 0.22865 shift mean:   0.002 shift max:   0.020 78
r_work: 0.22852 shift mean:   0.002 shift max:   0.019 79
r_work: 0.22840 shift mean:   0.002 shift max:   0.019 80
r_work: 0.22829 shift mean:   0.002 shift max:   0.019 81
r_work: 0.22818 shift mean:   0.002 shift max:   0.017 82
r_work: 0.22808 shift mean:   0.002 shift max:   0.016 83
r_work: 0.22797 shift mean:   0.002 shift max:   0.018 84
r_work: 0.22790 shift mean:   0.002 shift max:   0.016 85
r_work: 0.22781 shift mean:   0.002 shift max:   0.019 86
r_work: 0.22773 shift mean:   0.001 shift max:   0.017 87
r_work: 0.22764 shift mean:   0.002 shift max:   0.018 88
r_work: 0.22759 shift mean:   0.002 shift max:   0.017 89
r_work: 0.22753 shift mean:   0.001 shift max:   0.015 90
r_work: 0.22747 shift mean:   0.002 shift max:   0.016 91
r_work: 0.22742 shift mean:   0.001 shift max:   0.013 92
r_work: 0.22735 shift mean:   0.001 shift max:   0.014 93
r_work: 0.22733 shift mean:   0.001 shift max:   0.012 94
r_work: 0.22727 shift mean:   0.001 shift max:   0.013 95
r_work: 0.22724 shift mean:   0.001 shift max:   0.014 96
r_work: 0.22719 shift mean:   0.001 shift max:   0.013 97
r_work: 0.22715 shift mean:   0.001 shift max:   0.015 98
r_work: 0.22710 shift mean:   0.001 shift max:   0.015 99
r_work: 0.22704 shift mean:   0.001 shift max:   0.016 100
r_work: 0.22699 shift mean:   0.001 shift max:   0.016 101
r_work: 0.22695 shift mean:   0.001 shift max:   0.017 102
r_work: 0.22691 shift mean:   0.002 shift max:   0.018 103
0: Rw: 0.2269 Rf: 0.2753 Rf-Rw: 0.0484 bond: 0.009 angle: 1.67 clash: 0.3 rota: 2.69 rama: f: 96.05 o: 0.79 Z: -2.12 cb: 0.21 shift start/prev: 0.176 0.159 rws(prev):  1.000 rws:  1.000 n_fev: 103
0: Rw: 0.2269 Rf: 0.2753 Rf-Rw: 0.0484 bond: 0.009 angle: 1.67 clash: 0.3 rota: 2.69 rama: f: 96.05 o: 0.79 Z: -2.12 cb: 0.21 shift start/prev: 0.176 0.159 rws(prev):  1.000 rws:  0.667 n_fev: 103 (NEXT)
r_work: 0.26493 shift mean:   0.000 shift max:   0.000 1
r_work: 0.26468 shift mean:   0.000 shift max:   0.200 2
r_work: 0.26462 shift mean:   0.000 shift max:   0.022 3
r_work: 0.26462 shift mean:   0.000 shift max:   0.000 4
r_work: 0.26430 shift mean:   0.000 shift max:   0.095 5
r_work: 0.26407 shift mean:   0.000 shift max:   0.042 6
r_work: 0.26374 shift mean:   0.000 shift max:   0.040 7
r_work: 0.26320 shift mean:   0.001 shift max:   0.045 8
r_work: 0.26320 shift mean:   0.000 shift max:   0.000 9
r_work: 0.26138 shift mean:   0.003 shift max:   0.187 10
r_work: 0.26071 shift mean:   0.001 shift max:   0.063 11
r_work: 0.25983 shift mean:   0.001 shift max:   0.075 12
r_work: 0.25888 shift mean:   0.002 shift max:   0.067 13
r_work: 0.25779 shift mean:   0.002 shift max:   0.073 14
r_work: 0.25653 shift mean:   0.002 shift max:   0.080 15
r_work: 0.25522 shift mean:   0.003 shift max:   0.084 16
r_work: 0.25376 shift mean:   0.003 shift max:   0.099 17
r_work: 0.25236 shift mean:   0.003 shift max:   0.102 18
r_work: 0.25087 shift mean:   0.004 shift max:   0.111 19
r_work: 0.24957 shift mean:   0.003 shift max:   0.100 20
r_work: 0.24835 shift mean:   0.003 shift max:   0.098 21
r_work: 0.24717 shift mean:   0.003 shift max:   0.096 22
r_work: 0.24603 shift mean:   0.003 shift max:   0.094 23
r_work: 0.24490 shift mean:   0.003 shift max:   0.094 24
r_work: 0.24388 shift mean:   0.003 shift max:   0.086 25
r_work: 0.24281 shift mean:   0.004 shift max:   0.090 26
r_work: 0.24188 shift mean:   0.003 shift max:   0.078 27
r_work: 0.24098 shift mean:   0.004 shift max:   0.079 28
r_work: 0.24017 shift mean:   0.003 shift max:   0.074 29
r_work: 0.23932 shift mean:   0.004 shift max:   0.085 30
r_work: 0.23861 shift mean:   0.003 shift max:   0.072 31
r_work: 0.23775 shift mean:   0.004 shift max:   0.086 32
r_work: 0.23709 shift mean:   0.003 shift max:   0.069 33
r_work: 0.23629 shift mean:   0.004 shift max:   0.080 34
r_work: 0.23554 shift mean:   0.004 shift max:   0.077 35
r_work: 0.23475 shift mean:   0.004 shift max:   0.081 36
r_work: 0.23402 shift mean:   0.004 shift max:   0.074 37
r_work: 0.23335 shift mean:   0.004 shift max:   0.065 38
r_work: 0.23259 shift mean:   0.004 shift max:   0.074 39
r_work: 0.23205 shift mean:   0.003 shift max:   0.051 40
r_work: 0.23143 shift mean:   0.004 shift max:   0.058 41
r_work: 0.23086 shift mean:   0.004 shift max:   0.049 42
r_work: 0.23035 shift mean:   0.003 shift max:   0.041 43
r_work: 0.22973 shift mean:   0.004 shift max:   0.046 44
r_work: 0.22934 shift mean:   0.003 shift max:   0.031 45
r_work: 0.22888 shift mean:   0.003 shift max:   0.032 46
r_work: 0.22836 shift mean:   0.004 shift max:   0.035 47
r_work: 0.22786 shift mean:   0.004 shift max:   0.029 48
r_work: 0.22736 shift mean:   0.004 shift max:   0.035 49
r_work: 0.22702 shift mean:   0.003 shift max:   0.028 50
r_work: 0.22660 shift mean:   0.004 shift max:   0.036 51
r_work: 0.22627 shift mean:   0.003 shift max:   0.031 52
r_work: 0.22594 shift mean:   0.003 shift max:   0.033 53
r_work: 0.22552 shift mean:   0.004 shift max:   0.042 54
r_work: 0.22522 shift mean:   0.003 shift max:   0.032 55
r_work: 0.22485 shift mean:   0.004 shift max:   0.039 56
r_work: 0.22454 shift mean:   0.003 shift max:   0.034 57
r_work: 0.22419 shift mean:   0.003 shift max:   0.037 58
r_work: 0.22390 shift mean:   0.003 shift max:   0.034 59
r_work: 0.22361 shift mean:   0.003 shift max:   0.033 60
r_work: 0.22332 shift mean:   0.003 shift max:   0.034 61
r_work: 0.22305 shift mean:   0.003 shift max:   0.032 62
r_work: 0.22281 shift mean:   0.003 shift max:   0.030 63
r_work: 0.22259 shift mean:   0.003 shift max:   0.028 64
r_work: 0.22233 shift mean:   0.003 shift max:   0.031 65
r_work: 0.22216 shift mean:   0.002 shift max:   0.027 66
r_work: 0.22196 shift mean:   0.003 shift max:   0.027 67
r_work: 0.22175 shift mean:   0.002 shift max:   0.026 68
r_work: 0.22156 shift mean:   0.002 shift max:   0.025 69
r_work: 0.22137 shift mean:   0.002 shift max:   0.025 70
r_work: 0.22120 shift mean:   0.002 shift max:   0.025 71
r_work: 0.22104 shift mean:   0.002 shift max:   0.024 72
r_work: 0.22086 shift mean:   0.002 shift max:   0.024 73
r_work: 0.22071 shift mean:   0.002 shift max:   0.021 74
r_work: 0.22054 shift mean:   0.002 shift max:   0.025 75
r_work: 0.22042 shift mean:   0.002 shift max:   0.019 76
r_work: 0.22026 shift mean:   0.002 shift max:   0.022 77
r_work: 0.22015 shift mean:   0.002 shift max:   0.018 78
r_work: 0.22004 shift mean:   0.002 shift max:   0.020 79
r_work: 0.21993 shift mean:   0.002 shift max:   0.019 80
r_work: 0.21982 shift mean:   0.002 shift max:   0.019 81
r_work: 0.21969 shift mean:   0.002 shift max:   0.020 82
r_work: 0.21958 shift mean:   0.002 shift max:   0.017 83
r_work: 0.21947 shift mean:   0.002 shift max:   0.020 84
r_work: 0.21937 shift mean:   0.002 shift max:   0.017 85
r_work: 0.21927 shift mean:   0.002 shift max:   0.020 86
r_work: 0.21918 shift mean:   0.002 shift max:   0.019 87
r_work: 0.21910 shift mean:   0.002 shift max:   0.016 88
r_work: 0.21901 shift mean:   0.002 shift max:   0.018 89
r_work: 0.21895 shift mean:   0.001 shift max:   0.013 90
r_work: 0.21889 shift mean:   0.002 shift max:   0.013 91
r_work: 0.21884 shift mean:   0.002 shift max:   0.013 92
r_work: 0.21877 shift mean:   0.002 shift max:   0.014 93
r_work: 0.21870 shift mean:   0.002 shift max:   0.014 94
r_work: 0.21865 shift mean:   0.001 shift max:   0.013 95
r_work: 0.21860 shift mean:   0.002 shift max:   0.016 96
r_work: 0.21856 shift mean:   0.001 shift max:   0.012 97
r_work: 0.21851 shift mean:   0.002 shift max:   0.014 98
r_work: 0.21846 shift mean:   0.002 shift max:   0.014 99
r_work: 0.21843 shift mean:   0.001 shift max:   0.013 100
r_work: 0.21838 shift mean:   0.002 shift max:   0.017 101
r_work: 0.21834 shift mean:   0.001 shift max:   0.013 102
r_work: 0.21829 shift mean:   0.002 shift max:   0.016 103
1: Rw: 0.2183 Rf: 0.2731 Rf-Rw: 0.0548 bond: 0.009 angle: 1.70 clash: 0.4 rota: 2.91 rama: f: 95.85 o: 0.79 Z: -2.24 cb: 0.21 shift start/prev: 0.207 0.042 rws(prev):  0.667 rws:  0.667 n_fev: 103
1: Rw: 0.2183 Rf: 0.2731 Rf-Rw: 0.0548 bond: 0.009 angle: 1.70 clash: 0.4 rota: 2.91 rama: f: 95.85 o: 0.79 Z: -2.24 cb: 0.21 shift start/prev: 0.207 0.042 rws(prev):  0.667 rws:  1.000 n_fev: 103 (NEXT)
Flip happened. Stopping weight search.
Best Rfree from above: 0.2753
Best restraints scale: 1.0
Best Rwork, Rfree (at refinement start): 0.2301 0.2772
At refinement start
 Rw: 0.2301 Rf: 0.2772 Rf-Rw: 0.0471 bond: 0.009 angle: 1.67 clash: 0.3 rota: 2.69 rama: f: 96.05 o: 0.79 Z: -2.12 cb: 0.21 shift start/prev: 0.176 0.042 
Refinement:
r_work: 0.23005 shift mean:   0.000 shift max:   0.000 1
r_work: 0.22852 shift mean:   0.003 shift max:   0.032 2
r_work: 0.22877 shift mean:   0.000 shift max:   0.005 3
r_work: 0.22894 shift mean:   0.000 shift max:   0.004 4
r_work: 0.22907 shift mean:   0.000 shift max:   0.003 5
r_work: 0.22915 shift mean:   0.000 shift max:   0.003 6
r_work: 0.22921 shift mean:   0.000 shift max:   0.002 7
r_work: 0.22924 shift mean:   0.000 shift max:   0.002 8
r_work: 0.22926 shift mean:   0.000 shift max:   0.002 9
r_work: 0.22927 shift mean:   0.000 shift max:   0.001 10
r_work: 0.22928 shift mean:   0.000 shift max:   0.001 11
r_work: 0.22928 shift mean:   0.000 shift max:   0.001 12
r_work: 0.22929 shift mean:   0.000 shift max:   0.001 13
r_work: 0.22928 shift mean:   0.000 shift max:   0.002 14
r_work: 0.22926 shift mean:   0.000 shift max:   0.002 15
r_work: 0.22921 shift mean:   0.000 shift max:   0.003 16
r_work: 0.22914 shift mean:   0.000 shift max:   0.005 17
r_work: 0.22900 shift mean:   0.001 shift max:   0.008 18
r_work: 0.22874 shift mean:   0.001 shift max:   0.013 19
r_work: 0.22849 shift mean:   0.001 shift max:   0.012 20
r_work: 0.22820 shift mean:   0.001 shift max:   0.012 21
r_work: 0.22785 shift mean:   0.001 shift max:   0.015 22
r_work: 0.22760 shift mean:   0.001 shift max:   0.011 23
r_work: 0.22729 shift mean:   0.001 shift max:   0.012 24
r_work: 0.22706 shift mean:   0.001 shift max:   0.009 25
r_work: 0.22681 shift mean:   0.001 shift max:   0.011 26
r_work: 0.22647 shift mean:   0.002 shift max:   0.015 27
r_work: 0.22620 shift mean:   0.001 shift max:   0.014 28
r_work: 0.22584 shift mean:   0.002 shift max:   0.020 29
r_work: 0.22557 shift mean:   0.002 shift max:   0.016 30
r_work: 0.22520 shift mean:   0.002 shift max:   0.022 31
r_work: 0.22490 shift mean:   0.002 shift max:   0.020 32
r_work: 0.22458 shift mean:   0.002 shift max:   0.023 33
r_work: 0.22430 shift mean:   0.002 shift max:   0.022 34
r_work: 0.22402 shift mean:   0.002 shift max:   0.023 35
r_work: 0.22374 shift mean:   0.002 shift max:   0.023 36
r_work: 0.22350 shift mean:   0.002 shift max:   0.023 37
r_work: 0.22327 shift mean:   0.002 shift max:   0.023 38
r_work: 0.22306 shift mean:   0.002 shift max:   0.023 39
r_work: 0.22287 shift mean:   0.002 shift max:   0.021 40
r_work: 0.22267 shift mean:   0.002 shift max:   0.024 41
r_work: 0.22252 shift mean:   0.002 shift max:   0.018 42
r_work: 0.22237 shift mean:   0.002 shift max:   0.020 43
r_work: 0.22223 shift mean:   0.002 shift max:   0.020 44
r_work: 0.22209 shift mean:   0.002 shift max:   0.019 45
r_work: 0.22197 shift mean:   0.002 shift max:   0.019 46
r_work: 0.22188 shift mean:   0.002 shift max:   0.016 47
r_work: 0.22178 shift mean:   0.002 shift max:   0.018 48
r_work: 0.22170 shift mean:   0.001 shift max:   0.015 49
r_work: 0.22162 shift mean:   0.001 shift max:   0.015 50
r_work: 0.22154 shift mean:   0.002 shift max:   0.016 51
r_work: 0.22149 shift mean:   0.001 shift max:   0.013 52
0: Rw: 0.2215 Rf: 0.2726 Rf-Rw: 0.0511 bond: 0.009 angle: 1.70 clash: 0.4 rota: 2.69 rama: f: 95.85 o: 0.79 Z: -2.32 cb: 0.21 shift start/prev: 0.217 0.055 n_fev: 52
r_work: 0.22149 shift mean:   0.000 shift max:   0.000 1
r_work: 0.22101 shift mean:   0.002 shift max:   0.072 2
r_work: 0.22137 shift mean:   0.002 shift max:   0.054 3
r_work: 0.22139 shift mean:   0.000 shift max:   0.003 4
r_work: 0.22140 shift mean:   0.000 shift max:   0.002 5
r_work: 0.22140 shift mean:   0.000 shift max:   0.002 6
r_work: 0.22140 shift mean:   0.000 shift max:   0.002 7
r_work: 0.22139 shift mean:   0.000 shift max:   0.002 8
r_work: 0.22139 shift mean:   0.000 shift max:   0.002 9
r_work: 0.22139 shift mean:   0.000 shift max:   0.002 10
r_work: 0.22138 shift mean:   0.000 shift max:   0.001 11
r_work: 0.22137 shift mean:   0.000 shift max:   0.001 12
r_work: 0.22137 shift mean:   0.000 shift max:   0.001 13
r_work: 0.22136 shift mean:   0.000 shift max:   0.002 14
r_work: 0.22132 shift mean:   0.000 shift max:   0.003 15
r_work: 0.22128 shift mean:   0.000 shift max:   0.004 16
r_work: 0.22121 shift mean:   0.001 shift max:   0.006 17
r_work: 0.22112 shift mean:   0.001 shift max:   0.009 18
r_work: 0.22101 shift mean:   0.001 shift max:   0.011 19
r_work: 0.22094 shift mean:   0.001 shift max:   0.006 20
r_work: 0.22088 shift mean:   0.001 shift max:   0.005 21
r_work: 0.22081 shift mean:   0.001 shift max:   0.006 22
r_work: 0.22075 shift mean:   0.001 shift max:   0.004 23
r_work: 0.22069 shift mean:   0.001 shift max:   0.006 24
r_work: 0.22064 shift mean:   0.001 shift max:   0.005 25
r_work: 0.22059 shift mean:   0.001 shift max:   0.007 26
r_work: 0.22053 shift mean:   0.001 shift max:   0.007 27
r_work: 0.22047 shift mean:   0.001 shift max:   0.009 28
r_work: 0.22040 shift mean:   0.001 shift max:   0.010 29
r_work: 0.22033 shift mean:   0.001 shift max:   0.011 30
r_work: 0.22029 shift mean:   0.001 shift max:   0.011 31
r_work: 0.22025 shift mean:   0.001 shift max:   0.013 32
r_work: 0.22020 shift mean:   0.001 shift max:   0.013 33
r_work: 0.22016 shift mean:   0.001 shift max:   0.014 34
r_work: 0.22014 shift mean:   0.002 shift max:   0.015 35
r_work: 0.22011 shift mean:   0.002 shift max:   0.015 36
r_work: 0.22010 shift mean:   0.002 shift max:   0.015 37
r_work: 0.22009 shift mean:   0.002 shift max:   0.016 38
r_work: 0.22009 shift mean:   0.002 shift max:   0.014 39
r_work: 0.22009 shift mean:   0.002 shift max:   0.016 40
r_work: 0.22012 shift mean:   0.001 shift max:   0.013 41
r_work: 0.22011 shift mean:   0.001 shift max:   0.015 42
r_work: 0.22013 shift mean:   0.001 shift max:   0.013 43
r_work: 0.22015 shift mean:   0.001 shift max:   0.014 44
r_work: 0.22015 shift mean:   0.001 shift max:   0.015 45
r_work: 0.22017 shift mean:   0.001 shift max:   0.015 46
r_work: 0.22016 shift mean:   0.001 shift max:   0.016 47
r_work: 0.22014 shift mean:   0.001 shift max:   0.019 48
r_work: 0.22015 shift mean:   0.001 shift max:   0.017 49
r_work: 0.22009 shift mean:   0.002 shift max:   0.028 50
r_work: 0.22007 shift mean:   0.001 shift max:   0.021 51
r_work: 0.22002 shift mean:   0.002 shift max:   0.035 52
1: Rw: 0.2200 Rf: 0.2705 Rf-Rw: 0.0505 bond: 0.009 angle: 1.69 clash: 0.4 rota: 2.69 rama: f: 95.85 o: 0.79 Z: -2.18 cb: 0.21 shift start/prev: 0.236 0.038 n_fev: 52
r_work: 0.22002 shift mean:   0.000 shift max:   0.000 1
r_work: 0.21951 shift mean:   0.002 shift max:   0.170 2
r_work: 0.21987 shift mean:   0.001 shift max:   0.120 3
r_work: 0.21989 shift mean:   0.000 shift max:   0.008 4
r_work: 0.21991 shift mean:   0.000 shift max:   0.008 5
r_work: 0.21991 shift mean:   0.000 shift max:   0.006 6
r_work: 0.21991 shift mean:   0.000 shift max:   0.005 7
r_work: 0.21991 shift mean:   0.000 shift max:   0.004 8
r_work: 0.21990 shift mean:   0.000 shift max:   0.003 9
r_work: 0.21990 shift mean:   0.000 shift max:   0.002 10
r_work: 0.21988 shift mean:   0.000 shift max:   0.002 11
r_work: 0.21987 shift mean:   0.000 shift max:   0.002 12
r_work: 0.21986 shift mean:   0.000 shift max:   0.002 13
r_work: 0.21984 shift mean:   0.000 shift max:   0.003 14
r_work: 0.21982 shift mean:   0.000 shift max:   0.003 15
r_work: 0.21978 shift mean:   0.000 shift max:   0.005 16
r_work: 0.21973 shift mean:   0.000 shift max:   0.007 17
r_work: 0.21965 shift mean:   0.000 shift max:   0.011 18
r_work: 0.21954 shift mean:   0.001 shift max:   0.017 19
r_work: 0.21933 shift mean:   0.001 shift max:   0.035 20
r_work: 0.21920 shift mean:   0.000 shift max:   0.017 21
r_work: 0.21912 shift mean:   0.000 shift max:   0.016 22
r_work: 0.21900 shift mean:   0.001 shift max:   0.021 23
r_work: 0.21890 shift mean:   0.001 shift max:   0.020 24
r_work: 0.21880 shift mean:   0.001 shift max:   0.020 25
r_work: 0.21871 shift mean:   0.000 shift max:   0.019 26
r_work: 0.21860 shift mean:   0.001 shift max:   0.022 27
r_work: 0.21849 shift mean:   0.001 shift max:   0.026 28
r_work: 0.21832 shift mean:   0.001 shift max:   0.038 29
r_work: 0.21822 shift mean:   0.001 shift max:   0.025 30
r_work: 0.21809 shift mean:   0.001 shift max:   0.032 31
r_work: 0.21801 shift mean:   0.001 shift max:   0.023 32
r_work: 0.21793 shift mean:   0.001 shift max:   0.022 33
r_work: 0.21787 shift mean:   0.001 shift max:   0.023 34
r_work: 0.21782 shift mean:   0.000 shift max:   0.015 35
r_work: 0.21775 shift mean:   0.001 shift max:   0.021 36
r_work: 0.21770 shift mean:   0.001 shift max:   0.015 37
r_work: 0.21765 shift mean:   0.001 shift max:   0.018 38
r_work: 0.21760 shift mean:   0.001 shift max:   0.018 39
r_work: 0.21757 shift mean:   0.001 shift max:   0.017 40
r_work: 0.21751 shift mean:   0.001 shift max:   0.020 41
r_work: 0.21748 shift mean:   0.001 shift max:   0.016 42
r_work: 0.21743 shift mean:   0.001 shift max:   0.018 43
r_work: 0.21741 shift mean:   0.001 shift max:   0.015 44
r_work: 0.21739 shift mean:   0.001 shift max:   0.015 45
r_work: 0.21735 shift mean:   0.001 shift max:   0.013 46
r_work: 0.21733 shift mean:   0.001 shift max:   0.012 47
r_work: 0.21729 shift mean:   0.001 shift max:   0.012 48
r_work: 0.21726 shift mean:   0.001 shift max:   0.011 49
r_work: 0.21721 shift mean:   0.001 shift max:   0.012 50
r_work: 0.21717 shift mean:   0.001 shift max:   0.012 51
r_work: 0.21713 shift mean:   0.001 shift max:   0.014 52
2: Rw: 0.2171 Rf: 0.2695 Rf-Rw: 0.0524 bond: 0.009 angle: 1.71 clash: 0.4 rota: 2.69 rama: f: 95.85 o: 0.79 Z: -2.29 cb: 0.21 shift start/prev: 0.249 0.021 n_fev: 52
r_work: 0.21713 shift mean:   0.000 shift max:   0.000 1
r_work: 0.21699 shift mean:   0.001 shift max:   0.024 2
r_work: 0.21705 shift mean:   0.000 shift max:   0.010 3
r_work: 0.21705 shift mean:   0.000 shift max:   0.002 4
r_work: 0.21706 shift mean:   0.000 shift max:   0.002 5
r_work: 0.21707 shift mean:   0.000 shift max:   0.002 6
r_work: 0.21707 shift mean:   0.000 shift max:   0.001 7
r_work: 0.21706 shift mean:   0.000 shift max:   0.001 8
r_work: 0.21706 shift mean:   0.000 shift max:   0.001 9
r_work: 0.21705 shift mean:   0.000 shift max:   0.001 10
r_work: 0.21704 shift mean:   0.000 shift max:   0.001 11
r_work: 0.21704 shift mean:   0.000 shift max:   0.002 12
r_work: 0.21703 shift mean:   0.000 shift max:   0.002 13
r_work: 0.21702 shift mean:   0.000 shift max:   0.002 14
r_work: 0.21701 shift mean:   0.000 shift max:   0.004 15
r_work: 0.21698 shift mean:   0.000 shift max:   0.005 16
r_work: 0.21695 shift mean:   0.000 shift max:   0.008 17
r_work: 0.21689 shift mean:   0.001 shift max:   0.013 18
r_work: 0.21686 shift mean:   0.000 shift max:   0.010 19
r_work: 0.21682 shift mean:   0.000 shift max:   0.009 20
r_work: 0.21678 shift mean:   0.001 shift max:   0.012 21
r_work: 0.21674 shift mean:   0.000 shift max:   0.009 22
r_work: 0.21670 shift mean:   0.000 shift max:   0.010 23
r_work: 0.21667 shift mean:   0.001 shift max:   0.011 24
r_work: 0.21664 shift mean:   0.001 shift max:   0.011 25
r_work: 0.21660 shift mean:   0.001 shift max:   0.015 26
r_work: 0.21657 shift mean:   0.001 shift max:   0.011 27
r_work: 0.21654 shift mean:   0.001 shift max:   0.018 28
r_work: 0.21652 shift mean:   0.001 shift max:   0.013 29
r_work: 0.21648 shift mean:   0.001 shift max:   0.019 30
r_work: 0.21646 shift mean:   0.001 shift max:   0.018 31
r_work: 0.21644 shift mean:   0.001 shift max:   0.021 32
r_work: 0.21642 shift mean:   0.001 shift max:   0.022 33
r_work: 0.21640 shift mean:   0.001 shift max:   0.022 34
r_work: 0.21640 shift mean:   0.001 shift max:   0.026 35
r_work: 0.21640 shift mean:   0.001 shift max:   0.022 36
r_work: 0.21640 shift mean:   0.001 shift max:   0.023 37
r_work: 0.21641 shift mean:   0.001 shift max:   0.023 38
r_work: 0.21642 shift mean:   0.001 shift max:   0.017 39
r_work: 0.21643 shift mean:   0.001 shift max:   0.018 40
r_work: 0.21643 shift mean:   0.001 shift max:   0.016 41
r_work: 0.21642 shift mean:   0.001 shift max:   0.018 42
r_work: 0.21642 shift mean:   0.001 shift max:   0.018 43
r_work: 0.21641 shift mean:   0.001 shift max:   0.018 44
r_work: 0.21640 shift mean:   0.001 shift max:   0.022 45
r_work: 0.21639 shift mean:   0.001 shift max:   0.021 46
r_work: 0.21638 shift mean:   0.001 shift max:   0.024 47
r_work: 0.21634 shift mean:   0.001 shift max:   0.030 48
r_work: 0.21631 shift mean:   0.001 shift max:   0.027 49
r_work: 0.21624 shift mean:   0.002 shift max:   0.046 50
r_work: 0.21618 shift mean:   0.001 shift max:   0.033 51
r_work: 0.21609 shift mean:   0.002 shift max:   0.050 52
3: Rw: 0.2161 Rf: 0.2700 Rf-Rw: 0.0539 bond: 0.009 angle: 1.71 clash: 0.4 rota: 2.69 rama: f: 95.65 o: 0.79 Z: -2.23 cb: 0.21 shift start/prev: 0.265 0.030 n_fev: 52
r_work: 0.21609 shift mean:   0.000 shift max:   0.000 1
r_work: 0.21587 shift mean:   0.002 shift max:   0.113 2
r_work: 0.21606 shift mean:   0.001 shift max:   0.091 3
r_work: 0.21606 shift mean:   0.000 shift max:   0.003 4
r_work: 0.21606 shift mean:   0.000 shift max:   0.003 5
r_work: 0.21606 shift mean:   0.000 shift max:   0.002 6
r_work: 0.21606 shift mean:   0.000 shift max:   0.002 7
r_work: 0.21606 shift mean:   0.000 shift max:   0.002 8
r_work: 0.21605 shift mean:   0.000 shift max:   0.002 9
r_work: 0.21604 shift mean:   0.000 shift max:   0.001 10
r_work: 0.21603 shift mean:   0.000 shift max:   0.002 11
r_work: 0.21602 shift mean:   0.000 shift max:   0.002 12
r_work: 0.21600 shift mean:   0.000 shift max:   0.002 13
r_work: 0.21598 shift mean:   0.000 shift max:   0.003 14
r_work: 0.21595 shift mean:   0.000 shift max:   0.005 15
r_work: 0.21591 shift mean:   0.000 shift max:   0.007 16
r_work: 0.21584 shift mean:   0.000 shift max:   0.012 17
r_work: 0.21577 shift mean:   0.000 shift max:   0.015 18
r_work: 0.21571 shift mean:   0.000 shift max:   0.010 19
r_work: 0.21566 shift mean:   0.000 shift max:   0.012 20
r_work: 0.21561 shift mean:   0.000 shift max:   0.013 21
r_work: 0.21555 shift mean:   0.000 shift max:   0.013 22
r_work: 0.21548 shift mean:   0.000 shift max:   0.018 23
r_work: 0.21544 shift mean:   0.000 shift max:   0.014 24
r_work: 0.21536 shift mean:   0.000 shift max:   0.020 25
r_work: 0.21531 shift mean:   0.000 shift max:   0.016 26
r_work: 0.21525 shift mean:   0.000 shift max:   0.020 27
r_work: 0.21520 shift mean:   0.000 shift max:   0.017 28
r_work: 0.21515 shift mean:   0.000 shift max:   0.017 29
r_work: 0.21511 shift mean:   0.000 shift max:   0.018 30
r_work: 0.21508 shift mean:   0.000 shift max:   0.016 31
r_work: 0.21504 shift mean:   0.000 shift max:   0.017 32
r_work: 0.21502 shift mean:   0.000 shift max:   0.014 33
r_work: 0.21499 shift mean:   0.000 shift max:   0.016 34
r_work: 0.21495 shift mean:   0.000 shift max:   0.015 35
r_work: 0.21493 shift mean:   0.000 shift max:   0.016 36
r_work: 0.21491 shift mean:   0.001 shift max:   0.017 37
r_work: 0.21491 shift mean:   0.000 shift max:   0.014 38
r_work: 0.21488 shift mean:   0.001 shift max:   0.018 39
r_work: 0.21487 shift mean:   0.000 shift max:   0.013 40
r_work: 0.21486 shift mean:   0.001 shift max:   0.013 41
r_work: 0.21485 shift mean:   0.001 shift max:   0.012 42
r_work: 0.21484 shift mean:   0.001 shift max:   0.010 43
r_work: 0.21485 shift mean:   0.001 shift max:   0.011 44
r_work: 0.21485 shift mean:   0.000 shift max:   0.009 45
r_work: 0.21485 shift mean:   0.000 shift max:   0.011 46
r_work: 0.21484 shift mean:   0.000 shift max:   0.009 47
r_work: 0.21485 shift mean:   0.000 shift max:   0.010 48
r_work: 0.21485 shift mean:   0.000 shift max:   0.011 49
r_work: 0.21485 shift mean:   0.000 shift max:   0.010 50
r_work: 0.21484 shift mean:   0.001 shift max:   0.016 51
r_work: 0.21483 shift mean:   0.000 shift max:   0.014 52
4: Rw: 0.2148 Rf: 0.2703 Rf-Rw: 0.0555 bond: 0.009 angle: 1.72 clash: 0.4 rota: 2.69 rama: f: 95.65 o: 0.79 Z: -2.33 cb: 0.41 shift start/prev: 0.271 0.013 n_fev: 52
At refinement end:
 Rw: 0.2148 Rf: 0.2703 Rf-Rw: 0.0555 bond: 0.009 angle: 1.72 clash: 0.4 rota: 2.69 rama: f: 95.65 o: 0.79 Z: -2.33 cb: 0.41 shift start/prev: 0.271 0.013 
Best Rwork, Rfree (after refinement): 0.2148 0.2703
See 1w60_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 1595.53 seconds
wall clock time: 23 minutes 39.70 seconds (1419.70 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)