Starting qr.refine
on Fri Jun 21 15:03:00 2024 by afonine
===============================================================================

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

  Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//5ZGL.mtz
  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/5ZGL.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//5ZGL.mtz"
    }
    default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//5ZGL.mtz"
    model {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/5ZGL.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/5ZGL.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)=0.1130 0.1114 0.1267 n_refl.: 2791
       re-set all scales: r(all,work,free)=0.1130 0.1114 0.1267 n_refl.: 2791
         remove outliers: r(all,work,free)=0.1136 0.1119 0.1288 n_refl.: 2770
bulk-solvent and scaling: r(all,work,free)=0.1010 0.0987 0.1210 n_refl.: 2770
         remove outliers: r(all,work,free)=0.0994 0.0970 0.1210 n_refl.: 2763
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 11.771-3.014    85.47    90    10 0.0981    32.963    32.405 1.000 1.008 0.000
  3.010-2.425    97.09    90    10 0.0849    28.154    28.228 1.000 1.002 0.000
  2.414-1.937    93.43   167    18 0.0696    29.608    29.368 1.000 1.004 0.000
  1.935-1.553    94.91   318    36 0.0910    18.292    17.747 1.000 1.004 0.000
  1.553-1.246    91.70   587    65 0.1015    12.078    11.645 1.000 1.008 0.000
  1.245-0.950    74.40  1238   134 0.1100     7.563     7.721 1.000 1.013 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0049   b_overall=-0.0058 
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.0970 r_free=0.1210
-------------------------------------------------------------------------------
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: 152
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 70
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 70
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 0.04, per 1000 atoms: 0.26
  Number of scatterers: 152
  At special positions: 0
  Unit cell: (11.957, 10.141, 21.372, 90, 100.112, 90)
  Space group: P 1 21 1 (No. 4)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O      24      8.00
     N      14      7.00
     C      44      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: 0.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  8

  Time building geometry restraints manager: 0.06 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: 16
        1.27 -     1.42: 28
        1.42 -     1.56: 34
  Bond restraints: 148
  Sorted by residual:
  bond pdb=" N   SER A 240 "
       pdb=" H   SER A 240 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.44e+01
  bond pdb=" N   GLY B 235 "
       pdb=" H   GLY B 235 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.43e+01
  bond pdb=" N   SER B 240 "
       pdb=" H   SER B 240 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.43e+01
  bond pdb=" N   GLY A 236 "
       pdb=" H   GLY A 236 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.43e+01
  bond pdb=" N   GLY A 239 "
       pdb=" H   GLY A 239 "
    ideal  model  delta    sigma   weight residual
    1.020  0.860  0.160 2.00e-02 2.50e+03 6.40e+01
  ... (remaining 143 not shown)

  Histogram of bond angle deviations from ideal:
      103.65 -   108.02: 10
      108.02 -   112.38: 113
      112.38 -   116.75: 27
      116.75 -   121.12: 49
      121.12 -   125.48: 43
  Bond angle restraints: 242
  Sorted by residual:
  angle pdb=" N   SER A 240 "
        pdb=" CA  SER A 240 "
        pdb=" C   SER A 240 "
      ideal   model   delta    sigma   weight residual
     111.00  105.45    5.55 2.80e+00 1.28e-01 3.92e+00
  angle pdb=" C   GLY A 238 "
        pdb=" N   GLY A 239 "
        pdb=" CA  GLY A 239 "
      ideal   model   delta    sigma   weight residual
     121.70  118.91    2.79 1.80e+00 3.09e-01 2.40e+00
  angle pdb=" CB  SER A 240 "
        pdb=" CA  SER A 240 "
        pdb=" HA  SER A 240 "
      ideal   model   delta    sigma   weight residual
     109.00  105.12    3.88 3.00e+00 1.11e-01 1.68e+00
  angle pdb=" CA  TYR A 237 "
        pdb=" CB  TYR A 237 "
        pdb=" CG  TYR A 237 "
      ideal   model   delta    sigma   weight residual
     113.90  111.58    2.32 1.80e+00 3.09e-01 1.66e+00
  angle pdb=" C   SER B 240 "
        pdb=" CA  SER B 240 "
        pdb=" CB  SER B 240 "
      ideal   model   delta    sigma   weight residual
     110.10  112.44   -2.34 1.90e+00 2.77e-01 1.52e+00
  ... (remaining 237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.12 -    11.95: 44
       11.95 -    23.78: 2
       23.78 -    35.62: 3
       35.62 -    47.45: 4
       47.45 -    59.28: 11
  Dihedral angle restraints: 64
    sinusoidal: 34
      harmonic: 30
  Sorted by residual:
  dihedral pdb=" CA  TYR A 237 "
           pdb=" C   TYR A 237 "
           pdb=" N   GLY A 238 "
           pdb=" CA  GLY A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.06   20.94     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" N   TYR A 237 "
           pdb=" CA  TYR A 237 "
           pdb=" CB  TYR A 237 "
           pdb=" CG  TYR A 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   86.57  -26.57     3      1.50e+01 4.44e-03 3.89e+00
  dihedral pdb=" N   SER B 240 "
           pdb=" CA  SER B 240 "
           pdb=" C   SER B 240 "
           pdb=" OXT SER B 240 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -20.00   34.99  -54.99     2      3.00e+01 1.11e-03 3.58e+00
  ... (remaining 61 not shown)

  Histogram of chiral volume deviations from ideal:
       0.040 -    0.061: 1
       0.061 -    0.081: 0
       0.081 -    0.102: 2
       0.102 -    0.123: 0
       0.123 -    0.143: 1
  Chirality restraints: 4
  Sorted by residual:
  chirality pdb=" CA  TYR B 237 "
            pdb=" N   TYR B 237 "
            pdb=" C   TYR B 237 "
            pdb=" CB  TYR B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  SER B 240 "
            pdb=" N   SER B 240 "
            pdb=" C   SER B 240 "
            pdb=" CB  SER B 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.41    0.10 2.00e-01 2.50e+01 2.46e-01
  chirality pdb=" CA  TYR A 237 "
            pdb=" N   TYR A 237 "
            pdb=" C   TYR A 237 "
            pdb=" CB  TYR A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.60   -0.09 2.00e-01 2.50e+01 2.23e-01
  ... (remaining 1 not shown)

  Planarity restraints: 28
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 237 "    0.102 2.00e-02 2.50e+03   4.06e-02 4.95e+01
        pdb=" CG  TYR A 237 "    0.000 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 237 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 237 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 237 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 237 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 237 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A 237 "    0.043 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 237 "   -0.053 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 237 "   -0.058 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 237 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 237 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 237 "   -0.039 2.00e-02 2.50e+03   1.54e-02 7.09e+00
        pdb=" CG  TYR B 237 "    0.005 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 237 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 237 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 237 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 237 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 237 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 237 "   -0.014 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 237 "    0.016 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 237 "    0.022 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 237 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 237 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 236 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   GLY A 236 "    0.021 2.00e-02 2.50e+03
        pdb=" O   GLY A 236 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TYR A 237 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 25 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.22: 55
        2.22 -     2.79: 350
        2.79 -     3.36: 666
        3.36 -     3.93: 1104
        3.93 -     4.50: 1668
  Nonbonded interactions: 3843
  Sorted by model distance:
  nonbonded pdb=" O   SER A 240 "
            pdb=" H2  GLY A 234 "
     model   vdw sym.op.
     1.655 1.800 x-1,y,z+1
  nonbonded pdb=" H2  GLY A 234 "
            pdb=" O   SER A 240 "
     model   vdw sym.op.
     1.655 1.800 x+1,y,z-1
  nonbonded pdb=" HH  TYR B 237 "
            pdb=" O   HOH B 301 "
     model   vdw
     1.783 1.800
  nonbonded pdb=" O   SER A 240 "
            pdb=" H1  GLY A 234 "
     model   vdw sym.op.
     1.787 1.800 x-1,y,z+1
  nonbonded pdb=" H1  GLY A 234 "
            pdb=" O   SER A 240 "
     model   vdw sym.op.
     1.787 1.800 x+1,y,z-1
  ... (remaining 3838 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      24      7.97       2
   N      14      6.97       2
   C      44      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: 0.0970 Rf: 0.1210 Rf-Rw: 0.0240 bond: 0.012 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.05 cb: 0.00 shift start/prev: 0.000 0.000 
Optimal weight search:
Data weight (initial): 380.2914813881846
r_work: 0.09695 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16894 shift mean:   0.070 shift max:   0.200 2
r_work: 0.16894 shift mean:   0.000 shift max:   0.000 3
r_work: 0.15033 shift mean:   0.010 shift max:   0.030 4
r_work: 0.13190 shift mean:   0.010 shift max:   0.034 5
r_work: 0.11988 shift mean:   0.006 shift max:   0.024 6
r_work: 0.11221 shift mean:   0.004 shift max:   0.018 7
r_work: 0.10674 shift mean:   0.003 shift max:   0.014 8
r_work: 0.10305 shift mean:   0.003 shift max:   0.012 9
r_work: 0.10034 shift mean:   0.002 shift max:   0.009 10
r_work: 0.09853 shift mean:   0.002 shift max:   0.007 11
r_work: 0.09710 shift mean:   0.002 shift max:   0.006 12
r_work: 0.09611 shift mean:   0.002 shift max:   0.006 13
r_work: 0.09533 shift mean:   0.002 shift max:   0.005 14
r_work: 0.09478 shift mean:   0.002 shift max:   0.005 15
r_work: 0.09442 shift mean:   0.003 shift max:   0.006 16
r_work: 0.09409 shift mean:   0.003 shift max:   0.008 17
r_work: 0.09385 shift mean:   0.003 shift max:   0.010 18
r_work: 0.09362 shift mean:   0.004 shift max:   0.012 19
r_work: 0.09349 shift mean:   0.005 shift max:   0.015 20
r_work: 0.09344 shift mean:   0.005 shift max:   0.015 21
r_work: 0.09338 shift mean:   0.004 shift max:   0.013 22
r_work: 0.09332 shift mean:   0.004 shift max:   0.012 23
r_work: 0.09325 shift mean:   0.003 shift max:   0.009 24
r_work: 0.09320 shift mean:   0.003 shift max:   0.008 25
r_work: 0.09320 shift mean:   0.002 shift max:   0.006 26
r_work: 0.09319 shift mean:   0.002 shift max:   0.006 27
r_work: 0.09316 shift mean:   0.002 shift max:   0.005 28
r_work: 0.09313 shift mean:   0.002 shift max:   0.005 29
r_work: 0.09308 shift mean:   0.002 shift max:   0.005 30
r_work: 0.09305 shift mean:   0.002 shift max:   0.006 31
r_work: 0.09300 shift mean:   0.002 shift max:   0.007 32
r_work: 0.09292 shift mean:   0.002 shift max:   0.008 33
r_work: 0.09284 shift mean:   0.002 shift max:   0.009 34
r_work: 0.09270 shift mean:   0.003 shift max:   0.012 35
r_work: 0.09260 shift mean:   0.002 shift max:   0.010 36
r_work: 0.09246 shift mean:   0.003 shift max:   0.012 37
r_work: 0.09236 shift mean:   0.003 shift max:   0.012 38
r_work: 0.09222 shift mean:   0.003 shift max:   0.011 39
r_work: 0.09210 shift mean:   0.003 shift max:   0.010 40
r_work: 0.09199 shift mean:   0.002 shift max:   0.009 41
r_work: 0.09189 shift mean:   0.002 shift max:   0.009 42
r_work: 0.09182 shift mean:   0.002 shift max:   0.008 43
r_work: 0.09177 shift mean:   0.002 shift max:   0.007 44
r_work: 0.09171 shift mean:   0.002 shift max:   0.006 45
r_work: 0.09167 shift mean:   0.002 shift max:   0.005 46
r_work: 0.09162 shift mean:   0.002 shift max:   0.006 47
r_work: 0.09158 shift mean:   0.001 shift max:   0.005 48
r_work: 0.09154 shift mean:   0.001 shift max:   0.005 49
r_work: 0.09150 shift mean:   0.001 shift max:   0.004 50
r_work: 0.09151 shift mean:   0.001 shift max:   0.004 51
r_work: 0.09144 shift mean:   0.001 shift max:   0.004 52
r_work: 0.09143 shift mean:   0.001 shift max:   0.003 53
r_work: 0.09139 shift mean:   0.001 shift max:   0.004 54
r_work: 0.09138 shift mean:   0.001 shift max:   0.004 55
r_work: 0.09140 shift mean:   0.001 shift max:   0.004 56
r_work: 0.09142 shift mean:   0.001 shift max:   0.003 57
r_work: 0.09141 shift mean:   0.001 shift max:   0.004 58
r_work: 0.09146 shift mean:   0.001 shift max:   0.004 59
r_work: 0.09145 shift mean:   0.001 shift max:   0.003 60
r_work: 0.09144 shift mean:   0.001 shift max:   0.004 61
r_work: 0.09145 shift mean:   0.001 shift max:   0.003 62
r_work: 0.09147 shift mean:   0.001 shift max:   0.004 63
r_work: 0.09149 shift mean:   0.001 shift max:   0.003 64
r_work: 0.09150 shift mean:   0.001 shift max:   0.004 65
r_work: 0.09151 shift mean:   0.001 shift max:   0.003 66
r_work: 0.09152 shift mean:   0.001 shift max:   0.004 67
r_work: 0.09154 shift mean:   0.001 shift max:   0.003 68
r_work: 0.09154 shift mean:   0.001 shift max:   0.004 69
r_work: 0.09156 shift mean:   0.001 shift max:   0.003 70
r_work: 0.09160 shift mean:   0.001 shift max:   0.003 71
r_work: 0.09161 shift mean:   0.001 shift max:   0.003 72
r_work: 0.09163 shift mean:   0.001 shift max:   0.003 73
r_work: 0.09165 shift mean:   0.001 shift max:   0.003 74
r_work: 0.09168 shift mean:   0.001 shift max:   0.003 75
r_work: 0.09167 shift mean:   0.001 shift max:   0.003 76
r_work: 0.09168 shift mean:   0.000 shift max:   0.002 77
r_work: 0.09168 shift mean:   0.001 shift max:   0.003 78
r_work: 0.09168 shift mean:   0.000 shift max:   0.002 79
r_work: 0.09166 shift mean:   0.001 shift max:   0.003 80
r_work: 0.09165 shift mean:   0.001 shift max:   0.003 81
r_work: 0.09163 shift mean:   0.001 shift max:   0.003 82
r_work: 0.09163 shift mean:   0.001 shift max:   0.004 83
r_work: 0.09161 shift mean:   0.000 shift max:   0.003 84
r_work: 0.09161 shift mean:   0.001 shift max:   0.003 85
r_work: 0.09159 shift mean:   0.001 shift max:   0.003 86
r_work: 0.09158 shift mean:   0.000 shift max:   0.003 87
r_work: 0.09154 shift mean:   0.001 shift max:   0.004 88
r_work: 0.09151 shift mean:   0.000 shift max:   0.003 89
r_work: 0.09149 shift mean:   0.001 shift max:   0.003 90
r_work: 0.09147 shift mean:   0.001 shift max:   0.004 91
r_work: 0.09143 shift mean:   0.001 shift max:   0.003 92
r_work: 0.09140 shift mean:   0.000 shift max:   0.003 93
r_work: 0.09139 shift mean:   0.001 shift max:   0.004 94
r_work: 0.09139 shift mean:   0.000 shift max:   0.003 95
r_work: 0.09135 shift mean:   0.001 shift max:   0.003 96
r_work: 0.09134 shift mean:   0.000 shift max:   0.003 97
r_work: 0.09134 shift mean:   0.001 shift max:   0.003 98
r_work: 0.09133 shift mean:   0.000 shift max:   0.003 99
r_work: 0.09133 shift mean:   0.000 shift max:   0.003 100
r_work: 0.09132 shift mean:   0.001 shift max:   0.003 101
r_work: 0.09131 shift mean:   0.001 shift max:   0.004 102
0: Rw: 0.0913 Rf: 0.1159 Rf-Rw: 0.0246 bond: 0.023 angle: 3.11 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.37 cb: 0.00 shift start/prev: 0.090 0.090 rws(prev):  1.000 rws:  1.000 n_fev: 102
0: Rw: 0.0913 Rf: 0.1159 Rf-Rw: 0.0246 bond: 0.023 angle: 3.11 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.37 cb: 0.00 shift start/prev: 0.090 0.090 rws(prev):  1.000 rws:  1.500 n_fev: 102 (NEXT)
r_work: 0.09695 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16440 shift mean:   0.073 shift max:   0.191 2
r_work: 0.16998 shift mean:   0.004 shift max:   0.009 3
r_work: 0.15208 shift mean:   0.010 shift max:   0.028 4
r_work: 0.13269 shift mean:   0.011 shift max:   0.038 5
r_work: 0.12062 shift mean:   0.007 shift max:   0.025 6
r_work: 0.11289 shift mean:   0.004 shift max:   0.018 7
r_work: 0.10750 shift mean:   0.003 shift max:   0.014 8
r_work: 0.10368 shift mean:   0.003 shift max:   0.011 9
r_work: 0.10099 shift mean:   0.003 shift max:   0.009 10
r_work: 0.09896 shift mean:   0.003 shift max:   0.008 11
r_work: 0.09753 shift mean:   0.003 shift max:   0.006 12
r_work: 0.09639 shift mean:   0.003 shift max:   0.005 13
r_work: 0.09565 shift mean:   0.003 shift max:   0.005 14
r_work: 0.09511 shift mean:   0.003 shift max:   0.006 15
r_work: 0.09468 shift mean:   0.003 shift max:   0.007 16
r_work: 0.09439 shift mean:   0.003 shift max:   0.009 17
r_work: 0.09407 shift mean:   0.004 shift max:   0.011 18
r_work: 0.09394 shift mean:   0.004 shift max:   0.012 19
r_work: 0.09385 shift mean:   0.004 shift max:   0.013 20
r_work: 0.09384 shift mean:   0.004 shift max:   0.012 21
r_work: 0.09367 shift mean:   0.003 shift max:   0.011 22
r_work: 0.09367 shift mean:   0.003 shift max:   0.009 23
r_work: 0.09364 shift mean:   0.002 shift max:   0.008 24
r_work: 0.09360 shift mean:   0.002 shift max:   0.006 25
r_work: 0.09359 shift mean:   0.002 shift max:   0.006 26
r_work: 0.09356 shift mean:   0.002 shift max:   0.006 27
r_work: 0.09352 shift mean:   0.002 shift max:   0.006 28
r_work: 0.09349 shift mean:   0.001 shift max:   0.005 29
r_work: 0.09348 shift mean:   0.002 shift max:   0.008 30
r_work: 0.09340 shift mean:   0.002 shift max:   0.007 31
r_work: 0.09332 shift mean:   0.002 shift max:   0.010 32
r_work: 0.09324 shift mean:   0.002 shift max:   0.010 33
r_work: 0.09316 shift mean:   0.003 shift max:   0.012 34
r_work: 0.09306 shift mean:   0.003 shift max:   0.013 35
r_work: 0.09294 shift mean:   0.003 shift max:   0.013 36
r_work: 0.09282 shift mean:   0.003 shift max:   0.012 37
r_work: 0.09269 shift mean:   0.003 shift max:   0.013 38
r_work: 0.09261 shift mean:   0.002 shift max:   0.010 39
r_work: 0.09249 shift mean:   0.003 shift max:   0.011 40
r_work: 0.09239 shift mean:   0.002 shift max:   0.008 41
r_work: 0.09229 shift mean:   0.002 shift max:   0.008 42
r_work: 0.09223 shift mean:   0.001 shift max:   0.005 43
r_work: 0.09218 shift mean:   0.002 shift max:   0.005 44
r_work: 0.09217 shift mean:   0.001 shift max:   0.005 45
r_work: 0.09213 shift mean:   0.001 shift max:   0.005 46
r_work: 0.09214 shift mean:   0.001 shift max:   0.004 47
r_work: 0.09213 shift mean:   0.001 shift max:   0.004 48
r_work: 0.09209 shift mean:   0.001 shift max:   0.004 49
r_work: 0.09211 shift mean:   0.001 shift max:   0.004 50
r_work: 0.09209 shift mean:   0.001 shift max:   0.004 51
r_work: 0.09211 shift mean:   0.001 shift max:   0.004 52
r_work: 0.09212 shift mean:   0.001 shift max:   0.005 53
r_work: 0.09212 shift mean:   0.001 shift max:   0.005 54
r_work: 0.09213 shift mean:   0.001 shift max:   0.005 55
r_work: 0.09213 shift mean:   0.001 shift max:   0.006 56
r_work: 0.09214 shift mean:   0.001 shift max:   0.005 57
r_work: 0.09215 shift mean:   0.001 shift max:   0.006 58
r_work: 0.09218 shift mean:   0.001 shift max:   0.006 59
r_work: 0.09216 shift mean:   0.001 shift max:   0.005 60
r_work: 0.09219 shift mean:   0.001 shift max:   0.005 61
r_work: 0.09220 shift mean:   0.001 shift max:   0.005 62
r_work: 0.09223 shift mean:   0.001 shift max:   0.005 63
r_work: 0.09222 shift mean:   0.001 shift max:   0.004 64
r_work: 0.09226 shift mean:   0.001 shift max:   0.004 65
r_work: 0.09228 shift mean:   0.001 shift max:   0.005 66
r_work: 0.09230 shift mean:   0.001 shift max:   0.004 67
r_work: 0.09230 shift mean:   0.001 shift max:   0.005 68
r_work: 0.09231 shift mean:   0.001 shift max:   0.004 69
r_work: 0.09231 shift mean:   0.001 shift max:   0.005 70
r_work: 0.09235 shift mean:   0.001 shift max:   0.004 71
r_work: 0.09235 shift mean:   0.001 shift max:   0.005 72
r_work: 0.09235 shift mean:   0.001 shift max:   0.004 73
r_work: 0.09234 shift mean:   0.001 shift max:   0.004 74
r_work: 0.09232 shift mean:   0.001 shift max:   0.004 75
r_work: 0.09232 shift mean:   0.001 shift max:   0.004 76
r_work: 0.09228 shift mean:   0.001 shift max:   0.004 77
r_work: 0.09228 shift mean:   0.001 shift max:   0.004 78
r_work: 0.09226 shift mean:   0.001 shift max:   0.004 79
r_work: 0.09224 shift mean:   0.001 shift max:   0.004 80
r_work: 0.09221 shift mean:   0.001 shift max:   0.003 81
r_work: 0.09220 shift mean:   0.001 shift max:   0.004 82
r_work: 0.09221 shift mean:   0.001 shift max:   0.004 83
r_work: 0.09221 shift mean:   0.001 shift max:   0.004 84
r_work: 0.09216 shift mean:   0.001 shift max:   0.004 85
r_work: 0.09215 shift mean:   0.001 shift max:   0.003 86
r_work: 0.09215 shift mean:   0.001 shift max:   0.004 87
r_work: 0.09215 shift mean:   0.001 shift max:   0.004 88
r_work: 0.09213 shift mean:   0.001 shift max:   0.003 89
r_work: 0.09212 shift mean:   0.001 shift max:   0.004 90
r_work: 0.09210 shift mean:   0.001 shift max:   0.004 91
r_work: 0.09210 shift mean:   0.001 shift max:   0.004 92
r_work: 0.09208 shift mean:   0.001 shift max:   0.004 93
r_work: 0.09210 shift mean:   0.001 shift max:   0.004 94
r_work: 0.09209 shift mean:   0.001 shift max:   0.004 95
r_work: 0.09210 shift mean:   0.001 shift max:   0.004 96
r_work: 0.09210 shift mean:   0.001 shift max:   0.004 97
r_work: 0.09209 shift mean:   0.000 shift max:   0.003 98
r_work: 0.09208 shift mean:   0.001 shift max:   0.004 99
r_work: 0.09209 shift mean:   0.000 shift max:   0.003 100
r_work: 0.09209 shift mean:   0.000 shift max:   0.003 101
r_work: 0.09211 shift mean:   0.001 shift max:   0.004 102
1: Rw: 0.0921 Rf: 0.1156 Rf-Rw: 0.0235 bond: 0.022 angle: 3.03 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.37 cb: 0.00 shift start/prev: 0.090 0.015 rws(prev):  1.500 rws:  1.500 n_fev: 102
1: Rw: 0.0921 Rf: 0.1156 Rf-Rw: 0.0235 bond: 0.022 angle: 3.03 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.37 cb: 0.00 shift start/prev: 0.090 0.015 rws(prev):  1.500 rws:  2.250 n_fev: 102 (NEXT)
r_work: 0.09695 shift mean:   0.000 shift max:   0.000 1
r_work: 0.15839 shift mean:   0.073 shift max:   0.172 2
r_work: 0.17529 shift mean:   0.012 shift max:   0.028 3
r_work: 0.15736 shift mean:   0.010 shift max:   0.028 4
r_work: 0.13706 shift mean:   0.011 shift max:   0.039 5
r_work: 0.12325 shift mean:   0.008 shift max:   0.029 6
r_work: 0.11458 shift mean:   0.005 shift max:   0.019 7
r_work: 0.10870 shift mean:   0.004 shift max:   0.014 8
r_work: 0.10452 shift mean:   0.003 shift max:   0.011 9
r_work: 0.10164 shift mean:   0.003 shift max:   0.008 10
r_work: 0.09957 shift mean:   0.003 shift max:   0.007 11
r_work: 0.09808 shift mean:   0.003 shift max:   0.006 12
r_work: 0.09695 shift mean:   0.003 shift max:   0.006 13
r_work: 0.09611 shift mean:   0.003 shift max:   0.006 14
r_work: 0.09550 shift mean:   0.003 shift max:   0.006 15
r_work: 0.09509 shift mean:   0.003 shift max:   0.007 16
r_work: 0.09479 shift mean:   0.003 shift max:   0.009 17
r_work: 0.09450 shift mean:   0.004 shift max:   0.010 18
r_work: 0.09439 shift mean:   0.004 shift max:   0.011 19
r_work: 0.09425 shift mean:   0.004 shift max:   0.012 20
r_work: 0.09420 shift mean:   0.003 shift max:   0.010 21
r_work: 0.09416 shift mean:   0.003 shift max:   0.009 22
r_work: 0.09413 shift mean:   0.002 shift max:   0.008 23
r_work: 0.09409 shift mean:   0.002 shift max:   0.008 24
r_work: 0.09408 shift mean:   0.002 shift max:   0.007 25
r_work: 0.09404 shift mean:   0.002 shift max:   0.008 26
r_work: 0.09402 shift mean:   0.002 shift max:   0.008 27
r_work: 0.09397 shift mean:   0.002 shift max:   0.009 28
r_work: 0.09392 shift mean:   0.002 shift max:   0.009 29
r_work: 0.09389 shift mean:   0.002 shift max:   0.012 30
r_work: 0.09378 shift mean:   0.002 shift max:   0.012 31
r_work: 0.09369 shift mean:   0.003 shift max:   0.016 32
r_work: 0.09356 shift mean:   0.003 shift max:   0.015 33
r_work: 0.09347 shift mean:   0.003 shift max:   0.016 34
r_work: 0.09334 shift mean:   0.003 shift max:   0.015 35
r_work: 0.09323 shift mean:   0.003 shift max:   0.014 36
r_work: 0.09316 shift mean:   0.002 shift max:   0.012 37
r_work: 0.09310 shift mean:   0.002 shift max:   0.011 38
r_work: 0.09302 shift mean:   0.002 shift max:   0.010 39
r_work: 0.09295 shift mean:   0.002 shift max:   0.009 40
r_work: 0.09294 shift mean:   0.002 shift max:   0.008 41
r_work: 0.09290 shift mean:   0.002 shift max:   0.007 42
r_work: 0.09286 shift mean:   0.001 shift max:   0.006 43
r_work: 0.09282 shift mean:   0.001 shift max:   0.006 44
r_work: 0.09282 shift mean:   0.001 shift max:   0.007 45
r_work: 0.09281 shift mean:   0.001 shift max:   0.006 46
r_work: 0.09282 shift mean:   0.001 shift max:   0.008 47
r_work: 0.09282 shift mean:   0.001 shift max:   0.006 48
r_work: 0.09285 shift mean:   0.001 shift max:   0.009 49
r_work: 0.09285 shift mean:   0.001 shift max:   0.008 50
r_work: 0.09283 shift mean:   0.001 shift max:   0.009 51
r_work: 0.09283 shift mean:   0.001 shift max:   0.008 52
r_work: 0.09288 shift mean:   0.001 shift max:   0.010 53
r_work: 0.09289 shift mean:   0.001 shift max:   0.008 54
r_work: 0.09292 shift mean:   0.001 shift max:   0.008 55
r_work: 0.09290 shift mean:   0.001 shift max:   0.008 56
r_work: 0.09290 shift mean:   0.001 shift max:   0.006 57
r_work: 0.09294 shift mean:   0.001 shift max:   0.006 58
r_work: 0.09295 shift mean:   0.001 shift max:   0.007 59
r_work: 0.09296 shift mean:   0.001 shift max:   0.006 60
r_work: 0.09296 shift mean:   0.001 shift max:   0.007 61
r_work: 0.09297 shift mean:   0.001 shift max:   0.007 62
r_work: 0.09301 shift mean:   0.001 shift max:   0.007 63
r_work: 0.09300 shift mean:   0.001 shift max:   0.007 64
r_work: 0.09304 shift mean:   0.001 shift max:   0.008 65
r_work: 0.09304 shift mean:   0.001 shift max:   0.006 66
r_work: 0.09303 shift mean:   0.001 shift max:   0.008 67
r_work: 0.09306 shift mean:   0.001 shift max:   0.007 68
r_work: 0.09302 shift mean:   0.001 shift max:   0.007 69
r_work: 0.09303 shift mean:   0.001 shift max:   0.008 70
r_work: 0.09302 shift mean:   0.001 shift max:   0.007 71
r_work: 0.09302 shift mean:   0.001 shift max:   0.008 72
r_work: 0.09302 shift mean:   0.001 shift max:   0.007 73
r_work: 0.09303 shift mean:   0.001 shift max:   0.007 74
r_work: 0.09300 shift mean:   0.001 shift max:   0.009 75
r_work: 0.09300 shift mean:   0.001 shift max:   0.006 76
r_work: 0.09302 shift mean:   0.001 shift max:   0.008 77
r_work: 0.09299 shift mean:   0.001 shift max:   0.008 78
r_work: 0.09301 shift mean:   0.001 shift max:   0.008 79
r_work: 0.09299 shift mean:   0.001 shift max:   0.008 80
r_work: 0.09299 shift mean:   0.001 shift max:   0.008 81
r_work: 0.09297 shift mean:   0.001 shift max:   0.008 82
r_work: 0.09297 shift mean:   0.001 shift max:   0.008 83
r_work: 0.09296 shift mean:   0.001 shift max:   0.007 84
r_work: 0.09293 shift mean:   0.001 shift max:   0.009 85
r_work: 0.09295 shift mean:   0.001 shift max:   0.007 86
r_work: 0.09292 shift mean:   0.001 shift max:   0.008 87
r_work: 0.09292 shift mean:   0.001 shift max:   0.009 88
r_work: 0.09288 shift mean:   0.001 shift max:   0.009 89
r_work: 0.09290 shift mean:   0.001 shift max:   0.008 90
r_work: 0.09286 shift mean:   0.001 shift max:   0.010 91
r_work: 0.09285 shift mean:   0.001 shift max:   0.008 92
r_work: 0.09284 shift mean:   0.001 shift max:   0.011 93
r_work: 0.09284 shift mean:   0.001 shift max:   0.009 94
r_work: 0.09282 shift mean:   0.001 shift max:   0.010 95
r_work: 0.09279 shift mean:   0.001 shift max:   0.010 96
r_work: 0.09276 shift mean:   0.001 shift max:   0.011 97
r_work: 0.09277 shift mean:   0.001 shift max:   0.010 98
r_work: 0.09277 shift mean:   0.001 shift max:   0.011 99
r_work: 0.09274 shift mean:   0.001 shift max:   0.010 100
r_work: 0.09272 shift mean:   0.001 shift max:   0.011 101
r_work: 0.09272 shift mean:   0.001 shift max:   0.011 102
2: Rw: 0.0927 Rf: 0.1155 Rf-Rw: 0.0228 bond: 0.020 angle: 2.93 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.36 cb: 0.00 shift start/prev: 0.101 0.026 rws(prev):  2.250 rws:  2.250 n_fev: 102
Optimal weight found. Stopping weight search.
Best Rfree from above: 0.0927
Best restraints scale: 2.25
Best Rwork, Rfree (at refinement start): 0.0919 0.1150
At refinement start
 Rw: 0.0919 Rf: 0.1150 Rf-Rw: 0.0232 bond: 0.020 angle: 2.93 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.36 cb: 0.00 shift start/prev: 0.101 0.000 
Refinement:
r_work: 0.09188 shift mean:   0.000 shift max:   0.000 1
r_work: 0.17905 shift mean:   0.046 shift max:   0.200 2
r_work: 0.10939 shift mean:   0.028 shift max:   0.123 3
r_work: 0.10328 shift mean:   0.003 shift max:   0.015 4
r_work: 0.09907 shift mean:   0.003 shift max:   0.013 5
r_work: 0.09635 shift mean:   0.002 shift max:   0.010 6
r_work: 0.09466 shift mean:   0.002 shift max:   0.008 7
r_work: 0.09354 shift mean:   0.001 shift max:   0.006 8
r_work: 0.09287 shift mean:   0.001 shift max:   0.005 9
r_work: 0.09244 shift mean:   0.001 shift max:   0.004 10
r_work: 0.09214 shift mean:   0.001 shift max:   0.003 11
r_work: 0.09200 shift mean:   0.000 shift max:   0.002 12
r_work: 0.09191 shift mean:   0.000 shift max:   0.002 13
r_work: 0.09185 shift mean:   0.000 shift max:   0.002 14
r_work: 0.09183 shift mean:   0.000 shift max:   0.001 15
r_work: 0.09180 shift mean:   0.000 shift max:   0.001 16
r_work: 0.09181 shift mean:   0.000 shift max:   0.001 17
r_work: 0.09181 shift mean:   0.000 shift max:   0.001 18
r_work: 0.09181 shift mean:   0.000 shift max:   0.001 19
r_work: 0.09183 shift mean:   0.000 shift max:   0.001 20
r_work: 0.09183 shift mean:   0.000 shift max:   0.001 21
r_work: 0.09183 shift mean:   0.000 shift max:   0.001 22
r_work: 0.09185 shift mean:   0.000 shift max:   0.001 23
r_work: 0.09185 shift mean:   0.000 shift max:   0.001 24
r_work: 0.09186 shift mean:   0.000 shift max:   0.001 25
r_work: 0.09186 shift mean:   0.000 shift max:   0.001 26
r_work: 0.09185 shift mean:   0.000 shift max:   0.002 27
r_work: 0.09186 shift mean:   0.000 shift max:   0.003 28
r_work: 0.09187 shift mean:   0.000 shift max:   0.004 29
r_work: 0.09186 shift mean:   0.001 shift max:   0.005 30
r_work: 0.09186 shift mean:   0.001 shift max:   0.008 31
r_work: 0.09189 shift mean:   0.001 shift max:   0.009 32
r_work: 0.09189 shift mean:   0.001 shift max:   0.009 33
r_work: 0.09189 shift mean:   0.001 shift max:   0.007 34
r_work: 0.09192 shift mean:   0.001 shift max:   0.007 35
r_work: 0.09193 shift mean:   0.001 shift max:   0.007 36
r_work: 0.09194 shift mean:   0.001 shift max:   0.006 37
r_work: 0.09196 shift mean:   0.001 shift max:   0.007 38
r_work: 0.09203 shift mean:   0.001 shift max:   0.010 39
r_work: 0.09205 shift mean:   0.001 shift max:   0.012 40
r_work: 0.09210 shift mean:   0.001 shift max:   0.016 41
r_work: 0.09212 shift mean:   0.001 shift max:   0.016 42
r_work: 0.09214 shift mean:   0.002 shift max:   0.024 43
r_work: 0.09217 shift mean:   0.002 shift max:   0.025 44
r_work: 0.09221 shift mean:   0.002 shift max:   0.025 45
r_work: 0.09219 shift mean:   0.001 shift max:   0.020 46
r_work: 0.09218 shift mean:   0.001 shift max:   0.025 47
r_work: 0.09214 shift mean:   0.001 shift max:   0.016 48
r_work: 0.09210 shift mean:   0.001 shift max:   0.018 49
r_work: 0.09210 shift mean:   0.001 shift max:   0.014 50
r_work: 0.09206 shift mean:   0.001 shift max:   0.014 51
r_work: 0.09207 shift mean:   0.001 shift max:   0.012 52
0: Rw: 0.0921 Rf: 0.1155 Rf-Rw: 0.0235 bond: 0.020 angle: 2.94 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.35 cb: 0.00 shift start/prev: 0.106 0.021 n_fev: 52
r_work: 0.09207 shift mean:   0.000 shift max:   0.000 1
r_work: 0.15295 shift mean:   0.049 shift max:   0.200 2
r_work: 0.09363 shift mean:   0.044 shift max:   0.179 3
r_work: 0.09318 shift mean:   0.001 shift max:   0.003 4
r_work: 0.09294 shift mean:   0.001 shift max:   0.002 5
r_work: 0.09271 shift mean:   0.001 shift max:   0.002 6
r_work: 0.09259 shift mean:   0.000 shift max:   0.002 7
r_work: 0.09246 shift mean:   0.000 shift max:   0.001 8
r_work: 0.09239 shift mean:   0.000 shift max:   0.001 9
r_work: 0.09232 shift mean:   0.000 shift max:   0.001 10
r_work: 0.09227 shift mean:   0.000 shift max:   0.001 11
r_work: 0.09223 shift mean:   0.000 shift max:   0.000 12
r_work: 0.09218 shift mean:   0.000 shift max:   0.001 13
r_work: 0.09217 shift mean:   0.000 shift max:   0.001 14
r_work: 0.09216 shift mean:   0.000 shift max:   0.000 15
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 16
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 17
r_work: 0.09209 shift mean:   0.000 shift max:   0.001 18
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 19
r_work: 0.09205 shift mean:   0.000 shift max:   0.001 20
r_work: 0.09204 shift mean:   0.000 shift max:   0.002 21
r_work: 0.09203 shift mean:   0.000 shift max:   0.002 22
r_work: 0.09200 shift mean:   0.000 shift max:   0.003 23
r_work: 0.09198 shift mean:   0.001 shift max:   0.004 24
r_work: 0.09196 shift mean:   0.001 shift max:   0.004 25
r_work: 0.09194 shift mean:   0.001 shift max:   0.005 26
r_work: 0.09192 shift mean:   0.001 shift max:   0.005 27
r_work: 0.09191 shift mean:   0.001 shift max:   0.005 28
r_work: 0.09191 shift mean:   0.001 shift max:   0.004 29
r_work: 0.09190 shift mean:   0.000 shift max:   0.004 30
r_work: 0.09191 shift mean:   0.000 shift max:   0.004 31
r_work: 0.09192 shift mean:   0.000 shift max:   0.003 32
r_work: 0.09194 shift mean:   0.000 shift max:   0.002 33
r_work: 0.09193 shift mean:   0.000 shift max:   0.002 34
r_work: 0.09196 shift mean:   0.000 shift max:   0.002 35
r_work: 0.09196 shift mean:   0.000 shift max:   0.002 36
r_work: 0.09196 shift mean:   0.000 shift max:   0.002 37
r_work: 0.09195 shift mean:   0.000 shift max:   0.003 38
r_work: 0.09195 shift mean:   0.000 shift max:   0.003 39
r_work: 0.09196 shift mean:   0.000 shift max:   0.004 40
r_work: 0.09196 shift mean:   0.000 shift max:   0.005 41
r_work: 0.09196 shift mean:   0.000 shift max:   0.005 42
r_work: 0.09196 shift mean:   0.000 shift max:   0.006 43
r_work: 0.09197 shift mean:   0.001 shift max:   0.007 44
r_work: 0.09197 shift mean:   0.001 shift max:   0.007 45
r_work: 0.09196 shift mean:   0.001 shift max:   0.007 46
r_work: 0.09194 shift mean:   0.001 shift max:   0.007 47
r_work: 0.09194 shift mean:   0.001 shift max:   0.007 48
r_work: 0.09194 shift mean:   0.000 shift max:   0.006 49
r_work: 0.09194 shift mean:   0.000 shift max:   0.007 50
r_work: 0.09192 shift mean:   0.000 shift max:   0.005 51
r_work: 0.09191 shift mean:   0.000 shift max:   0.005 52
1: Rw: 0.0919 Rf: 0.1158 Rf-Rw: 0.0238 bond: 0.020 angle: 2.93 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.35 cb: 0.00 shift start/prev: 0.109 0.013 n_fev: 52
r_work: 0.09191 shift mean:   0.000 shift max:   0.000 1
r_work: 0.14352 shift mean:   0.047 shift max:   0.146 2
r_work: 0.09236 shift mean:   0.045 shift max:   0.139 3
r_work: 0.09227 shift mean:   0.000 shift max:   0.001 4
r_work: 0.09219 shift mean:   0.000 shift max:   0.001 5
r_work: 0.09214 shift mean:   0.000 shift max:   0.001 6
r_work: 0.09210 shift mean:   0.000 shift max:   0.001 7
r_work: 0.09207 shift mean:   0.000 shift max:   0.000 8
r_work: 0.09207 shift mean:   0.000 shift max:   0.000 9
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 10
r_work: 0.09202 shift mean:   0.000 shift max:   0.000 11
r_work: 0.09201 shift mean:   0.000 shift max:   0.000 12
r_work: 0.09200 shift mean:   0.000 shift max:   0.000 13
r_work: 0.09198 shift mean:   0.000 shift max:   0.000 14
r_work: 0.09197 shift mean:   0.000 shift max:   0.000 15
r_work: 0.09196 shift mean:   0.000 shift max:   0.000 16
r_work: 0.09195 shift mean:   0.000 shift max:   0.000 17
r_work: 0.09196 shift mean:   0.000 shift max:   0.001 18
r_work: 0.09193 shift mean:   0.000 shift max:   0.001 19
r_work: 0.09193 shift mean:   0.000 shift max:   0.001 20
r_work: 0.09193 shift mean:   0.000 shift max:   0.001 21
r_work: 0.09191 shift mean:   0.000 shift max:   0.002 22
r_work: 0.09193 shift mean:   0.000 shift max:   0.003 23
r_work: 0.09195 shift mean:   0.000 shift max:   0.003 24
r_work: 0.09195 shift mean:   0.000 shift max:   0.003 25
r_work: 0.09197 shift mean:   0.001 shift max:   0.005 26
r_work: 0.09199 shift mean:   0.001 shift max:   0.004 27
r_work: 0.09202 shift mean:   0.000 shift max:   0.004 28
r_work: 0.09205 shift mean:   0.000 shift max:   0.004 29
r_work: 0.09205 shift mean:   0.000 shift max:   0.003 30
r_work: 0.09207 shift mean:   0.000 shift max:   0.002 31
r_work: 0.09207 shift mean:   0.000 shift max:   0.002 32
r_work: 0.09208 shift mean:   0.000 shift max:   0.002 33
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 34
r_work: 0.09209 shift mean:   0.000 shift max:   0.002 35
r_work: 0.09209 shift mean:   0.000 shift max:   0.001 36
r_work: 0.09210 shift mean:   0.000 shift max:   0.002 37
r_work: 0.09211 shift mean:   0.000 shift max:   0.001 38
r_work: 0.09212 shift mean:   0.000 shift max:   0.001 39
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 40
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 41
r_work: 0.09212 shift mean:   0.000 shift max:   0.001 42
r_work: 0.09211 shift mean:   0.000 shift max:   0.001 43
r_work: 0.09211 shift mean:   0.000 shift max:   0.002 44
r_work: 0.09210 shift mean:   0.000 shift max:   0.002 45
r_work: 0.09209 shift mean:   0.000 shift max:   0.002 46
r_work: 0.09210 shift mean:   0.000 shift max:   0.003 47
r_work: 0.09210 shift mean:   0.000 shift max:   0.003 48
r_work: 0.09211 shift mean:   0.000 shift max:   0.004 49
r_work: 0.09211 shift mean:   0.000 shift max:   0.003 50
r_work: 0.09211 shift mean:   0.000 shift max:   0.004 51
r_work: 0.09212 shift mean:   0.000 shift max:   0.005 52
2: Rw: 0.0921 Rf: 0.1156 Rf-Rw: 0.0235 bond: 0.020 angle: 2.93 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.34 cb: 0.00 shift start/prev: 0.109 0.008 n_fev: 52
r_work: 0.09212 shift mean:   0.000 shift max:   0.000 1
r_work: 0.15735 shift mean:   0.046 shift max:   0.196 2
r_work: 0.09216 shift mean:   0.044 shift max:   0.189 3
r_work: 0.09216 shift mean:   0.000 shift max:   0.001 4
r_work: 0.09215 shift mean:   0.000 shift max:   0.001 5
r_work: 0.09211 shift mean:   0.000 shift max:   0.001 6
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 7
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 8
r_work: 0.09211 shift mean:   0.000 shift max:   0.000 9
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 10
r_work: 0.09212 shift mean:   0.000 shift max:   0.000 11
r_work: 0.09212 shift mean:   0.000 shift max:   0.000 12
r_work: 0.09211 shift mean:   0.000 shift max:   0.000 13
r_work: 0.09211 shift mean:   0.000 shift max:   0.000 14
r_work: 0.09212 shift mean:   0.000 shift max:   0.000 15
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 16
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 17
r_work: 0.09214 shift mean:   0.000 shift max:   0.000 18
r_work: 0.09214 shift mean:   0.000 shift max:   0.000 19
r_work: 0.09214 shift mean:   0.000 shift max:   0.000 20
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 21
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 22
r_work: 0.09213 shift mean:   0.000 shift max:   0.000 23
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 24
r_work: 0.09213 shift mean:   0.000 shift max:   0.001 25
r_work: 0.09212 shift mean:   0.000 shift max:   0.001 26
r_work: 0.09210 shift mean:   0.000 shift max:   0.002 27
r_work: 0.09209 shift mean:   0.000 shift max:   0.002 28
r_work: 0.09209 shift mean:   0.000 shift max:   0.003 29
r_work: 0.09207 shift mean:   0.000 shift max:   0.003 30
r_work: 0.09207 shift mean:   0.000 shift max:   0.003 31
r_work: 0.09207 shift mean:   0.000 shift max:   0.005 32
r_work: 0.09204 shift mean:   0.000 shift max:   0.005 33
r_work: 0.09206 shift mean:   0.000 shift max:   0.004 34
r_work: 0.09206 shift mean:   0.000 shift max:   0.003 35
r_work: 0.09207 shift mean:   0.000 shift max:   0.004 36
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 37
r_work: 0.09205 shift mean:   0.000 shift max:   0.002 38
r_work: 0.09205 shift mean:   0.000 shift max:   0.002 39
r_work: 0.09204 shift mean:   0.000 shift max:   0.002 40
r_work: 0.09205 shift mean:   0.000 shift max:   0.001 41
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 42
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 43
r_work: 0.09206 shift mean:   0.000 shift max:   0.001 44
r_work: 0.09207 shift mean:   0.000 shift max:   0.002 45
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 46
r_work: 0.09206 shift mean:   0.000 shift max:   0.001 47
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 48
r_work: 0.09204 shift mean:   0.000 shift max:   0.002 49
r_work: 0.09204 shift mean:   0.000 shift max:   0.002 50
r_work: 0.09203 shift mean:   0.000 shift max:   0.003 51
r_work: 0.09203 shift mean:   0.000 shift max:   0.003 52
3: Rw: 0.0920 Rf: 0.1158 Rf-Rw: 0.0238 bond: 0.020 angle: 2.95 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.33 cb: 0.00 shift start/prev: 0.111 0.005 n_fev: 52
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 1
r_work: 0.13750 shift mean:   0.037 shift max:   0.111 2
r_work: 0.09217 shift mean:   0.035 shift max:   0.108 3
r_work: 0.09215 shift mean:   0.000 shift max:   0.001 4
r_work: 0.09212 shift mean:   0.000 shift max:   0.001 5
r_work: 0.09210 shift mean:   0.000 shift max:   0.000 6
r_work: 0.09208 shift mean:   0.000 shift max:   0.000 7
r_work: 0.09206 shift mean:   0.000 shift max:   0.000 8
r_work: 0.09205 shift mean:   0.000 shift max:   0.000 9
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 10
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 11
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 12
r_work: 0.09205 shift mean:   0.000 shift max:   0.000 13
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 14
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 15
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 16
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 17
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 18
r_work: 0.09202 shift mean:   0.000 shift max:   0.000 19
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 20
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 21
r_work: 0.09203 shift mean:   0.000 shift max:   0.000 22
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 23
r_work: 0.09204 shift mean:   0.000 shift max:   0.000 24
r_work: 0.09206 shift mean:   0.000 shift max:   0.001 25
r_work: 0.09205 shift mean:   0.000 shift max:   0.001 26
r_work: 0.09205 shift mean:   0.000 shift max:   0.001 27
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 28
r_work: 0.09206 shift mean:   0.000 shift max:   0.002 29
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 30
r_work: 0.09207 shift mean:   0.000 shift max:   0.002 31
r_work: 0.09209 shift mean:   0.000 shift max:   0.002 32
r_work: 0.09209 shift mean:   0.000 shift max:   0.002 33
r_work: 0.09208 shift mean:   0.000 shift max:   0.002 34
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 35
r_work: 0.09207 shift mean:   0.000 shift max:   0.002 36
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 37
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 38
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 39
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 40
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 41
r_work: 0.09208 shift mean:   0.000 shift max:   0.000 42
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 43
r_work: 0.09208 shift mean:   0.000 shift max:   0.000 44
r_work: 0.09207 shift mean:   0.000 shift max:   0.000 45
r_work: 0.09208 shift mean:   0.000 shift max:   0.000 46
r_work: 0.09208 shift mean:   0.000 shift max:   0.000 47
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 48
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 49
r_work: 0.09208 shift mean:   0.000 shift max:   0.001 50
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 51
r_work: 0.09207 shift mean:   0.000 shift max:   0.001 52
4: Rw: 0.0921 Rf: 0.1157 Rf-Rw: 0.0236 bond: 0.020 angle: 2.94 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.33 cb: 0.00 shift start/prev: 0.111 0.003 n_fev: 52
At refinement end:
 Rw: 0.0921 Rf: 0.1157 Rf-Rw: 0.0236 bond: 0.020 angle: 2.94 clash: 0.0 rota: 0.00 rama: f: 100.00 o: 0.00 Z: -4.33 cb: 0.00 shift start/prev: 0.111 0.003 
Best Rwork, Rfree (after refinement): 0.0921 0.1157
See 5ZGL_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 192.84 seconds
wall clock time: 3 minutes 23.80 seconds (203.80 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)