Starting qr.refine
on Mon May 20 21:52:37 2024 by afonine
===============================================================================

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

  Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/2ogu/2ogu.mtz
  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/qrefine_optimized/2ogu.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/2ogu.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/qrefine_optimized/2ogu.pdb"
    miller_array {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/2ogu/2ogu.mtz"
    }
    default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/original/2ogu/2ogu.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)=0.4453 0.4429 0.4961 n_refl.: 6717
       re-set all scales: r(all,work,free)=0.4453 0.4429 0.4961 n_refl.: 6717
         remove outliers: r(all,work,free)=0.4446 0.4422 0.4961 n_refl.: 6712
bulk-solvent and scaling: r(all,work,free)=0.2911 0.2889 0.3383 n_refl.: 6712
         remove outliers: r(all,work,free)=0.2911 0.2889 0.3383 n_refl.: 6712
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 28.612-12.706   81.97    93     7 0.2818  2174.673  2095.160 2.263 0.983 0.353
 12.682-10.260   91.59    95     3 0.1648  2568.632  2457.471 2.177 0.984 0.340
 10.240-8.268    91.43   185     7 0.1468  2276.148  2235.504 1.961 0.982 0.275
  8.239-6.652    93.16   358    10 0.2317  1390.923  1364.547 1.875 0.982 0.256
  6.641-5.360    94.83   677    38 0.2953   842.563   796.600 1.591 0.984 0.220
  5.359-4.320    95.50  1280    57 0.2931   779.801   734.819 1.505 0.983 0.160
  4.319-3.481    96.04  2452   119 0.3562   439.540   405.839 1.655 0.984 0.072
  3.480-3.231    96.10  1253    78 0.4182   247.485   211.126 1.753 0.981 0.010

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.6637   b_overall=3.8591  
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.2889 r_free=0.3383
-------------------------------------------------------------------------------
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 GLU  144": "OE1" <-> "OE2"
  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: 3448
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 3448
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 213}
  Time building chain proxies: 0.49, per 1000 atoms: 0.14
  Number of scatterers: 3448
  At special positions: 0
  Unit cell: (165.889, 165.889, 82.223, 90, 90, 120)
  Space group: R 3 2 :H (No. 155)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       7     16.00
     O     338      8.00
     N     305      7.00
     C    1069      6.00
     H    1729      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: 0.66
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  406

  Time building geometry restraints manager: 0.78 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: 1726
        1.13 -     1.30: 312
        1.30 -     1.47: 648
        1.47 -     1.64: 772
        1.64 -     1.82: 11
  Bond restraints: 3469
  Sorted by residual:
  bond pdb=" ND1 HIS A 161 "
       pdb=" CE1 HIS A 161 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.45e+00
  bond pdb=" ND1 HIS A 193 "
       pdb=" CE1 HIS A 193 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.23e+00
  bond pdb=" ND1 HIS A 286 "
       pdb=" CE1 HIS A 286 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.50e+00
  bond pdb=" SG  CYS A 130 "
       pdb=" HG  CYS A 130 "
    ideal  model  delta    sigma   weight residual
    1.300  1.339 -0.039 2.00e-02 2.50e+03 3.75e+00
  bond pdb=" CE1 HIS A 117 "
       pdb=" NE2 HIS A 117 "
    ideal  model  delta    sigma   weight residual
    1.321  1.340 -0.019 1.00e-02 1.00e+04 3.59e+00
  ... (remaining 3464 not shown)

  Histogram of bond angle deviations from ideal:
       94.91 -   102.71: 11
      102.71 -   110.51: 3043
      110.51 -   118.32: 1833
      118.32 -   126.12: 1363
      126.12 -   133.92: 36
  Bond angle restraints: 6286
  Sorted by residual:
  angle pdb=" CA  ASP A 145 "
        pdb=" CB  ASP A 145 "
        pdb=" CG  ASP A 145 "
      ideal   model   delta    sigma   weight residual
     112.60  120.14   -7.54 1.00e+00 1.00e+00 5.68e+01
  angle pdb=" CD2 HIS A 193 "
        pdb=" NE2 HIS A 193 "
        pdb=" CE1 HIS A 193 "
      ideal   model   delta    sigma   weight residual
     109.00  104.86    4.14 1.00e+00 1.00e+00 1.71e+01
  angle pdb=" CD2 HIS A 286 "
        pdb=" NE2 HIS A 286 "
        pdb=" CE1 HIS A 286 "
      ideal   model   delta    sigma   weight residual
     109.00  105.00    4.00 1.00e+00 1.00e+00 1.60e+01
  angle pdb=" CD2 HIS A 161 "
        pdb=" NE2 HIS A 161 "
        pdb=" CE1 HIS A 161 "
      ideal   model   delta    sigma   weight residual
     109.00  105.11    3.89 1.00e+00 1.00e+00 1.51e+01
  angle pdb=" CG  HIS A 193 "
        pdb=" CD2 HIS A 193 "
        pdb=" NE2 HIS A 193 "
      ideal   model   delta    sigma   weight residual
     107.20  110.87   -3.67 1.00e+00 1.00e+00 1.35e+01
  ... (remaining 6281 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.57: 1446
       17.57 -    35.14: 103
       35.14 -    52.70: 29
       52.70 -    70.27: 18
       70.27 -    87.83: 2
  Dihedral angle restraints: 1598
    sinusoidal: 909
      harmonic: 689
  Sorted by residual:
  dihedral pdb=" CA  VAL A 288 "
           pdb=" C   VAL A 288 "
           pdb=" N   THR A 289 "
           pdb=" CA  THR A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.34  -24.66     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ASP A 300 "
           pdb=" C   ASP A 300 "
           pdb=" N   GLU A 301 "
           pdb=" CA  GLU A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.40   19.60     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ARG A 263 "
           pdb=" C   ARG A 263 "
           pdb=" N   MET A 264 "
           pdb=" CA  MET A 264 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 1595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 176
       0.084 -    0.168: 58
       0.168 -    0.252: 27
       0.252 -    0.336: 7
       0.336 -    0.420: 3
  Chirality restraints: 271
  Sorted by residual:
  chirality pdb=" CA  SER A 242 "
            pdb=" N   SER A 242 "
            pdb=" C   SER A 242 "
            pdb=" CB  SER A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.40e+00
  chirality pdb=" CA  ASP A 300 "
            pdb=" N   ASP A 300 "
            pdb=" C   ASP A 300 "
            pdb=" CB  ASP A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CB  ILE A 294 "
            pdb=" CA  ILE A 294 "
            pdb=" CG1 ILE A 294 "
            pdb=" CG2 ILE A 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.88e+00
  ... (remaining 268 not shown)

  Planarity restraints: 524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 166 "   -0.494 9.50e-02 1.11e+02   1.92e-01 2.45e+02
        pdb=" NE  ARG A 166 "    0.045 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 166 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 166 "   -0.167 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 166 "    0.119 2.00e-02 2.50e+03
        pdb="HH11 ARG A 166 "    0.127 2.00e-02 2.50e+03
        pdb="HH12 ARG A 166 "   -0.059 2.00e-02 2.50e+03
        pdb="HH21 ARG A 166 "   -0.127 2.00e-02 2.50e+03
        pdb="HH22 ARG A 166 "    0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 179 "    0.225 9.50e-02 1.11e+02   1.20e-01 2.04e+02
        pdb=" NE  ARG A 179 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 179 "    0.051 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 179 "    0.131 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 179 "    0.064 2.00e-02 2.50e+03
        pdb="HH11 ARG A 179 "   -0.191 2.00e-02 2.50e+03
        pdb="HH12 ARG A 179 "    0.076 2.00e-02 2.50e+03
        pdb="HH21 ARG A 179 "   -0.044 2.00e-02 2.50e+03
        pdb="HH22 ARG A 179 "   -0.104 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 298 "    0.193 9.50e-02 1.11e+02   1.10e-01 1.82e+02
        pdb=" NE  ARG A 298 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 298 "    0.052 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 298 "    0.058 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 298 "    0.146 2.00e-02 2.50e+03
        pdb="HH11 ARG A 298 "   -0.144 2.00e-02 2.50e+03
        pdb="HH12 ARG A 298 "    0.060 2.00e-02 2.50e+03
        pdb="HH21 ARG A 298 "   -0.105 2.00e-02 2.50e+03
        pdb="HH22 ARG A 298 "   -0.091 2.00e-02 2.50e+03
  ... (remaining 521 not shown)

  Histogram of nonbonded interaction distances:
        1.31 -     1.97: 114
        1.97 -     2.63: 4272
        2.63 -     3.29: 11096
        3.29 -     3.94: 14362
        3.94 -     4.60: 21935
  Nonbonded interactions: 51779
  Sorted by model distance:
  nonbonded pdb=" HE2 LYS A 150 "
            pdb=" HD1 HIS A 161 "
     model   vdw sym.op.
     1.315 2.170 -y+2,x-y+1,z
  nonbonded pdb=" HB3 SER A 126 "
            pdb=" HD1 PHE A 232 "
     model   vdw sym.op.
     1.428 2.170 -x+2,-x+y+1,-z+1
  nonbonded pdb="HD11 LEU A 134 "
            pdb="HD11 ILE A 243 "
     model   vdw sym.op.
     1.569 2.340 -x+2,-x+y+1,-z+1
  nonbonded pdb=" HG3 GLU A 133 "
            pdb=" HG  SER A 240 "
     model   vdw sym.op.
     1.611 2.170 -x+2,-x+y+1,-z+1
  nonbonded pdb="HH12 ARG A 206 "
            pdb=" O   SER A 242 "
     model   vdw sym.op.
     1.649 1.800 -x+2,-x+y+1,-z+1
  ... (remaining 51774 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       7     15.96       2
   O     338      7.97       2
   N     305      6.97       2
   C    1069      5.97       2
   H    1729      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: 0.2889 Rf: 0.3383 Rf-Rw: 0.0494 bond: 0.008 angle: 1.52 clash: 1.2 rota: 6.35 rama: f: 96.80 o: 0.00 Z: -1.07 cb: 0.00 shift start/prev: 0.001 0.001 
Optimal weight search:
Data weight (initial): 114.78262975910948
r_work: 0.28891 shift mean:   0.000 shift max:   0.000 1
r_work: 0.28663 shift mean:   0.004 shift max:   0.200 2
r_work: 0.28663 shift mean:   0.000 shift max:   0.000 3
r_work: 0.28674 shift mean:   0.000 shift max:   0.020 4
r_work: 0.28680 shift mean:   0.000 shift max:   0.010 5
r_work: 0.28679 shift mean:   0.000 shift max:   0.010 6
r_work: 0.28674 shift mean:   0.000 shift max:   0.011 7
r_work: 0.28661 shift mean:   0.000 shift max:   0.013 8
r_work: 0.28644 shift mean:   0.000 shift max:   0.013 9
r_work: 0.28624 shift mean:   0.001 shift max:   0.013 10
r_work: 0.28598 shift mean:   0.001 shift max:   0.014 11
r_work: 0.28569 shift mean:   0.001 shift max:   0.016 12
r_work: 0.28524 shift mean:   0.001 shift max:   0.021 13
r_work: 0.28462 shift mean:   0.001 shift max:   0.030 14
r_work: 0.28373 shift mean:   0.002 shift max:   0.043 15
r_work: 0.28238 shift mean:   0.003 shift max:   0.066 16
r_work: 0.28043 shift mean:   0.005 shift max:   0.099 17
r_work: 0.27919 shift mean:   0.003 shift max:   0.064 18
r_work: 0.27790 shift mean:   0.004 shift max:   0.077 19
r_work: 0.27682 shift mean:   0.003 shift max:   0.061 20
r_work: 0.27581 shift mean:   0.003 shift max:   0.064 21
r_work: 0.27477 shift mean:   0.004 shift max:   0.072 22
r_work: 0.27388 shift mean:   0.003 shift max:   0.064 23
r_work: 0.27294 shift mean:   0.004 shift max:   0.076 24
r_work: 0.27222 shift mean:   0.003 shift max:   0.064 25
r_work: 0.27144 shift mean:   0.004 shift max:   0.073 26
r_work: 0.27082 shift mean:   0.003 shift max:   0.061 27
r_work: 0.27023 shift mean:   0.003 shift max:   0.059 28
r_work: 0.26963 shift mean:   0.004 shift max:   0.059 29
r_work: 0.26913 shift mean:   0.003 shift max:   0.053 30
r_work: 0.26862 shift mean:   0.004 shift max:   0.053 31
r_work: 0.26817 shift mean:   0.003 shift max:   0.048 32
r_work: 0.26775 shift mean:   0.004 shift max:   0.047 33
r_work: 0.26731 shift mean:   0.003 shift max:   0.042 34
r_work: 0.26690 shift mean:   0.004 shift max:   0.041 35
r_work: 0.26653 shift mean:   0.003 shift max:   0.036 36
r_work: 0.26614 shift mean:   0.004 shift max:   0.035 37
r_work: 0.26581 shift mean:   0.003 shift max:   0.031 38
r_work: 0.26544 shift mean:   0.004 shift max:   0.029 39
r_work: 0.26510 shift mean:   0.004 shift max:   0.027 40
r_work: 0.26474 shift mean:   0.004 shift max:   0.026 41
r_work: 0.26444 shift mean:   0.004 shift max:   0.024 42
r_work: 0.26410 shift mean:   0.004 shift max:   0.023 43
r_work: 0.26379 shift mean:   0.004 shift max:   0.023 44
r_work: 0.26350 shift mean:   0.003 shift max:   0.020 45
r_work: 0.26317 shift mean:   0.004 shift max:   0.022 46
r_work: 0.26292 shift mean:   0.003 shift max:   0.019 47
r_work: 0.26262 shift mean:   0.003 shift max:   0.021 48
r_work: 0.26236 shift mean:   0.003 shift max:   0.018 49
r_work: 0.26207 shift mean:   0.003 shift max:   0.019 50
r_work: 0.26184 shift mean:   0.003 shift max:   0.018 51
r_work: 0.26155 shift mean:   0.003 shift max:   0.019 52
r_work: 0.26131 shift mean:   0.003 shift max:   0.018 53
r_work: 0.26102 shift mean:   0.003 shift max:   0.019 54
r_work: 0.26075 shift mean:   0.003 shift max:   0.019 55
r_work: 0.26049 shift mean:   0.003 shift max:   0.020 56
r_work: 0.26023 shift mean:   0.003 shift max:   0.020 57
r_work: 0.25996 shift mean:   0.003 shift max:   0.021 58
r_work: 0.25969 shift mean:   0.003 shift max:   0.022 59
r_work: 0.25946 shift mean:   0.003 shift max:   0.023 60
r_work: 0.25918 shift mean:   0.003 shift max:   0.025 61
r_work: 0.25895 shift mean:   0.003 shift max:   0.024 62
r_work: 0.25873 shift mean:   0.003 shift max:   0.026 63
r_work: 0.25851 shift mean:   0.003 shift max:   0.025 64
r_work: 0.25833 shift mean:   0.002 shift max:   0.026 65
r_work: 0.25815 shift mean:   0.002 shift max:   0.026 66
r_work: 0.25798 shift mean:   0.002 shift max:   0.025 67
r_work: 0.25782 shift mean:   0.002 shift max:   0.025 68
r_work: 0.25767 shift mean:   0.002 shift max:   0.024 69
r_work: 0.25752 shift mean:   0.002 shift max:   0.024 70
r_work: 0.25741 shift mean:   0.002 shift max:   0.022 71
r_work: 0.25730 shift mean:   0.002 shift max:   0.021 72
r_work: 0.25719 shift mean:   0.002 shift max:   0.020 73
r_work: 0.25712 shift mean:   0.002 shift max:   0.018 74
r_work: 0.25704 shift mean:   0.002 shift max:   0.017 75
r_work: 0.25699 shift mean:   0.002 shift max:   0.015 76
r_work: 0.25694 shift mean:   0.002 shift max:   0.016 77
r_work: 0.25690 shift mean:   0.002 shift max:   0.015 78
r_work: 0.25688 shift mean:   0.002 shift max:   0.016 79
r_work: 0.25686 shift mean:   0.002 shift max:   0.015 80
r_work: 0.25683 shift mean:   0.002 shift max:   0.014 81
r_work: 0.25680 shift mean:   0.002 shift max:   0.014 82
r_work: 0.25679 shift mean:   0.002 shift max:   0.012 83
r_work: 0.25676 shift mean:   0.002 shift max:   0.012 84
r_work: 0.25671 shift mean:   0.001 shift max:   0.010 85
r_work: 0.25668 shift mean:   0.002 shift max:   0.010 86
r_work: 0.25664 shift mean:   0.002 shift max:   0.010 87
r_work: 0.25662 shift mean:   0.002 shift max:   0.009 88
r_work: 0.25656 shift mean:   0.002 shift max:   0.009 89
r_work: 0.25653 shift mean:   0.001 shift max:   0.009 90
r_work: 0.25649 shift mean:   0.002 shift max:   0.009 91
r_work: 0.25644 shift mean:   0.001 shift max:   0.009 92
r_work: 0.25640 shift mean:   0.001 shift max:   0.008 93
r_work: 0.25632 shift mean:   0.001 shift max:   0.010 94
r_work: 0.25629 shift mean:   0.001 shift max:   0.008 95
r_work: 0.25624 shift mean:   0.001 shift max:   0.010 96
r_work: 0.25619 shift mean:   0.001 shift max:   0.009 97
r_work: 0.25613 shift mean:   0.001 shift max:   0.011 98
r_work: 0.25608 shift mean:   0.001 shift max:   0.010 99
r_work: 0.25603 shift mean:   0.001 shift max:   0.011 100
r_work: 0.25598 shift mean:   0.001 shift max:   0.011 101
r_work: 0.25593 shift mean:   0.001 shift max:   0.011 102
0: Rw: 0.2559 Rf: 0.3240 Rf-Rw: 0.0680 bond: 0.009 angle: 1.60 clash: 1.2 rota: 6.88 rama: f: 95.43 o: 0.00 Z: -1.16 cb: 0.49 shift start/prev: 0.172 0.170 rws(prev):  1.000 rws:  1.000 n_fev: 102
0: Rw: 0.2559 Rf: 0.3240 Rf-Rw: 0.0680 bond: 0.009 angle: 1.60 clash: 1.2 rota: 6.88 rama: f: 95.43 o: 0.00 Z: -1.16 cb: 0.49 shift start/prev: 0.172 0.170 rws(prev):  1.000 rws:  0.667 n_fev: 102 (NEXT)
r_work: 0.28891 shift mean:   0.000 shift max:   0.000 1
r_work: 0.28565 shift mean:   0.004 shift max:   0.200 2
r_work: 0.28565 shift mean:   0.000 shift max:   0.000 3
r_work: 0.28580 shift mean:   0.000 shift max:   0.019 4
r_work: 0.28585 shift mean:   0.000 shift max:   0.010 5
r_work: 0.28583 shift mean:   0.000 shift max:   0.011 6
r_work: 0.28570 shift mean:   0.000 shift max:   0.013 7
r_work: 0.28547 shift mean:   0.001 shift max:   0.014 8
r_work: 0.28518 shift mean:   0.001 shift max:   0.015 9
r_work: 0.28484 shift mean:   0.001 shift max:   0.015 10
r_work: 0.28441 shift mean:   0.001 shift max:   0.017 11
r_work: 0.28386 shift mean:   0.001 shift max:   0.021 12
r_work: 0.28309 shift mean:   0.002 shift max:   0.028 13
r_work: 0.28193 shift mean:   0.002 shift max:   0.041 14
r_work: 0.28029 shift mean:   0.003 shift max:   0.058 15
r_work: 0.27728 shift mean:   0.007 shift max:   0.109 16
r_work: 0.27594 shift mean:   0.003 shift max:   0.052 17
r_work: 0.27464 shift mean:   0.003 shift max:   0.052 18
r_work: 0.27319 shift mean:   0.004 shift max:   0.061 19
r_work: 0.27191 shift mean:   0.004 shift max:   0.057 20
r_work: 0.27084 shift mean:   0.003 shift max:   0.052 21
r_work: 0.26980 shift mean:   0.004 shift max:   0.054 22
r_work: 0.26876 shift mean:   0.004 shift max:   0.056 23
r_work: 0.26772 shift mean:   0.004 shift max:   0.060 24
r_work: 0.26666 shift mean:   0.005 shift max:   0.067 25
r_work: 0.26575 shift mean:   0.004 shift max:   0.059 26
r_work: 0.26483 shift mean:   0.005 shift max:   0.067 27
r_work: 0.26408 shift mean:   0.004 shift max:   0.055 28
r_work: 0.26329 shift mean:   0.005 shift max:   0.056 29
r_work: 0.26265 shift mean:   0.004 shift max:   0.049 30
r_work: 0.26201 shift mean:   0.005 shift max:   0.049 31
r_work: 0.26151 shift mean:   0.004 shift max:   0.039 32
r_work: 0.26089 shift mean:   0.005 shift max:   0.042 33
r_work: 0.26032 shift mean:   0.005 shift max:   0.040 34
r_work: 0.25976 shift mean:   0.005 shift max:   0.038 35
r_work: 0.25916 shift mean:   0.005 shift max:   0.036 36
r_work: 0.25869 shift mean:   0.005 shift max:   0.029 37
r_work: 0.25815 shift mean:   0.006 shift max:   0.033 38
r_work: 0.25778 shift mean:   0.004 shift max:   0.022 39
r_work: 0.25734 shift mean:   0.005 shift max:   0.027 40
r_work: 0.25699 shift mean:   0.004 shift max:   0.021 41
r_work: 0.25669 shift mean:   0.004 shift max:   0.021 42
r_work: 0.25633 shift mean:   0.005 shift max:   0.022 43
r_work: 0.25597 shift mean:   0.004 shift max:   0.019 44
r_work: 0.25563 shift mean:   0.004 shift max:   0.022 45
r_work: 0.25536 shift mean:   0.004 shift max:   0.019 46
r_work: 0.25502 shift mean:   0.004 shift max:   0.021 47
r_work: 0.25475 shift mean:   0.003 shift max:   0.018 48
r_work: 0.25450 shift mean:   0.004 shift max:   0.021 49
r_work: 0.25427 shift mean:   0.003 shift max:   0.017 50
r_work: 0.25400 shift mean:   0.004 shift max:   0.020 51
r_work: 0.25378 shift mean:   0.003 shift max:   0.017 52
r_work: 0.25352 shift mean:   0.003 shift max:   0.020 53
r_work: 0.25328 shift mean:   0.003 shift max:   0.023 54
r_work: 0.25304 shift mean:   0.003 shift max:   0.023 55
r_work: 0.25276 shift mean:   0.004 shift max:   0.027 56
r_work: 0.25249 shift mean:   0.003 shift max:   0.025 57
r_work: 0.25223 shift mean:   0.003 shift max:   0.027 58
r_work: 0.25192 shift mean:   0.003 shift max:   0.029 59
r_work: 0.25172 shift mean:   0.002 shift max:   0.021 60
r_work: 0.25148 shift mean:   0.003 shift max:   0.026 61
r_work: 0.25128 shift mean:   0.002 shift max:   0.021 62
r_work: 0.25105 shift mean:   0.003 shift max:   0.022 63
r_work: 0.25084 shift mean:   0.003 shift max:   0.023 64
r_work: 0.25067 shift mean:   0.003 shift max:   0.021 65
r_work: 0.25046 shift mean:   0.003 shift max:   0.021 66
r_work: 0.25030 shift mean:   0.002 shift max:   0.016 67
r_work: 0.25014 shift mean:   0.002 shift max:   0.017 68
r_work: 0.25002 shift mean:   0.002 shift max:   0.014 69
r_work: 0.24989 shift mean:   0.002 shift max:   0.014 70
r_work: 0.24978 shift mean:   0.002 shift max:   0.017 71
r_work: 0.24968 shift mean:   0.002 shift max:   0.013 72
r_work: 0.24956 shift mean:   0.002 shift max:   0.019 73
r_work: 0.24949 shift mean:   0.002 shift max:   0.016 74
r_work: 0.24940 shift mean:   0.002 shift max:   0.020 75
r_work: 0.24933 shift mean:   0.002 shift max:   0.019 76
r_work: 0.24926 shift mean:   0.002 shift max:   0.019 77
r_work: 0.24920 shift mean:   0.002 shift max:   0.020 78
r_work: 0.24915 shift mean:   0.002 shift max:   0.014 79
r_work: 0.24912 shift mean:   0.002 shift max:   0.016 80
r_work: 0.24908 shift mean:   0.002 shift max:   0.012 81
r_work: 0.24904 shift mean:   0.002 shift max:   0.013 82
r_work: 0.24899 shift mean:   0.002 shift max:   0.015 83
r_work: 0.24895 shift mean:   0.002 shift max:   0.011 84
r_work: 0.24889 shift mean:   0.002 shift max:   0.015 85
r_work: 0.24884 shift mean:   0.002 shift max:   0.012 86
r_work: 0.24877 shift mean:   0.002 shift max:   0.013 87
r_work: 0.24873 shift mean:   0.002 shift max:   0.012 88
r_work: 0.24866 shift mean:   0.002 shift max:   0.012 89
r_work: 0.24860 shift mean:   0.002 shift max:   0.012 90
r_work: 0.24854 shift mean:   0.002 shift max:   0.012 91
r_work: 0.24848 shift mean:   0.002 shift max:   0.012 92
r_work: 0.24842 shift mean:   0.002 shift max:   0.012 93
r_work: 0.24835 shift mean:   0.002 shift max:   0.012 94
r_work: 0.24828 shift mean:   0.002 shift max:   0.012 95
r_work: 0.24823 shift mean:   0.002 shift max:   0.012 96
r_work: 0.24814 shift mean:   0.002 shift max:   0.012 97
r_work: 0.24807 shift mean:   0.002 shift max:   0.011 98
r_work: 0.24800 shift mean:   0.002 shift max:   0.012 99
r_work: 0.24794 shift mean:   0.002 shift max:   0.012 100
r_work: 0.24786 shift mean:   0.002 shift max:   0.011 101
r_work: 0.24778 shift mean:   0.002 shift max:   0.012 102
1: Rw: 0.2478 Rf: 0.3194 Rf-Rw: 0.0716 bond: 0.009 angle: 1.65 clash: 1.7 rota: 6.35 rama: f: 95.43 o: 0.00 Z: -1.41 cb: 0.49 shift start/prev: 0.200 0.042 rws(prev):  0.667 rws:  0.667 n_fev: 102
1: Rw: 0.2478 Rf: 0.3194 Rf-Rw: 0.0716 bond: 0.009 angle: 1.65 clash: 1.7 rota: 6.35 rama: f: 95.43 o: 0.00 Z: -1.41 cb: 0.49 shift start/prev: 0.200 0.042 rws(prev):  0.667 rws:  0.444 n_fev: 102 (NEXT)
r_work: 0.28891 shift mean:   0.000 shift max:   0.000 1
r_work: 0.28424 shift mean:   0.006 shift max:   0.200 2
r_work: 0.28424 shift mean:   0.000 shift max:   0.000 3
r_work: 0.28435 shift mean:   0.000 shift max:   0.019 4
r_work: 0.28438 shift mean:   0.000 shift max:   0.010 5
r_work: 0.28427 shift mean:   0.000 shift max:   0.013 6
r_work: 0.28398 shift mean:   0.001 shift max:   0.015 7
r_work: 0.28349 shift mean:   0.001 shift max:   0.018 8
r_work: 0.28293 shift mean:   0.001 shift max:   0.019 9
r_work: 0.28228 shift mean:   0.001 shift max:   0.021 10
r_work: 0.28150 shift mean:   0.002 shift max:   0.024 11
r_work: 0.28040 shift mean:   0.002 shift max:   0.030 12
r_work: 0.27880 shift mean:   0.003 shift max:   0.042 13
r_work: 0.27659 shift mean:   0.005 shift max:   0.058 14
r_work: 0.27294 shift mean:   0.009 shift max:   0.101 15
r_work: 0.27111 shift mean:   0.004 shift max:   0.053 16
r_work: 0.26934 shift mean:   0.005 shift max:   0.054 17
r_work: 0.26731 shift mean:   0.006 shift max:   0.066 18
r_work: 0.26582 shift mean:   0.005 shift max:   0.053 19
r_work: 0.26455 shift mean:   0.005 shift max:   0.049 20
r_work: 0.26319 shift mean:   0.005 shift max:   0.054 21
r_work: 0.26208 shift mean:   0.005 shift max:   0.050 22
r_work: 0.26095 shift mean:   0.005 shift max:   0.052 23
r_work: 0.25966 shift mean:   0.006 shift max:   0.060 24
r_work: 0.25863 shift mean:   0.005 shift max:   0.051 25
r_work: 0.25753 shift mean:   0.007 shift max:   0.060 26
r_work: 0.25667 shift mean:   0.005 shift max:   0.045 27
r_work: 0.25575 shift mean:   0.006 shift max:   0.049 28
r_work: 0.25498 shift mean:   0.005 shift max:   0.040 29
r_work: 0.25423 shift mean:   0.006 shift max:   0.039 30
r_work: 0.25361 shift mean:   0.005 shift max:   0.032 31
r_work: 0.25295 shift mean:   0.006 shift max:   0.030 32
r_work: 0.25235 shift mean:   0.006 shift max:   0.030 33
r_work: 0.25177 shift mean:   0.006 shift max:   0.030 34
r_work: 0.25122 shift mean:   0.006 shift max:   0.029 35
r_work: 0.25071 shift mean:   0.006 shift max:   0.027 36
r_work: 0.25024 shift mean:   0.006 shift max:   0.028 37
r_work: 0.24985 shift mean:   0.005 shift max:   0.024 38
r_work: 0.24944 shift mean:   0.005 shift max:   0.025 39
r_work: 0.24912 shift mean:   0.005 shift max:   0.021 40
r_work: 0.24880 shift mean:   0.005 shift max:   0.022 41
r_work: 0.24847 shift mean:   0.005 shift max:   0.022 42
r_work: 0.24822 shift mean:   0.004 shift max:   0.018 43
r_work: 0.24792 shift mean:   0.005 shift max:   0.022 44
r_work: 0.24766 shift mean:   0.004 shift max:   0.019 45
r_work: 0.24743 shift mean:   0.004 shift max:   0.020 46
r_work: 0.24716 shift mean:   0.005 shift max:   0.023 47
r_work: 0.24695 shift mean:   0.004 shift max:   0.019 48
r_work: 0.24669 shift mean:   0.004 shift max:   0.024 49
r_work: 0.24652 shift mean:   0.003 shift max:   0.019 50
r_work: 0.24628 shift mean:   0.004 shift max:   0.022 51
r_work: 0.24603 shift mean:   0.004 shift max:   0.023 52
r_work: 0.24582 shift mean:   0.003 shift max:   0.021 53
r_work: 0.24555 shift mean:   0.004 shift max:   0.023 54
r_work: 0.24529 shift mean:   0.003 shift max:   0.021 55
r_work: 0.24502 shift mean:   0.004 shift max:   0.021 56
r_work: 0.24477 shift mean:   0.003 shift max:   0.019 57
r_work: 0.24449 shift mean:   0.003 shift max:   0.019 58
r_work: 0.24424 shift mean:   0.003 shift max:   0.018 59
r_work: 0.24394 shift mean:   0.003 shift max:   0.020 60
r_work: 0.24374 shift mean:   0.003 shift max:   0.016 61
r_work: 0.24349 shift mean:   0.003 shift max:   0.019 62
r_work: 0.24329 shift mean:   0.003 shift max:   0.016 63
r_work: 0.24306 shift mean:   0.003 shift max:   0.018 64
r_work: 0.24285 shift mean:   0.003 shift max:   0.018 65
r_work: 0.24268 shift mean:   0.003 shift max:   0.017 66
r_work: 0.24248 shift mean:   0.003 shift max:   0.019 67
r_work: 0.24231 shift mean:   0.003 shift max:   0.017 68
r_work: 0.24213 shift mean:   0.003 shift max:   0.018 69
r_work: 0.24198 shift mean:   0.003 shift max:   0.018 70
r_work: 0.24184 shift mean:   0.002 shift max:   0.015 71
r_work: 0.24173 shift mean:   0.003 shift max:   0.018 72
r_work: 0.24163 shift mean:   0.002 shift max:   0.014 73
r_work: 0.24153 shift mean:   0.002 shift max:   0.016 74
r_work: 0.24145 shift mean:   0.002 shift max:   0.015 75
r_work: 0.24136 shift mean:   0.002 shift max:   0.015 76
r_work: 0.24126 shift mean:   0.002 shift max:   0.015 77
r_work: 0.24119 shift mean:   0.002 shift max:   0.013 78
r_work: 0.24110 shift mean:   0.002 shift max:   0.014 79
r_work: 0.24105 shift mean:   0.002 shift max:   0.012 80
r_work: 0.24098 shift mean:   0.002 shift max:   0.012 81
r_work: 0.24092 shift mean:   0.002 shift max:   0.012 82
r_work: 0.24087 shift mean:   0.002 shift max:   0.011 83
r_work: 0.24083 shift mean:   0.002 shift max:   0.012 84
r_work: 0.24077 shift mean:   0.002 shift max:   0.010 85
r_work: 0.24071 shift mean:   0.002 shift max:   0.012 86
r_work: 0.24064 shift mean:   0.002 shift max:   0.011 87
r_work: 0.24058 shift mean:   0.002 shift max:   0.011 88
r_work: 0.24051 shift mean:   0.002 shift max:   0.011 89
r_work: 0.24046 shift mean:   0.002 shift max:   0.010 90
r_work: 0.24040 shift mean:   0.002 shift max:   0.011 91
r_work: 0.24033 shift mean:   0.002 shift max:   0.009 92
r_work: 0.24028 shift mean:   0.002 shift max:   0.010 93
r_work: 0.24023 shift mean:   0.002 shift max:   0.010 94
r_work: 0.24018 shift mean:   0.002 shift max:   0.010 95
r_work: 0.24010 shift mean:   0.002 shift max:   0.011 96
r_work: 0.24005 shift mean:   0.002 shift max:   0.011 97
r_work: 0.23997 shift mean:   0.002 shift max:   0.012 98
r_work: 0.23991 shift mean:   0.002 shift max:   0.011 99
r_work: 0.23983 shift mean:   0.002 shift max:   0.011 100
r_work: 0.23975 shift mean:   0.002 shift max:   0.012 101
r_work: 0.23970 shift mean:   0.002 shift max:   0.010 102
2: Rw: 0.2397 Rf: 0.3180 Rf-Rw: 0.0783 bond: 0.010 angle: 1.72 clash: 2.6 rota: 6.88 rama: f: 95.89 o: 0.00 Z: -1.82 cb: 0.49 shift start/prev: 0.231 0.045 rws(prev):  0.444 rws:  0.444 n_fev: 102
2: Rw: 0.2397 Rf: 0.3180 Rf-Rw: 0.0783 bond: 0.010 angle: 1.72 clash: 2.6 rota: 6.88 rama: f: 95.89 o: 0.00 Z: -1.82 cb: 0.49 shift start/prev: 0.231 0.045 rws(prev):  0.444 rws:  0.667 n_fev: 102 (NEXT)
Flip happened. Stopping weight search.
Best Rfree from above: 0.3194
Best restraints scale: 0.667
Best Rwork, Rfree (at refinement start): 0.2596 0.3165
At refinement start
 Rw: 0.2596 Rf: 0.3165 Rf-Rw: 0.0569 bond: 0.009 angle: 1.65 clash: 1.7 rota: 6.35 rama: f: 95.43 o: 0.00 Z: -1.41 cb: 0.49 shift start/prev: 0.200 0.045 
Refinement:
r_work: 0.25962 shift mean:   0.000 shift max:   0.000 1
r_work: 0.25769 shift mean:   0.004 shift max:   0.032 2
r_work: 0.25769 shift mean:   0.000 shift max:   0.000 3
r_work: 0.25789 shift mean:   0.000 shift max:   0.004 4
r_work: 0.25802 shift mean:   0.000 shift max:   0.003 5
r_work: 0.25808 shift mean:   0.000 shift max:   0.003 6
r_work: 0.25810 shift mean:   0.000 shift max:   0.002 7
r_work: 0.25809 shift mean:   0.000 shift max:   0.002 8
r_work: 0.25806 shift mean:   0.000 shift max:   0.002 9
r_work: 0.25800 shift mean:   0.000 shift max:   0.002 10
r_work: 0.25794 shift mean:   0.000 shift max:   0.003 11
r_work: 0.25787 shift mean:   0.000 shift max:   0.003 12
r_work: 0.25778 shift mean:   0.001 shift max:   0.004 13
r_work: 0.25762 shift mean:   0.001 shift max:   0.006 14
r_work: 0.25736 shift mean:   0.001 shift max:   0.009 15
r_work: 0.25692 shift mean:   0.002 shift max:   0.014 16
r_work: 0.25620 shift mean:   0.003 shift max:   0.023 17
r_work: 0.25567 shift mean:   0.002 shift max:   0.017 18
r_work: 0.25507 shift mean:   0.003 shift max:   0.020 19
r_work: 0.25447 shift mean:   0.003 shift max:   0.021 20
r_work: 0.25399 shift mean:   0.002 shift max:   0.018 21
r_work: 0.25346 shift mean:   0.003 shift max:   0.022 22
r_work: 0.25307 shift mean:   0.002 shift max:   0.016 23
r_work: 0.25268 shift mean:   0.002 shift max:   0.019 24
r_work: 0.25227 shift mean:   0.003 shift max:   0.022 25
r_work: 0.25192 shift mean:   0.003 shift max:   0.022 26
r_work: 0.25155 shift mean:   0.003 shift max:   0.026 27
r_work: 0.25124 shift mean:   0.003 shift max:   0.022 28
r_work: 0.25090 shift mean:   0.003 shift max:   0.026 29
r_work: 0.25067 shift mean:   0.003 shift max:   0.022 30
r_work: 0.25043 shift mean:   0.003 shift max:   0.024 31
r_work: 0.25026 shift mean:   0.003 shift max:   0.021 32
r_work: 0.25009 shift mean:   0.003 shift max:   0.021 33
r_work: 0.24993 shift mean:   0.003 shift max:   0.020 34
r_work: 0.24980 shift mean:   0.003 shift max:   0.020 35
r_work: 0.24970 shift mean:   0.003 shift max:   0.018 36
r_work: 0.24961 shift mean:   0.003 shift max:   0.017 37
r_work: 0.24954 shift mean:   0.003 shift max:   0.017 38
r_work: 0.24948 shift mean:   0.002 shift max:   0.016 39
r_work: 0.24942 shift mean:   0.002 shift max:   0.014 40
r_work: 0.24941 shift mean:   0.002 shift max:   0.014 41
r_work: 0.24936 shift mean:   0.002 shift max:   0.012 42
r_work: 0.24935 shift mean:   0.002 shift max:   0.012 43
r_work: 0.24933 shift mean:   0.002 shift max:   0.011 44
r_work: 0.24930 shift mean:   0.002 shift max:   0.010 45
r_work: 0.24927 shift mean:   0.002 shift max:   0.010 46
r_work: 0.24925 shift mean:   0.002 shift max:   0.010 47
r_work: 0.24924 shift mean:   0.002 shift max:   0.009 48
r_work: 0.24922 shift mean:   0.002 shift max:   0.010 49
r_work: 0.24921 shift mean:   0.002 shift max:   0.010 50
r_work: 0.24917 shift mean:   0.002 shift max:   0.012 51
r_work: 0.24917 shift mean:   0.002 shift max:   0.010 52
0: Rw: 0.2492 Rf: 0.3162 Rf-Rw: 0.0670 bond: 0.009 angle: 1.70 clash: 2.3 rota: 6.88 rama: f: 95.43 o: 0.00 Z: -1.49 cb: 0.49 shift start/prev: 0.262 0.079 n_fev: 52
r_work: 0.24917 shift mean:   0.000 shift max:   0.000 1
r_work: 0.24932 shift mean:   0.003 shift max:   0.062 2
r_work: 0.24921 shift mean:   0.002 shift max:   0.040 3
r_work: 0.24921 shift mean:   0.000 shift max:   0.004 4
r_work: 0.24920 shift mean:   0.000 shift max:   0.003 5
r_work: 0.24920 shift mean:   0.000 shift max:   0.002 6
r_work: 0.24920 shift mean:   0.000 shift max:   0.002 7
r_work: 0.24920 shift mean:   0.000 shift max:   0.002 8
r_work: 0.24919 shift mean:   0.000 shift max:   0.002 9
r_work: 0.24919 shift mean:   0.000 shift max:   0.001 10
r_work: 0.24919 shift mean:   0.000 shift max:   0.001 11
r_work: 0.24919 shift mean:   0.000 shift max:   0.001 12
r_work: 0.24919 shift mean:   0.000 shift max:   0.001 13
r_work: 0.24919 shift mean:   0.000 shift max:   0.001 14
r_work: 0.24919 shift mean:   0.000 shift max:   0.002 15
r_work: 0.24918 shift mean:   0.000 shift max:   0.002 16
r_work: 0.24919 shift mean:   0.001 shift max:   0.004 17
r_work: 0.24921 shift mean:   0.001 shift max:   0.006 18
r_work: 0.24920 shift mean:   0.002 shift max:   0.010 19
r_work: 0.24919 shift mean:   0.001 shift max:   0.004 20
r_work: 0.24919 shift mean:   0.001 shift max:   0.004 21
r_work: 0.24917 shift mean:   0.001 shift max:   0.004 22
r_work: 0.24915 shift mean:   0.001 shift max:   0.004 23
r_work: 0.24913 shift mean:   0.001 shift max:   0.004 24
r_work: 0.24911 shift mean:   0.001 shift max:   0.004 25
r_work: 0.24910 shift mean:   0.001 shift max:   0.006 26
r_work: 0.24906 shift mean:   0.001 shift max:   0.007 27
r_work: 0.24904 shift mean:   0.001 shift max:   0.007 28
r_work: 0.24901 shift mean:   0.001 shift max:   0.009 29
r_work: 0.24897 shift mean:   0.001 shift max:   0.010 30
r_work: 0.24892 shift mean:   0.002 shift max:   0.012 31
r_work: 0.24888 shift mean:   0.001 shift max:   0.010 32
r_work: 0.24885 shift mean:   0.002 shift max:   0.013 33
r_work: 0.24879 shift mean:   0.002 shift max:   0.014 34
r_work: 0.24876 shift mean:   0.002 shift max:   0.015 35
r_work: 0.24872 shift mean:   0.002 shift max:   0.016 36
r_work: 0.24871 shift mean:   0.002 shift max:   0.016 37
r_work: 0.24870 shift mean:   0.002 shift max:   0.017 38
r_work: 0.24868 shift mean:   0.002 shift max:   0.018 39
r_work: 0.24867 shift mean:   0.002 shift max:   0.016 40
r_work: 0.24870 shift mean:   0.002 shift max:   0.021 41
r_work: 0.24870 shift mean:   0.002 shift max:   0.016 42
r_work: 0.24873 shift mean:   0.002 shift max:   0.019 43
r_work: 0.24878 shift mean:   0.002 shift max:   0.017 44
r_work: 0.24883 shift mean:   0.002 shift max:   0.018 45
r_work: 0.24889 shift mean:   0.002 shift max:   0.018 46
r_work: 0.24892 shift mean:   0.002 shift max:   0.015 47
r_work: 0.24898 shift mean:   0.002 shift max:   0.015 48
r_work: 0.24902 shift mean:   0.001 shift max:   0.012 49
r_work: 0.24906 shift mean:   0.001 shift max:   0.012 50
r_work: 0.24907 shift mean:   0.001 shift max:   0.012 51
r_work: 0.24910 shift mean:   0.001 shift max:   0.010 52
1: Rw: 0.2491 Rf: 0.3163 Rf-Rw: 0.0672 bond: 0.009 angle: 1.67 clash: 2.6 rota: 5.82 rama: f: 96.35 o: 0.00 Z: -1.61 cb: 0.49 shift start/prev: 0.282 0.048 n_fev: 52
r_work: 0.24910 shift mean:   0.000 shift max:   0.000 1
r_work: 0.24892 shift mean:   0.001 shift max:   0.031 2
r_work: 0.24899 shift mean:   0.001 shift max:   0.011 3
r_work: 0.24901 shift mean:   0.000 shift max:   0.003 4
r_work: 0.24901 shift mean:   0.000 shift max:   0.002 5
r_work: 0.24901 shift mean:   0.000 shift max:   0.002 6
r_work: 0.24901 shift mean:   0.000 shift max:   0.002 7
r_work: 0.24900 shift mean:   0.000 shift max:   0.002 8
r_work: 0.24898 shift mean:   0.000 shift max:   0.002 9
r_work: 0.24897 shift mean:   0.000 shift max:   0.002 10
r_work: 0.24896 shift mean:   0.000 shift max:   0.001 11
r_work: 0.24894 shift mean:   0.000 shift max:   0.001 12
r_work: 0.24892 shift mean:   0.000 shift max:   0.001 13
r_work: 0.24889 shift mean:   0.000 shift max:   0.001 14
r_work: 0.24885 shift mean:   0.000 shift max:   0.002 15
r_work: 0.24879 shift mean:   0.000 shift max:   0.003 16
r_work: 0.24870 shift mean:   0.001 shift max:   0.005 17
r_work: 0.24855 shift mean:   0.001 shift max:   0.007 18
r_work: 0.24844 shift mean:   0.001 shift max:   0.006 19
r_work: 0.24833 shift mean:   0.001 shift max:   0.005 20
r_work: 0.24821 shift mean:   0.001 shift max:   0.007 21
r_work: 0.24812 shift mean:   0.001 shift max:   0.005 22
r_work: 0.24804 shift mean:   0.001 shift max:   0.006 23
r_work: 0.24796 shift mean:   0.001 shift max:   0.006 24
r_work: 0.24788 shift mean:   0.001 shift max:   0.006 25
r_work: 0.24779 shift mean:   0.001 shift max:   0.007 26
r_work: 0.24771 shift mean:   0.001 shift max:   0.005 27
r_work: 0.24762 shift mean:   0.001 shift max:   0.008 28
r_work: 0.24756 shift mean:   0.001 shift max:   0.006 29
r_work: 0.24748 shift mean:   0.001 shift max:   0.007 30
r_work: 0.24740 shift mean:   0.001 shift max:   0.008 31
r_work: 0.24734 shift mean:   0.001 shift max:   0.008 32
r_work: 0.24728 shift mean:   0.001 shift max:   0.009 33
r_work: 0.24723 shift mean:   0.001 shift max:   0.008 34
r_work: 0.24719 shift mean:   0.001 shift max:   0.010 35
r_work: 0.24714 shift mean:   0.001 shift max:   0.009 36
r_work: 0.24710 shift mean:   0.001 shift max:   0.009 37
r_work: 0.24707 shift mean:   0.001 shift max:   0.011 38
r_work: 0.24705 shift mean:   0.001 shift max:   0.008 39
r_work: 0.24702 shift mean:   0.001 shift max:   0.011 40
r_work: 0.24700 shift mean:   0.001 shift max:   0.009 41
r_work: 0.24698 shift mean:   0.001 shift max:   0.010 42
r_work: 0.24696 shift mean:   0.001 shift max:   0.011 43
r_work: 0.24695 shift mean:   0.001 shift max:   0.010 44
r_work: 0.24694 shift mean:   0.001 shift max:   0.012 45
r_work: 0.24695 shift mean:   0.001 shift max:   0.011 46
r_work: 0.24694 shift mean:   0.001 shift max:   0.013 47
r_work: 0.24695 shift mean:   0.001 shift max:   0.016 48
r_work: 0.24697 shift mean:   0.001 shift max:   0.014 49
r_work: 0.24698 shift mean:   0.002 shift max:   0.025 50
r_work: 0.24699 shift mean:   0.001 shift max:   0.016 51
r_work: 0.24700 shift mean:   0.002 shift max:   0.030 52
2: Rw: 0.2470 Rf: 0.3160 Rf-Rw: 0.0690 bond: 0.009 angle: 1.68 clash: 2.6 rota: 5.82 rama: f: 96.35 o: 0.00 Z: -1.45 cb: 0.49 shift start/prev: 0.302 0.034 n_fev: 52
r_work: 0.24700 shift mean:   0.000 shift max:   0.000 1
r_work: 0.24715 shift mean:   0.002 shift max:   0.072 2
r_work: 0.24706 shift mean:   0.001 shift max:   0.046 3
r_work: 0.24705 shift mean:   0.000 shift max:   0.004 4
r_work: 0.24704 shift mean:   0.000 shift max:   0.004 5
r_work: 0.24704 shift mean:   0.000 shift max:   0.003 6
r_work: 0.24704 shift mean:   0.000 shift max:   0.002 7
r_work: 0.24704 shift mean:   0.000 shift max:   0.002 8
r_work: 0.24704 shift mean:   0.000 shift max:   0.002 9
r_work: 0.24704 shift mean:   0.000 shift max:   0.001 10
r_work: 0.24704 shift mean:   0.000 shift max:   0.001 11
r_work: 0.24704 shift mean:   0.000 shift max:   0.001 12
r_work: 0.24704 shift mean:   0.000 shift max:   0.001 13
r_work: 0.24704 shift mean:   0.000 shift max:   0.001 14
r_work: 0.24705 shift mean:   0.000 shift max:   0.001 15
r_work: 0.24705 shift mean:   0.000 shift max:   0.001 16
r_work: 0.24705 shift mean:   0.000 shift max:   0.001 17
r_work: 0.24706 shift mean:   0.000 shift max:   0.002 18
r_work: 0.24708 shift mean:   0.000 shift max:   0.003 19
r_work: 0.24710 shift mean:   0.001 shift max:   0.005 20
r_work: 0.24711 shift mean:   0.000 shift max:   0.003 21
r_work: 0.24711 shift mean:   0.000 shift max:   0.003 22
r_work: 0.24711 shift mean:   0.000 shift max:   0.004 23
r_work: 0.24712 shift mean:   0.000 shift max:   0.003 24
r_work: 0.24713 shift mean:   0.000 shift max:   0.004 25
r_work: 0.24713 shift mean:   0.001 shift max:   0.005 26
r_work: 0.24714 shift mean:   0.000 shift max:   0.004 27
r_work: 0.24712 shift mean:   0.001 shift max:   0.007 28
r_work: 0.24713 shift mean:   0.001 shift max:   0.006 29
r_work: 0.24712 shift mean:   0.001 shift max:   0.009 30
r_work: 0.24712 shift mean:   0.001 shift max:   0.007 31
r_work: 0.24711 shift mean:   0.001 shift max:   0.009 32
r_work: 0.24712 shift mean:   0.001 shift max:   0.008 33
r_work: 0.24713 shift mean:   0.001 shift max:   0.008 34
r_work: 0.24715 shift mean:   0.001 shift max:   0.010 35
r_work: 0.24717 shift mean:   0.001 shift max:   0.009 36
r_work: 0.24718 shift mean:   0.001 shift max:   0.010 37
r_work: 0.24722 shift mean:   0.001 shift max:   0.012 38
r_work: 0.24723 shift mean:   0.001 shift max:   0.010 39
r_work: 0.24730 shift mean:   0.001 shift max:   0.017 40
r_work: 0.24734 shift mean:   0.001 shift max:   0.012 41
r_work: 0.24741 shift mean:   0.002 shift max:   0.020 42
r_work: 0.24746 shift mean:   0.001 shift max:   0.016 43
r_work: 0.24753 shift mean:   0.002 shift max:   0.019 44
r_work: 0.24763 shift mean:   0.002 shift max:   0.019 45
r_work: 0.24771 shift mean:   0.001 shift max:   0.014 46
r_work: 0.24779 shift mean:   0.001 shift max:   0.016 47
r_work: 0.24785 shift mean:   0.001 shift max:   0.011 48
r_work: 0.24790 shift mean:   0.001 shift max:   0.011 49
r_work: 0.24796 shift mean:   0.001 shift max:   0.012 50
r_work: 0.24799 shift mean:   0.001 shift max:   0.009 51
r_work: 0.24802 shift mean:   0.001 shift max:   0.012 52
3: Rw: 0.2480 Rf: 0.3168 Rf-Rw: 0.0688 bond: 0.009 angle: 1.67 clash: 2.9 rota: 5.29 rama: f: 96.35 o: 0.00 Z: -1.63 cb: 0.49 shift start/prev: 0.310 0.026 n_fev: 52
r_work: 0.24802 shift mean:   0.000 shift max:   0.000 1
r_work: 0.24796 shift mean:   0.001 shift max:   0.029 2
r_work: 0.24799 shift mean:   0.001 shift max:   0.019 3
r_work: 0.24799 shift mean:   0.000 shift max:   0.002 4
r_work: 0.24800 shift mean:   0.000 shift max:   0.001 5
r_work: 0.24800 shift mean:   0.000 shift max:   0.001 6
r_work: 0.24800 shift mean:   0.000 shift max:   0.001 7
r_work: 0.24800 shift mean:   0.000 shift max:   0.001 8
r_work: 0.24800 shift mean:   0.000 shift max:   0.001 9
r_work: 0.24799 shift mean:   0.000 shift max:   0.001 10
r_work: 0.24799 shift mean:   0.000 shift max:   0.001 11
r_work: 0.24799 shift mean:   0.000 shift max:   0.001 12
r_work: 0.24798 shift mean:   0.000 shift max:   0.001 13
r_work: 0.24797 shift mean:   0.000 shift max:   0.001 14
r_work: 0.24796 shift mean:   0.000 shift max:   0.001 15
r_work: 0.24795 shift mean:   0.000 shift max:   0.002 16
r_work: 0.24793 shift mean:   0.000 shift max:   0.003 17
r_work: 0.24790 shift mean:   0.000 shift max:   0.005 18
r_work: 0.24785 shift mean:   0.001 shift max:   0.008 19
r_work: 0.24774 shift mean:   0.001 shift max:   0.014 20
r_work: 0.24769 shift mean:   0.001 shift max:   0.007 21
r_work: 0.24765 shift mean:   0.001 shift max:   0.007 22
r_work: 0.24761 shift mean:   0.001 shift max:   0.009 23
r_work: 0.24757 shift mean:   0.001 shift max:   0.007 24
r_work: 0.24752 shift mean:   0.001 shift max:   0.009 25
r_work: 0.24747 shift mean:   0.001 shift max:   0.012 26
r_work: 0.24743 shift mean:   0.001 shift max:   0.010 27
r_work: 0.24738 shift mean:   0.001 shift max:   0.015 28
r_work: 0.24732 shift mean:   0.001 shift max:   0.015 29
r_work: 0.24726 shift mean:   0.001 shift max:   0.021 30
r_work: 0.24723 shift mean:   0.001 shift max:   0.017 31
r_work: 0.24718 shift mean:   0.001 shift max:   0.023 32
r_work: 0.24715 shift mean:   0.001 shift max:   0.020 33
r_work: 0.24711 shift mean:   0.001 shift max:   0.023 34
r_work: 0.24710 shift mean:   0.001 shift max:   0.025 35
r_work: 0.24708 shift mean:   0.001 shift max:   0.022 36
r_work: 0.24706 shift mean:   0.001 shift max:   0.025 37
r_work: 0.24703 shift mean:   0.001 shift max:   0.025 38
r_work: 0.24703 shift mean:   0.001 shift max:   0.021 39
r_work: 0.24702 shift mean:   0.001 shift max:   0.027 40
r_work: 0.24701 shift mean:   0.001 shift max:   0.018 41
r_work: 0.24701 shift mean:   0.001 shift max:   0.024 42
r_work: 0.24703 shift mean:   0.001 shift max:   0.021 43
r_work: 0.24704 shift mean:   0.001 shift max:   0.023 44
r_work: 0.24705 shift mean:   0.001 shift max:   0.023 45
r_work: 0.24707 shift mean:   0.001 shift max:   0.020 46
r_work: 0.24710 shift mean:   0.001 shift max:   0.023 47
r_work: 0.24713 shift mean:   0.001 shift max:   0.021 48
r_work: 0.24714 shift mean:   0.001 shift max:   0.022 49
r_work: 0.24718 shift mean:   0.001 shift max:   0.028 50
r_work: 0.24722 shift mean:   0.001 shift max:   0.021 51
r_work: 0.24728 shift mean:   0.001 shift max:   0.035 52
4: Rw: 0.2473 Rf: 0.3172 Rf-Rw: 0.0699 bond: 0.009 angle: 1.67 clash: 2.6 rota: 5.29 rama: f: 96.35 o: 0.00 Z: -1.41 cb: 0.49 shift start/prev: 0.321 0.021 n_fev: 52
At refinement end:
 Rw: 0.2473 Rf: 0.3172 Rf-Rw: 0.0699 bond: 0.009 angle: 1.67 clash: 2.6 rota: 5.29 rama: f: 96.35 o: 0.00 Z: -1.41 cb: 0.49 shift start/prev: 0.321 0.021 
Best Rwork, Rfree (after refinement): 0.2473 0.3172
See 2ogu_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 512.55 seconds
wall clock time: 8 minutes 48.28 seconds (528.28 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)