Starting qr.refine
on Thu Jun 20 16:36:56 2024 by afonine
===============================================================================

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

  Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4JP6.mtz
  Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.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 {
    model {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.pdb"
    }
    default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.pdb"
    miller_array {
      file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4JP6.mtz"
    }
    default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4JP6.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_angle_rmsd = 3.0
  }


Starting job
===============================================================================
Validate inputs:
-------------------------------------------------------------------------------
Refinement start
****************
-------------------------------------------------------------------------------
Extracting fmodel
*****************
                   start: r(all,work,free)=0.2334 0.2350 0.2150 n_refl.: 61516
       re-set all scales: r(all,work,free)=0.2334 0.2350 0.2150 n_refl.: 61516
         remove outliers: r(all,work,free)=0.2334 0.2351 0.2151 n_refl.: 61506
bulk-solvent and scaling: r(all,work,free)=0.1571 0.1558 0.1825 n_refl.: 61506
         remove outliers: r(all,work,free)=0.1571 0.1558 0.1825 n_refl.: 61505
   Resolution    Compl Nwork Nfree R_work    <Fobs>  <Fmodel> kiso   kani kmask
 36.755-9.175    99.01    95     5 0.2967   236.113   216.544 0.785 1.009 0.400
  9.162-7.294   100.00    96     5 0.2311   251.270   243.461 0.991 1.010 0.430
  7.286-5.810   100.00   171     9 0.2409   218.869   211.543 0.940 1.010 0.430
  5.802-4.623   100.00   314    17 0.1813   275.703   266.099 0.962 1.010 0.425
  4.620-3.682   100.00   633    33 0.1541   325.229   313.708 0.992 1.007 0.420
  3.680-2.930   100.00  1220    65 0.1830   263.204   253.695 1.035 1.005 0.082
  2.930-2.333    99.96  2355   124 0.1803   181.754   174.074 0.984 1.000 0.000
  2.333-1.857    99.98  4602   242 0.1660   139.625   132.461 1.063 0.992 0.000
  1.857-1.478    99.98  9002   473 0.1465    78.879    75.202 1.071 0.979 0.000
  1.478-1.177    99.97 17663   930 0.1379    49.725    47.565 1.117 0.958 0.000
  1.177-1.000    99.95 22279  1172 0.1375    33.240    32.178 1.167 0.932 0.000

  Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
    k_overall=1.0009   b_overall=-0.3839 
-------------------------------------------------------------------------------
Starting r-factors:
*******************
r_work=0.1558 r_free=0.1825
-------------------------------------------------------------------------------
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
    Residue "A ASP   33": "OD1" <-> "OD2"
    Residue "A GLU   75": "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: 2330
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1865
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA%NH3:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 465
          Classifications: {'water': 155}
          Link IDs: {None: 154}
  Time building chain proxies: 0.43, per 1000 atoms: 0.18
  Number of scatterers: 2330
  At special positions: 0
  Unit cell: (27.688, 54.971, 73.509, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     333      8.00
     N     176      7.00
     C     602      6.00
     H    1213      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  61 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  84 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 120 " distance=2.06
  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: 0.81
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  220

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1213
        1.03 -     1.23: 20
        1.23 -     1.43: 432
        1.43 -     1.62: 531
        1.62 -     1.82: 6
  Bond restraints: 2202
  Sorted by residual:
  bond pdb=" NH1 ARG A  66 "
       pdb="HH11 ARG A  66 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" NH1 ARG A  73 "
       pdb="HH12 ARG A  73 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.46e+01
  bond pdb=" N   ARG A   7 "
       pdb=" H   ARG A   7 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.46e+01
  bond pdb=" NH2 ARG A  79 "
       pdb="HH21 ARG A  79 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.46e+01
  bond pdb=" N   PHE A  49 "
       pdb=" H   PHE A  49 "
    ideal  model  delta    sigma   weight residual
    1.020  0.859  0.161 2.00e-02 2.50e+03 6.46e+01
  ... (remaining 2197 not shown)

  Histogram of bond angle deviations from ideal:
      101.78 -   108.42: 702
      108.42 -   115.05: 1676
      115.05 -   121.69: 724
      121.69 -   128.33: 417
      128.33 -   134.96: 13
  Bond angle restraints: 3532
  Sorted by residual:
  angle pdb=" C   ASN A 114 "
        pdb=" CA  ASN A 114 "
        pdb=" CB  ASN A 114 "
      ideal   model   delta    sigma   weight residual
     110.10  116.55   -6.45 1.90e+00 2.77e-01 1.15e+01
  angle pdb=" C   LEU A  91 "
        pdb=" CA  LEU A  91 "
        pdb=" CB  LEU A  91 "
      ideal   model   delta    sigma   weight residual
     110.10  105.41    4.69 1.90e+00 2.77e-01 6.08e+00
  angle pdb=" CA  TRP A  40 "
        pdb=" CB  TRP A  40 "
        pdb=" CG  TRP A  40 "
      ideal   model   delta    sigma   weight residual
     113.60  118.21   -4.61 1.90e+00 2.77e-01 5.88e+00
  angle pdb=" CB  ASN A 114 "
        pdb=" CA  ASN A 114 "
        pdb=" HA  ASN A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  101.78    7.22 3.00e+00 1.11e-01 5.79e+00
  angle pdb=" N   PCA A   1 "
        pdb=" CA  PCA A   1 "
        pdb=" CB  PCA A   1 "
      ideal   model   delta    sigma   weight residual
     110.50  106.44    4.06 1.70e+00 3.46e-01 5.69e+00
  ... (remaining 3527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.97: 790
       11.97 -    23.93: 80
       23.93 -    35.89: 13
       35.89 -    47.85: 14
       47.85 -    59.82: 10
  Dihedral angle restraints: 907
    sinusoidal: 472
      harmonic: 435
  Sorted by residual:
  dihedral pdb=" CA  THR A  47 "
           pdb=" C   THR A  47 "
           pdb=" N   ALA A  48 "
           pdb=" CA  ALA A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.03   23.97     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  VAL A 113 "
           pdb=" C   VAL A 113 "
           pdb=" N   ASN A 114 "
           pdb=" CA  ASN A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LEU A  65 "
           pdb=" C   LEU A  65 "
           pdb=" N   ARG A  66 "
           pdb=" CA  ARG A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.60   18.40     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 81
       0.065 -    0.129: 37
       0.129 -    0.193: 11
       0.193 -    0.257: 7
       0.257 -    0.321: 1
  Chirality restraints: 137
  Sorted by residual:
  chirality pdb=" CA  ASP A  35 "
            pdb=" N   ASP A  35 "
            pdb=" C   ASP A  35 "
            pdb=" CB  ASP A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  GLN A 116 "
            pdb=" N   GLN A 116 "
            pdb=" C   GLN A 116 "
            pdb=" CB  GLN A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ASP A 102 "
            pdb=" N   ASP A 102 "
            pdb=" C   ASP A 102 "
            pdb=" CB  ASP A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 134 not shown)

  Planarity restraints: 292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  12 "   -0.025 2.00e-02 2.50e+03   2.80e-02 2.35e+01
        pdb=" CG  PHE A  12 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  12 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  12 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  12 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  12 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  12 "   -0.021 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  12 "   -0.008 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  12 "    0.042 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  12 "    0.040 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  12 "   -0.066 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  49 "   -0.023 2.00e-02 2.50e+03   2.74e-02 2.26e+01
        pdb=" CG  PHE A  49 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  49 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  49 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  49 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  49 "    0.004 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  49 "    0.065 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  49 "    0.008 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  49 "   -0.052 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  49 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  49 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  96 "    0.030 2.00e-02 2.50e+03   2.60e-02 2.02e+01
        pdb=" CG  PHE A  96 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  96 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  96 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  96 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  96 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  96 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  96 "    0.004 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  96 "   -0.030 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  96 "    0.021 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  96 "    0.054 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  96 "   -0.037 2.00e-02 2.50e+03
  ... (remaining 289 not shown)

  Histogram of nonbonded interaction distances:
        1.14 -     1.83: 21
        1.83 -     2.52: 2153
        2.52 -     3.22: 8056
        3.22 -     3.91: 12483
        3.91 -     4.60: 18691
  Nonbonded interactions: 41404
  Sorted by model distance:
  nonbonded pdb="HH12 ARG A  73 "
            pdb=" O   HOH A 250 "
     model   vdw sym.op.
     1.141 1.800 -x+3/2,-y,z+1/2
  nonbonded pdb="HH21 ARG A  73 "
            pdb=" H2  HOH A 334 "
     model   vdw
     1.407 2.000
  nonbonded pdb="HH22 ARG A  73 "
            pdb=" H1  HOH A 334 "
     model   vdw
     1.449 2.000
  nonbonded pdb="HE21 GLN A 116 "
            pdb=" O   HOH A 251 "
     model   vdw
     1.553 1.800
  nonbonded pdb="HE22 GLN A 116 "
            pdb=" O   HOH A 316 "
     model   vdw
     1.557 1.800
  ... (remaining 41399 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       6     15.96       2
   O     333      7.97       2
   N     176      6.97       2
   C     602      5.97       2
   H    1213      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

Optimize H with d.o.f.
  start: r_work=0.1558 r_free=0.1825
  final: r_work=0.1584 r_free=0.1858
Start:
   Rw: 0.1584 Rf: 0.1858 Rf-Rw: 0.0273 bond: 0.009 angle: 1.35 clash: 3.8 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -1.03 cb: 0.00 shift start/prev: 0.079 0.083 
Optimal weight search:
Data weight (initial): 1446.3225870835863
r_work: 0.15844 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16256 shift mean:   0.015 shift max:   0.194 2
r_work: 0.16290 shift mean:   0.000 shift max:   0.006 3
r_work: 0.16112 shift mean:   0.001 shift max:   0.032 4
r_work: 0.15996 shift mean:   0.001 shift max:   0.016 5
r_work: 0.15915 shift mean:   0.001 shift max:   0.013 6
r_work: 0.15859 shift mean:   0.001 shift max:   0.011 7
r_work: 0.15822 shift mean:   0.001 shift max:   0.012 8
r_work: 0.15797 shift mean:   0.001 shift max:   0.011 9
r_work: 0.15781 shift mean:   0.001 shift max:   0.009 10
r_work: 0.15772 shift mean:   0.001 shift max:   0.008 11
r_work: 0.15766 shift mean:   0.001 shift max:   0.007 12
r_work: 0.15762 shift mean:   0.001 shift max:   0.010 13
r_work: 0.15760 shift mean:   0.001 shift max:   0.013 14
r_work: 0.15759 shift mean:   0.001 shift max:   0.007 15
r_work: 0.15760 shift mean:   0.001 shift max:   0.013 16
r_work: 0.15761 shift mean:   0.002 shift max:   0.019 17
r_work: 0.15764 shift mean:   0.002 shift max:   0.018 18
r_work: 0.15770 shift mean:   0.002 shift max:   0.028 19
r_work: 0.15772 shift mean:   0.002 shift max:   0.021 20
r_work: 0.15776 shift mean:   0.002 shift max:   0.031 21
r_work: 0.15778 shift mean:   0.002 shift max:   0.030 22
r_work: 0.15782 shift mean:   0.002 shift max:   0.033 23
r_work: 0.15783 shift mean:   0.003 shift max:   0.037 24
r_work: 0.15787 shift mean:   0.002 shift max:   0.030 25
r_work: 0.15794 shift mean:   0.002 shift max:   0.037 26
r_work: 0.15796 shift mean:   0.001 shift max:   0.018 27
r_work: 0.15799 shift mean:   0.001 shift max:   0.022 28
r_work: 0.15804 shift mean:   0.002 shift max:   0.033 29
r_work: 0.15807 shift mean:   0.002 shift max:   0.024 30
r_work: 0.15811 shift mean:   0.002 shift max:   0.025 31
r_work: 0.15814 shift mean:   0.002 shift max:   0.026 32
r_work: 0.15816 shift mean:   0.002 shift max:   0.025 33
r_work: 0.15819 shift mean:   0.002 shift max:   0.032 34
r_work: 0.15821 shift mean:   0.002 shift max:   0.024 35
r_work: 0.15823 shift mean:   0.002 shift max:   0.031 36
r_work: 0.15825 shift mean:   0.002 shift max:   0.032 37
r_work: 0.15826 shift mean:   0.002 shift max:   0.024 38
r_work: 0.15827 shift mean:   0.002 shift max:   0.027 39
r_work: 0.15828 shift mean:   0.002 shift max:   0.033 40
r_work: 0.15829 shift mean:   0.001 shift max:   0.021 41
r_work: 0.15832 shift mean:   0.002 shift max:   0.031 42
r_work: 0.15831 shift mean:   0.002 shift max:   0.023 43
r_work: 0.15831 shift mean:   0.002 shift max:   0.026 44
r_work: 0.15830 shift mean:   0.002 shift max:   0.025 45
r_work: 0.15828 shift mean:   0.002 shift max:   0.025 46
r_work: 0.15826 shift mean:   0.002 shift max:   0.024 47
r_work: 0.15823 shift mean:   0.002 shift max:   0.025 48
r_work: 0.15821 shift mean:   0.002 shift max:   0.027 49
r_work: 0.15817 shift mean:   0.002 shift max:   0.030 50
r_work: 0.15816 shift mean:   0.001 shift max:   0.019 51
r_work: 0.15811 shift mean:   0.002 shift max:   0.027 52
r_work: 0.15809 shift mean:   0.001 shift max:   0.021 53
r_work: 0.15805 shift mean:   0.001 shift max:   0.024 54
r_work: 0.15801 shift mean:   0.001 shift max:   0.027 55
r_work: 0.15798 shift mean:   0.001 shift max:   0.025 56
r_work: 0.15796 shift mean:   0.001 shift max:   0.023 57
r_work: 0.15793 shift mean:   0.002 shift max:   0.028 58
r_work: 0.15791 shift mean:   0.001 shift max:   0.025 59
r_work: 0.15789 shift mean:   0.002 shift max:   0.030 60
r_work: 0.15787 shift mean:   0.002 shift max:   0.029 61
r_work: 0.15785 shift mean:   0.001 shift max:   0.027 62
r_work: 0.15784 shift mean:   0.002 shift max:   0.029 63
r_work: 0.15783 shift mean:   0.002 shift max:   0.029 64
r_work: 0.15781 shift mean:   0.002 shift max:   0.030 65
r_work: 0.15781 shift mean:   0.002 shift max:   0.032 66
r_work: 0.15781 shift mean:   0.002 shift max:   0.029 67
r_work: 0.15781 shift mean:   0.002 shift max:   0.029 68
r_work: 0.15781 shift mean:   0.002 shift max:   0.030 69
r_work: 0.15781 shift mean:   0.001 shift max:   0.025 70
r_work: 0.15781 shift mean:   0.002 shift max:   0.027 71
r_work: 0.15781 shift mean:   0.002 shift max:   0.028 72
r_work: 0.15781 shift mean:   0.002 shift max:   0.027 73
r_work: 0.15782 shift mean:   0.001 shift max:   0.023 74
r_work: 0.15783 shift mean:   0.002 shift max:   0.027 75
r_work: 0.15783 shift mean:   0.001 shift max:   0.019 76
r_work: 0.15784 shift mean:   0.001 shift max:   0.023 77
r_work: 0.15784 shift mean:   0.001 shift max:   0.019 78
r_work: 0.15785 shift mean:   0.001 shift max:   0.022 79
r_work: 0.15785 shift mean:   0.001 shift max:   0.018 80
r_work: 0.15787 shift mean:   0.001 shift max:   0.020 81
r_work: 0.15787 shift mean:   0.001 shift max:   0.012 82
r_work: 0.15786 shift mean:   0.001 shift max:   0.016 83
r_work: 0.15787 shift mean:   0.001 shift max:   0.011 84
r_work: 0.15787 shift mean:   0.001 shift max:   0.014 85
r_work: 0.15787 shift mean:   0.001 shift max:   0.010 86
r_work: 0.15786 shift mean:   0.001 shift max:   0.010 87
r_work: 0.15785 shift mean:   0.001 shift max:   0.011 88
r_work: 0.15784 shift mean:   0.001 shift max:   0.010 89
r_work: 0.15784 shift mean:   0.001 shift max:   0.007 90
r_work: 0.15783 shift mean:   0.001 shift max:   0.009 91
r_work: 0.15782 shift mean:   0.001 shift max:   0.009 92
r_work: 0.15781 shift mean:   0.001 shift max:   0.008 93
r_work: 0.15780 shift mean:   0.001 shift max:   0.010 94
r_work: 0.15779 shift mean:   0.001 shift max:   0.009 95
r_work: 0.15779 shift mean:   0.001 shift max:   0.009 96
r_work: 0.15778 shift mean:   0.001 shift max:   0.010 97
r_work: 0.15777 shift mean:   0.001 shift max:   0.011 98
r_work: 0.15776 shift mean:   0.001 shift max:   0.008 99
r_work: 0.15775 shift mean:   0.001 shift max:   0.012 100
r_work: 0.15775 shift mean:   0.001 shift max:   0.008 101
r_work: 0.15774 shift mean:   0.001 shift max:   0.010 102
0: Rw: 0.1577 Rf: 0.1856 Rf-Rw: 0.0278 bond: 0.014 angle: 1.80 clash: 2.7 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.97 cb: 0.00 shift start/prev: 0.121 0.084 rws(prev):  1.000 rws:  1.000 n_fev: 102
Optimal weight found. Stopping weight search.
Best Rfree from above: 0.1856
Best restraints scale: 1.0
Best Rwork, Rfree (at refinement start): 0.1576 0.1853
At refinement start
 Rw: 0.1576 Rf: 0.1853 Rf-Rw: 0.0277 bond: 0.014 angle: 1.80 clash: 2.7 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.97 cb: 0.00 shift start/prev: 0.121 0.000 
Refinement:
r_work: 0.15760 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16852 shift mean:   0.006 shift max:   0.200 2
r_work: 0.16668 shift mean:   0.001 shift max:   0.020 3
r_work: 0.16374 shift mean:   0.001 shift max:   0.035 4
r_work: 0.16107 shift mean:   0.001 shift max:   0.041 5
r_work: 0.15969 shift mean:   0.001 shift max:   0.025 6
r_work: 0.15891 shift mean:   0.000 shift max:   0.017 7
r_work: 0.15846 shift mean:   0.000 shift max:   0.013 8
r_work: 0.15816 shift mean:   0.000 shift max:   0.010 9
r_work: 0.15797 shift mean:   0.000 shift max:   0.008 10
r_work: 0.15783 shift mean:   0.000 shift max:   0.006 11
r_work: 0.15776 shift mean:   0.000 shift max:   0.005 12
r_work: 0.15770 shift mean:   0.000 shift max:   0.004 13
r_work: 0.15766 shift mean:   0.000 shift max:   0.003 14
r_work: 0.15764 shift mean:   0.000 shift max:   0.003 15
r_work: 0.15762 shift mean:   0.000 shift max:   0.002 16
r_work: 0.15761 shift mean:   0.000 shift max:   0.002 17
r_work: 0.15760 shift mean:   0.000 shift max:   0.002 18
r_work: 0.15759 shift mean:   0.000 shift max:   0.002 19
r_work: 0.15758 shift mean:   0.000 shift max:   0.001 20
r_work: 0.15758 shift mean:   0.000 shift max:   0.001 21
r_work: 0.15758 shift mean:   0.000 shift max:   0.002 22
r_work: 0.15757 shift mean:   0.000 shift max:   0.001 23
r_work: 0.15758 shift mean:   0.000 shift max:   0.001 24
r_work: 0.15757 shift mean:   0.000 shift max:   0.001 25
r_work: 0.15757 shift mean:   0.000 shift max:   0.002 26
r_work: 0.15756 shift mean:   0.000 shift max:   0.003 27
r_work: 0.15757 shift mean:   0.001 shift max:   0.004 28
r_work: 0.15757 shift mean:   0.001 shift max:   0.006 29
r_work: 0.15757 shift mean:   0.001 shift max:   0.005 30
r_work: 0.15757 shift mean:   0.001 shift max:   0.005 31
r_work: 0.15757 shift mean:   0.001 shift max:   0.005 32
r_work: 0.15758 shift mean:   0.000 shift max:   0.004 33
r_work: 0.15758 shift mean:   0.001 shift max:   0.005 34
r_work: 0.15758 shift mean:   0.001 shift max:   0.006 35
r_work: 0.15758 shift mean:   0.000 shift max:   0.004 36
r_work: 0.15757 shift mean:   0.001 shift max:   0.006 37
r_work: 0.15759 shift mean:   0.001 shift max:   0.007 38
r_work: 0.15759 shift mean:   0.001 shift max:   0.007 39
r_work: 0.15759 shift mean:   0.001 shift max:   0.007 40
r_work: 0.15759 shift mean:   0.001 shift max:   0.011 41
r_work: 0.15760 shift mean:   0.001 shift max:   0.011 42
r_work: 0.15760 shift mean:   0.001 shift max:   0.016 43
r_work: 0.15761 shift mean:   0.001 shift max:   0.013 44
r_work: 0.15762 shift mean:   0.002 shift max:   0.018 45
r_work: 0.15763 shift mean:   0.001 shift max:   0.015 46
r_work: 0.15762 shift mean:   0.001 shift max:   0.018 47
r_work: 0.15764 shift mean:   0.001 shift max:   0.015 48
r_work: 0.15766 shift mean:   0.002 shift max:   0.021 49
r_work: 0.15766 shift mean:   0.001 shift max:   0.013 50
r_work: 0.15767 shift mean:   0.001 shift max:   0.018 51
r_work: 0.15769 shift mean:   0.002 shift max:   0.022 52
0: Rw: 0.1577 Rf: 0.1859 Rf-Rw: 0.0282 bond: 0.014 angle: 1.79 clash: 2.1 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.98 cb: 0.00 shift start/prev: 0.127 0.022 n_fev: 52
r_work: 0.15769 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16337 shift mean:   0.006 shift max:   0.200 2
r_work: 0.16337 shift mean:   0.000 shift max:   0.000 3
r_work: 0.16152 shift mean:   0.001 shift max:   0.038 4
r_work: 0.15994 shift mean:   0.001 shift max:   0.042 5
r_work: 0.15905 shift mean:   0.001 shift max:   0.028 6
r_work: 0.15855 shift mean:   0.000 shift max:   0.019 7
r_work: 0.15824 shift mean:   0.000 shift max:   0.014 8
r_work: 0.15804 shift mean:   0.000 shift max:   0.011 9
r_work: 0.15791 shift mean:   0.000 shift max:   0.009 10
r_work: 0.15783 shift mean:   0.000 shift max:   0.007 11
r_work: 0.15777 shift mean:   0.000 shift max:   0.006 12
r_work: 0.15773 shift mean:   0.000 shift max:   0.004 13
r_work: 0.15771 shift mean:   0.000 shift max:   0.004 14
r_work: 0.15769 shift mean:   0.000 shift max:   0.003 15
r_work: 0.15768 shift mean:   0.000 shift max:   0.003 16
r_work: 0.15767 shift mean:   0.000 shift max:   0.002 17
r_work: 0.15767 shift mean:   0.000 shift max:   0.001 18
r_work: 0.15767 shift mean:   0.000 shift max:   0.002 19
r_work: 0.15767 shift mean:   0.000 shift max:   0.001 20
r_work: 0.15767 shift mean:   0.000 shift max:   0.001 21
r_work: 0.15767 shift mean:   0.000 shift max:   0.001 22
r_work: 0.15766 shift mean:   0.000 shift max:   0.001 23
r_work: 0.15767 shift mean:   0.000 shift max:   0.001 24
r_work: 0.15767 shift mean:   0.000 shift max:   0.002 25
r_work: 0.15767 shift mean:   0.000 shift max:   0.004 26
r_work: 0.15766 shift mean:   0.000 shift max:   0.004 27
r_work: 0.15766 shift mean:   0.001 shift max:   0.006 28
r_work: 0.15766 shift mean:   0.001 shift max:   0.006 29
r_work: 0.15766 shift mean:   0.001 shift max:   0.006 30
r_work: 0.15766 shift mean:   0.001 shift max:   0.007 31
r_work: 0.15766 shift mean:   0.001 shift max:   0.006 32
r_work: 0.15767 shift mean:   0.001 shift max:   0.005 33
r_work: 0.15767 shift mean:   0.001 shift max:   0.006 34
r_work: 0.15767 shift mean:   0.000 shift max:   0.004 35
r_work: 0.15768 shift mean:   0.001 shift max:   0.005 36
r_work: 0.15769 shift mean:   0.000 shift max:   0.004 37
r_work: 0.15769 shift mean:   0.000 shift max:   0.005 38
r_work: 0.15769 shift mean:   0.000 shift max:   0.005 39
r_work: 0.15769 shift mean:   0.000 shift max:   0.005 40
r_work: 0.15770 shift mean:   0.000 shift max:   0.005 41
r_work: 0.15771 shift mean:   0.001 shift max:   0.007 42
r_work: 0.15772 shift mean:   0.001 shift max:   0.008 43
r_work: 0.15773 shift mean:   0.001 shift max:   0.008 44
r_work: 0.15775 shift mean:   0.001 shift max:   0.014 45
r_work: 0.15775 shift mean:   0.001 shift max:   0.009 46
r_work: 0.15776 shift mean:   0.001 shift max:   0.014 47
r_work: 0.15776 shift mean:   0.001 shift max:   0.014 48
r_work: 0.15777 shift mean:   0.001 shift max:   0.016 49
r_work: 0.15778 shift mean:   0.001 shift max:   0.014 50
r_work: 0.15778 shift mean:   0.001 shift max:   0.017 51
r_work: 0.15778 shift mean:   0.001 shift max:   0.014 52
1: Rw: 0.1578 Rf: 0.1853 Rf-Rw: 0.0275 bond: 0.014 angle: 1.82 clash: 2.1 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.132 0.016 n_fev: 52
r_work: 0.15778 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16576 shift mean:   0.007 shift max:   0.200 2
r_work: 0.15999 shift mean:   0.004 shift max:   0.098 3
r_work: 0.15924 shift mean:   0.001 shift max:   0.019 4
r_work: 0.15869 shift mean:   0.001 shift max:   0.018 5
r_work: 0.15836 shift mean:   0.000 shift max:   0.013 6
r_work: 0.15815 shift mean:   0.000 shift max:   0.010 7
r_work: 0.15802 shift mean:   0.000 shift max:   0.008 8
r_work: 0.15793 shift mean:   0.000 shift max:   0.006 9
r_work: 0.15787 shift mean:   0.000 shift max:   0.005 10
r_work: 0.15783 shift mean:   0.000 shift max:   0.004 11
r_work: 0.15780 shift mean:   0.000 shift max:   0.003 12
r_work: 0.15778 shift mean:   0.000 shift max:   0.003 13
r_work: 0.15777 shift mean:   0.000 shift max:   0.002 14
r_work: 0.15776 shift mean:   0.000 shift max:   0.001 15
r_work: 0.15776 shift mean:   0.000 shift max:   0.002 16
r_work: 0.15776 shift mean:   0.000 shift max:   0.001 17
r_work: 0.15776 shift mean:   0.000 shift max:   0.001 18
r_work: 0.15775 shift mean:   0.000 shift max:   0.001 19
r_work: 0.15775 shift mean:   0.000 shift max:   0.001 20
r_work: 0.15775 shift mean:   0.000 shift max:   0.001 21
r_work: 0.15775 shift mean:   0.000 shift max:   0.001 22
r_work: 0.15775 shift mean:   0.000 shift max:   0.001 23
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 24
r_work: 0.15774 shift mean:   0.000 shift max:   0.003 25
r_work: 0.15774 shift mean:   0.000 shift max:   0.003 26
r_work: 0.15774 shift mean:   0.000 shift max:   0.004 27
r_work: 0.15774 shift mean:   0.000 shift max:   0.006 28
r_work: 0.15773 shift mean:   0.001 shift max:   0.007 29
r_work: 0.15773 shift mean:   0.001 shift max:   0.006 30
r_work: 0.15772 shift mean:   0.001 shift max:   0.008 31
r_work: 0.15771 shift mean:   0.001 shift max:   0.007 32
r_work: 0.15771 shift mean:   0.000 shift max:   0.005 33
r_work: 0.15770 shift mean:   0.000 shift max:   0.006 34
r_work: 0.15770 shift mean:   0.000 shift max:   0.005 35
r_work: 0.15770 shift mean:   0.000 shift max:   0.004 36
r_work: 0.15770 shift mean:   0.000 shift max:   0.005 37
r_work: 0.15770 shift mean:   0.000 shift max:   0.003 38
r_work: 0.15770 shift mean:   0.000 shift max:   0.004 39
r_work: 0.15770 shift mean:   0.000 shift max:   0.006 40
r_work: 0.15770 shift mean:   0.000 shift max:   0.006 41
r_work: 0.15769 shift mean:   0.001 shift max:   0.009 42
r_work: 0.15769 shift mean:   0.001 shift max:   0.009 43
r_work: 0.15769 shift mean:   0.001 shift max:   0.011 44
r_work: 0.15769 shift mean:   0.001 shift max:   0.014 45
r_work: 0.15770 shift mean:   0.001 shift max:   0.012 46
r_work: 0.15770 shift mean:   0.001 shift max:   0.016 47
r_work: 0.15771 shift mean:   0.001 shift max:   0.015 48
r_work: 0.15772 shift mean:   0.001 shift max:   0.020 49
r_work: 0.15773 shift mean:   0.001 shift max:   0.016 50
r_work: 0.15774 shift mean:   0.001 shift max:   0.020 51
r_work: 0.15776 shift mean:   0.001 shift max:   0.023 52
2: Rw: 0.1578 Rf: 0.1850 Rf-Rw: 0.0272 bond: 0.014 angle: 1.79 clash: 1.6 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.137 0.015 n_fev: 52
r_work: 0.15776 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16616 shift mean:   0.009 shift max:   0.200 2
r_work: 0.15955 shift mean:   0.005 shift max:   0.109 3
r_work: 0.15892 shift mean:   0.001 shift max:   0.017 4
r_work: 0.15850 shift mean:   0.001 shift max:   0.015 5
r_work: 0.15822 shift mean:   0.000 shift max:   0.012 6
r_work: 0.15804 shift mean:   0.000 shift max:   0.009 7
r_work: 0.15794 shift mean:   0.000 shift max:   0.007 8
r_work: 0.15786 shift mean:   0.000 shift max:   0.006 9
r_work: 0.15782 shift mean:   0.000 shift max:   0.005 10
r_work: 0.15779 shift mean:   0.000 shift max:   0.004 11
r_work: 0.15777 shift mean:   0.000 shift max:   0.003 12
r_work: 0.15776 shift mean:   0.000 shift max:   0.002 13
r_work: 0.15775 shift mean:   0.000 shift max:   0.002 14
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 15
r_work: 0.15774 shift mean:   0.000 shift max:   0.002 16
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 17
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 18
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 19
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 20
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 21
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 22
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 23
r_work: 0.15774 shift mean:   0.000 shift max:   0.001 24
r_work: 0.15774 shift mean:   0.000 shift max:   0.002 25
r_work: 0.15774 shift mean:   0.000 shift max:   0.003 26
r_work: 0.15774 shift mean:   0.000 shift max:   0.004 27
r_work: 0.15774 shift mean:   0.000 shift max:   0.005 28
r_work: 0.15774 shift mean:   0.001 shift max:   0.006 29
r_work: 0.15775 shift mean:   0.001 shift max:   0.007 30
r_work: 0.15775 shift mean:   0.001 shift max:   0.006 31
r_work: 0.15776 shift mean:   0.001 shift max:   0.008 32
r_work: 0.15776 shift mean:   0.000 shift max:   0.005 33
r_work: 0.15776 shift mean:   0.000 shift max:   0.005 34
r_work: 0.15776 shift mean:   0.000 shift max:   0.004 35
r_work: 0.15776 shift mean:   0.000 shift max:   0.004 36
r_work: 0.15776 shift mean:   0.000 shift max:   0.004 37
r_work: 0.15777 shift mean:   0.000 shift max:   0.004 38
r_work: 0.15777 shift mean:   0.000 shift max:   0.005 39
r_work: 0.15778 shift mean:   0.000 shift max:   0.004 40
r_work: 0.15778 shift mean:   0.000 shift max:   0.006 41
r_work: 0.15778 shift mean:   0.000 shift max:   0.005 42
r_work: 0.15779 shift mean:   0.001 shift max:   0.009 43
r_work: 0.15778 shift mean:   0.000 shift max:   0.008 44
r_work: 0.15779 shift mean:   0.001 shift max:   0.009 45
r_work: 0.15779 shift mean:   0.001 shift max:   0.011 46
r_work: 0.15780 shift mean:   0.001 shift max:   0.011 47
r_work: 0.15781 shift mean:   0.001 shift max:   0.014 48
r_work: 0.15781 shift mean:   0.001 shift max:   0.013 49
r_work: 0.15781 shift mean:   0.001 shift max:   0.014 50
r_work: 0.15783 shift mean:   0.001 shift max:   0.014 51
r_work: 0.15783 shift mean:   0.001 shift max:   0.016 52
3: Rw: 0.1578 Rf: 0.1849 Rf-Rw: 0.0271 bond: 0.014 angle: 1.82 clash: 1.6 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.141 0.013 n_fev: 52
r_work: 0.15783 shift mean:   0.000 shift max:   0.000 1
r_work: 0.16965 shift mean:   0.012 shift max:   0.200 2
r_work: 0.15854 shift mean:   0.009 shift max:   0.152 3
r_work: 0.15830 shift mean:   0.000 shift max:   0.009 4
r_work: 0.15813 shift mean:   0.000 shift max:   0.008 5
r_work: 0.15802 shift mean:   0.000 shift max:   0.006 6
r_work: 0.15795 shift mean:   0.000 shift max:   0.005 7
r_work: 0.15790 shift mean:   0.000 shift max:   0.004 8
r_work: 0.15787 shift mean:   0.000 shift max:   0.004 9
r_work: 0.15785 shift mean:   0.000 shift max:   0.003 10
r_work: 0.15784 shift mean:   0.000 shift max:   0.002 11
r_work: 0.15783 shift mean:   0.000 shift max:   0.002 12
r_work: 0.15783 shift mean:   0.000 shift max:   0.001 13
r_work: 0.15782 shift mean:   0.000 shift max:   0.001 14
r_work: 0.15782 shift mean:   0.000 shift max:   0.001 15
r_work: 0.15782 shift mean:   0.000 shift max:   0.001 16
r_work: 0.15781 shift mean:   0.000 shift max:   0.001 17
r_work: 0.15781 shift mean:   0.000 shift max:   0.001 18
r_work: 0.15781 shift mean:   0.000 shift max:   0.001 19
r_work: 0.15782 shift mean:   0.000 shift max:   0.001 20
r_work: 0.15781 shift mean:   0.000 shift max:   0.001 21
r_work: 0.15781 shift mean:   0.000 shift max:   0.001 22
r_work: 0.15781 shift mean:   0.000 shift max:   0.002 23
r_work: 0.15782 shift mean:   0.000 shift max:   0.003 24
r_work: 0.15781 shift mean:   0.000 shift max:   0.004 25
r_work: 0.15782 shift mean:   0.000 shift max:   0.005 26
r_work: 0.15781 shift mean:   0.000 shift max:   0.006 27
r_work: 0.15782 shift mean:   0.001 shift max:   0.008 28
r_work: 0.15781 shift mean:   0.000 shift max:   0.006 29
r_work: 0.15781 shift mean:   0.001 shift max:   0.007 30
r_work: 0.15781 shift mean:   0.000 shift max:   0.006 31
r_work: 0.15780 shift mean:   0.000 shift max:   0.006 32
r_work: 0.15780 shift mean:   0.000 shift max:   0.006 33
r_work: 0.15779 shift mean:   0.000 shift max:   0.004 34
r_work: 0.15779 shift mean:   0.000 shift max:   0.005 35
r_work: 0.15778 shift mean:   0.000 shift max:   0.003 36
r_work: 0.15778 shift mean:   0.000 shift max:   0.005 37
r_work: 0.15778 shift mean:   0.000 shift max:   0.004 38
r_work: 0.15778 shift mean:   0.000 shift max:   0.006 39
r_work: 0.15778 shift mean:   0.000 shift max:   0.005 40
r_work: 0.15778 shift mean:   0.000 shift max:   0.008 41
r_work: 0.15778 shift mean:   0.000 shift max:   0.007 42
r_work: 0.15779 shift mean:   0.000 shift max:   0.008 43
r_work: 0.15779 shift mean:   0.000 shift max:   0.009 44
r_work: 0.15779 shift mean:   0.000 shift max:   0.009 45
r_work: 0.15779 shift mean:   0.000 shift max:   0.009 46
r_work: 0.15779 shift mean:   0.001 shift max:   0.011 47
r_work: 0.15780 shift mean:   0.001 shift max:   0.013 48
r_work: 0.15780 shift mean:   0.001 shift max:   0.015 49
r_work: 0.15781 shift mean:   0.001 shift max:   0.017 50
r_work: 0.15781 shift mean:   0.001 shift max:   0.017 51
r_work: 0.15782 shift mean:   0.001 shift max:   0.021 52
4: Rw: 0.1578 Rf: 0.1851 Rf-Rw: 0.0272 bond: 0.014 angle: 1.80 clash: 1.6 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.144 0.013 n_fev: 52
At refinement end:
 Rw: 0.1578 Rf: 0.1851 Rf-Rw: 0.0272 bond: 0.014 angle: 1.80 clash: 1.6 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.144 0.013 
Best Rwork, Rfree (after refinement): 0.1578 0.1851
See 4JP6_refined.pdb in pdb folder.

===============================================================================
Job complete
usr+sys time: 632.60 seconds
wall clock time: 10 minutes 50.00 seconds (650.00 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)