Starting phenix.real_space_refine
on Sat Jul 26 12:19:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vwh_21416/07_2025/6vwh_21416.cif"
  }
  resolution = 4.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    2726      2.51       5
     N     750      2.21       5
     O     808      1.98       5
     H    4139      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8461
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2196
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 10, 'TRANS': 125}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 6265
          Classifications: {'peptide': 403}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 377}
          Chain breaks: 4
  Time building chain proxies: 7.26, per 1000 atoms: 0.86
  Number of scatterers: 8461
  At special positions: 0
  Unit cell: (97.52, 119.78, 79.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     O     808      8.00
     N     750      7.00
     C    2726      6.00
     H    4139      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 776 " - pdb=" SG  CYS A 785 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B   3 " - pdb=" SG  CYS B  22 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 152 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 189 " - pdb=" SG  CYS B 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 209 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS B 218 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 221 " - pdb=" SG  CYS B 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 234 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 277 " - pdb=" SG  CYS B 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 294 " - pdb=" SG  CYS B 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 776 " - pdb=" SG  CYS B 785 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 3.02
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1026

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 13 sheets defined
      11.3% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 684 through 697
      removed outlier: 3.717A  pdb=" N   TYR A 688 " --> pdb=" O   GLU A 684 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 692 " --> pdb=" O   TYR A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 784
    Processing helix  chain 'B' and resid 12 through 17
      removed outlier: 3.529A  pdb=" N   LEU B  16 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 12 through 17'
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 4.334A  pdb=" N   ASN B  21 " --> pdb=" O   ARG B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.965A  pdb=" N   ILE B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 137
    Processing helix  chain 'B' and resid 144 through 149
    Processing helix  chain 'B' and resid 249 through 255
    Processing helix  chain 'B' and resid 779 through 784
    Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593
      removed outlier: 4.919A  pdb=" N   ASP A 586 " --> pdb=" O   ASN A 602 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN A 602 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ASN A 592 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   GLN A 596 " --> pdb=" O   ASN A 592 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752
      removed outlier: 3.536A  pdb=" N   TYR A 614 " --> pdb=" O   VAL A 752 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR A 769 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA A 793 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3
      removed outlier: 3.609A  pdb=" N   ILE B  25 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 10
      removed outlier: 6.735A  pdb=" N   ILE B   7 " --> pdb=" O   HIS B  30 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   LEU B  32 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B  29 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ILE B  31 " --> pdb=" O   PHE B  58 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LEU B  55 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   PHE B  90 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU B  57 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ARG B 112 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL B  88 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   GLU B 114 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   PHE B  90 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 165
    Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177
    Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195
    Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 209
      removed outlier: 8.147A  pdb=" N   SER B 208 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   CYS B 218 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 226
    Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 248
      removed outlier: 3.664A  pdb=" N   ARG B 245 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   CYS B 273 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ARG B 240 " --> pdb=" O   CYS B 273 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 281 through 283
    Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 590
      removed outlier: 4.801A  pdb=" N   ASP B 586 " --> pdb=" O   ASN B 602 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 602 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 747 through 751
      removed outlier: 4.145A  pdb=" N   TYR B 613 " --> pdb=" O   CYS B 776 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   CYS B 776 " --> pdb=" O   TYR B 613 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL B 791 " --> pdb=" O   ILE B 771 " (cutoff:3.500A)

    94 hydrogen bonds defined for protein.
    249 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.79

  Time building geometry restraints manager: 4.13 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 4137
        1.04 -     1.24: 526
        1.24 -     1.44: 1429
        1.44 -     1.64: 2432
        1.64 -     1.84: 44
  Bond restraints: 8568
  Sorted by residual:
  bond pdb=" CB  CYS B 205 "
       pdb=" SG  CYS B 205 "
    ideal  model  delta    sigma   weight residual
    1.808  1.737  0.071 3.30e-02 9.18e+02 4.57e+00
  bond pdb=" CB  CYS B 218 "
       pdb=" SG  CYS B 218 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.89e+00
  bond pdb=" N   ASN A 577 "
       pdb=" H   ASN A 577 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.31e+00
  bond pdb=" N   GLU A 682 "
       pdb=" CA  GLU A 682 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.09e+00
  bond pdb=" C   ARG B 620 "
       pdb=" N   GLN B 621 "
    ideal  model  delta    sigma   weight residual
    1.340  1.260  0.080 5.87e-02 2.90e+02 1.87e+00
  ... (remaining 8563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 14251
        1.55 -     3.09: 1015
        3.09 -     4.64: 125
        4.64 -     6.18: 17
        6.18 -     7.73: 5
  Bond angle restraints: 15413
  Sorted by residual:
  angle pdb=" N   ASN B  94 "
        pdb=" CA  ASN B  94 "
        pdb=" C   ASN B  94 "
      ideal   model   delta    sigma   weight residual
     113.28  120.89   -7.61 1.57e+00 4.06e-01 2.35e+01
  angle pdb=" N   ASN B  94 "
        pdb=" CA  ASN B  94 "
        pdb=" CB  ASN B  94 "
      ideal   model   delta    sigma   weight residual
     114.17  108.88    5.29 1.14e+00 7.69e-01 2.16e+01
  angle pdb=" N   LEU B 256 "
        pdb=" CA  LEU B 256 "
        pdb=" C   LEU B 256 "
      ideal   model   delta    sigma   weight residual
     110.20  103.33    6.87 1.58e+00 4.01e-01 1.89e+01
  angle pdb=" N   ASN B 602 "
        pdb=" CA  ASN B 602 "
        pdb=" C   ASN B 602 "
      ideal   model   delta    sigma   weight residual
     110.10  115.17   -5.07 1.53e+00 4.27e-01 1.10e+01
  angle pdb=" CA  TYR B 628 "
        pdb=" CB  TYR B 628 "
        pdb=" CG  TYR B 628 "
      ideal   model   delta    sigma   weight residual
     113.90  119.31   -5.41 1.80e+00 3.09e-01 9.04e+00
  ... (remaining 15408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 3757
       17.84 -    35.68: 258
       35.68 -    53.52: 80
       53.52 -    71.36: 38
       71.36 -    89.20: 5
  Dihedral angle restraints: 4138
    sinusoidal: 2235
      harmonic: 1903
  Sorted by residual:
  dihedral pdb=" CB  CYS B 205 "
           pdb=" SG  CYS B 205 "
           pdb=" SG  CYS B 218 "
           pdb=" CB  CYS B 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.70   55.70     1      1.00e+01 1.00e-02 4.19e+01
  dihedral pdb=" CA  SER A 788 "
           pdb=" C   SER A 788 "
           pdb=" N   ASN A 789 "
           pdb=" CA  ASN A 789 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.77   29.23     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  SER B 788 "
           pdb=" C   SER B 788 "
           pdb=" N   ASN B 789 "
           pdb=" CA  ASN B 789 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.22   28.78     0      5.00e+00 4.00e-02 3.31e+01
  ... (remaining 4135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 362
       0.045 -    0.089: 194
       0.089 -    0.134: 68
       0.134 -    0.179: 13
       0.179 -    0.223: 3
  Chirality restraints: 640
  Sorted by residual:
  chirality pdb=" CA  PHE B 766 "
            pdb=" N   PHE B 766 "
            pdb=" C   PHE B 766 "
            pdb=" CB  PHE B 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ASN B  94 "
            pdb=" N   ASN B  94 "
            pdb=" C   ASN B  94 "
            pdb=" CB  ASN B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" CB  ILE B 615 "
            pdb=" CA  ILE B 615 "
            pdb=" CG1 ILE B 615 "
            pdb=" CG2 ILE B 615 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.36e-01
  ... (remaining 637 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 770 "   -0.095 9.50e-02 1.11e+02   4.64e-02 2.69e+01
        pdb=" NE  ARG A 770 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 770 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 770 "    0.058 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 770 "    0.039 2.00e-02 2.50e+03
        pdb="HH11 ARG A 770 "   -0.014 2.00e-02 2.50e+03
        pdb="HH12 ARG A 770 "   -0.011 2.00e-02 2.50e+03
        pdb="HH21 ARG A 770 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 770 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 283 "    0.060 9.50e-02 1.11e+02   3.92e-02 2.60e+01
        pdb=" NE  ARG B 283 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 283 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 283 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 283 "   -0.049 2.00e-02 2.50e+03
        pdb="HH11 ARG B 283 "    0.009 2.00e-02 2.50e+03
        pdb="HH12 ARG B 283 "    0.038 2.00e-02 2.50e+03
        pdb="HH21 ARG B 283 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B 283 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 689 "    0.034 9.50e-02 1.11e+02   3.42e-02 2.36e+01
        pdb=" NE  ARG A 689 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 689 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 689 "   -0.074 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 689 "    0.011 2.00e-02 2.50e+03
        pdb="HH11 ARG A 689 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG A 689 "    0.057 2.00e-02 2.50e+03
        pdb="HH21 ARG A 689 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 689 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 273
        2.10 -     2.72: 14639
        2.72 -     3.35: 23897
        3.35 -     3.97: 29803
        3.97 -     4.60: 46113
  Nonbonded interactions: 114725
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 614 "
            pdb=" H   VAL B 752 "
     model   vdw
     1.470 2.450
  nonbonded pdb=" O   TYR A 626 "
            pdb=" H   TYR A 628 "
     model   vdw
     1.485 2.450
  nonbonded pdb=" HG  SER B 257 "
            pdb=" O   GLU B 264 "
     model   vdw
     1.490 2.450
  nonbonded pdb=" O   ARG A 764 "
            pdb=" HG1 THR A 767 "
     model   vdw
     1.517 2.450
  nonbonded pdb=" O   TYR B 626 "
            pdb=" H   TYR B 628 "
     model   vdw
     1.517 2.450
  ... (remaining 114720 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             54.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.140
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     33.810
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   94.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5785
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   4444  Z= 0.245
  Angle     :  1.073   7.731   6040  Z= 0.615
  Chirality :  0.058   0.223    640
  Planarity :  0.005   0.053    787
  Dihedral  : 13.745  89.202   1642
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  6.69 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.97 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.34), residues: 523
  helix: -3.57 (0.58), residues: 40
  sheet: -0.34 (0.46), residues: 131
  loop : -1.21 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.006   TRP B 618 
 HIS   0.012   0.003   HIS B 774 
 PHE   0.018   0.003   PHE B  90 
 TYR   0.042   0.006   TYR B 769 
 ARG   0.079   0.007   ARG A 770 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28841 (   94)
  hydrogen bonds       : angle      12.07725 (  249)
  SS BOND              : bond        0.00535 (   15)
  SS BOND              : angle       2.38139 (   30)
  covalent geometry    : bond        0.00560 ( 4429)
  covalent geometry    : angle       1.06292 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 ILE cc_start: 0.8430 (mt) cc_final: 0.8204 (mm)
REVERT: B  184 MET cc_start: 0.7692 (mtp) cc_final: 0.7432 (mtt)
REVERT: B  242 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7453 (mm-30)
REVERT: B  270 ASP cc_start: 0.6463 (t0) cc_final: 0.6110 (t0)
REVERT: B  601 TRP cc_start: 0.6939 (p90) cc_final: 0.6050 (p90)
REVERT: B  613 TYR cc_start: 0.4841 (p90) cc_final: 0.4202 (p90)
  outliers start: 4
  outliers final: 1
  residues processed: 89
  average time/residue: 0.4003
  time to fit residues: 44.1175
Evaluate side-chains
  56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN
A 697 HIS
B  14 GLN
B  72 ASN
B  94 ASN
B 102 ASN
B 136 ASN
B 198 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.125470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.109989 restraints weight = 58813.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.113833 restraints weight = 30579.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.116419 restraints weight = 19077.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5924
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4444  Z= 0.165
  Angle     :  0.699   5.155   6040  Z= 0.382
  Chirality :  0.048   0.162    640
  Planarity :  0.005   0.047    787
  Dihedral  :  6.857  29.167    597
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.12 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.35), residues: 523
  helix: -2.70 (0.67), residues: 36
  sheet: -0.80 (0.43), residues: 130
  loop : -0.72 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 618 
 HIS   0.010   0.002   HIS A 774 
 PHE   0.010   0.001   PHE B  90 
 TYR   0.019   0.002   TYR B 626 
 ARG   0.004   0.001   ARG B 620 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04569 (   94)
  hydrogen bonds       : angle       9.18397 (  249)
  SS BOND              : bond        0.00353 (   15)
  SS BOND              : angle       1.46118 (   30)
  covalent geometry    : bond        0.00360 ( 4429)
  covalent geometry    : angle       0.69357 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  582 SER cc_start: 0.8294 (t) cc_final: 0.8080 (m)
REVERT: A  598 ILE cc_start: 0.7747 (pt) cc_final: 0.7498 (mp)
REVERT: B  601 TRP cc_start: 0.6996 (p90) cc_final: 0.5984 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.3050
  time to fit residues: 27.7525
Evaluate side-chains
  50 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0970
   chunk 31 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 619 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.124891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.108774 restraints weight = 58760.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.112853 restraints weight = 29684.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.115570 restraints weight = 18033.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5951
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4444  Z= 0.123
  Angle     :  0.587   4.337   6040  Z= 0.320
  Chirality :  0.046   0.145    640
  Planarity :  0.005   0.038    787
  Dihedral  :  6.067  25.445    597
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.31 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.36), residues: 523
  helix: -1.89 (0.74), residues: 28
  sheet: -0.94 (0.44), residues: 124
  loop : -0.62 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 618 
 HIS   0.007   0.001   HIS A 774 
 PHE   0.011   0.001   PHE A 747 
 TYR   0.016   0.002   TYR B 628 
 ARG   0.002   0.000   ARG B 757 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (   94)
  hydrogen bonds       : angle       8.02162 (  249)
  SS BOND              : bond        0.00254 (   15)
  SS BOND              : angle       1.06317 (   30)
  covalent geometry    : bond        0.00275 ( 4429)
  covalent geometry    : angle       0.58363 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  582 SER cc_start: 0.8402 (t) cc_final: 0.8177 (m)
REVERT: A  598 ILE cc_start: 0.7864 (pt) cc_final: 0.7603 (mp)
REVERT: B  136 ASN cc_start: 0.8502 (t0) cc_final: 0.8254 (t0)
REVERT: B  242 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8284 (mm-30)
REVERT: B  244 TRP cc_start: 0.6626 (p-90) cc_final: 0.6366 (p-90)
REVERT: B  601 TRP cc_start: 0.6955 (p90) cc_final: 0.5925 (p90)
REVERT: B  773 ILE cc_start: 0.7821 (mt) cc_final: 0.7431 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.3001
  time to fit residues: 24.8896
Evaluate side-chains
  46 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.127733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.115959 restraints weight = 66140.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.118890 restraints weight = 36853.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.120863 restraints weight = 23835.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5995
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4444  Z= 0.141
  Angle     :  0.587   4.895   6040  Z= 0.319
  Chirality :  0.046   0.148    640
  Planarity :  0.005   0.036    787
  Dihedral  :  5.834  26.475    597
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.41 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.36), residues: 523
  helix: -1.44 (0.76), residues: 28
  sheet: -1.38 (0.42), residues: 130
  loop : -0.74 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 618 
 HIS   0.006   0.001   HIS A 774 
 PHE   0.009   0.001   PHE B  82 
 TYR   0.016   0.002   TYR B 628 
 ARG   0.003   0.000   ARG B 770 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (   94)
  hydrogen bonds       : angle       7.71312 (  249)
  SS BOND              : bond        0.00314 (   15)
  SS BOND              : angle       1.21934 (   30)
  covalent geometry    : bond        0.00319 ( 4429)
  covalent geometry    : angle       0.58204 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7935 (pt) cc_final: 0.7699 (mp)
REVERT: B  136 ASN cc_start: 0.8513 (t0) cc_final: 0.8275 (t0)
REVERT: B  244 TRP cc_start: 0.7066 (p-90) cc_final: 0.6531 (p-90)
REVERT: B  601 TRP cc_start: 0.7057 (p90) cc_final: 0.5936 (p90)
REVERT: B  773 ILE cc_start: 0.7991 (mt) cc_final: 0.7631 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2803
  time to fit residues: 22.6164
Evaluate side-chains
  49 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.127586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.115130 restraints weight = 66423.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.118216 restraints weight = 35848.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.120373 restraints weight = 22786.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6002
moved from start:          0.5514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4444  Z= 0.121
  Angle     :  0.559   3.907   6040  Z= 0.300
  Chirality :  0.045   0.143    640
  Planarity :  0.004   0.036    787
  Dihedral  :  5.589  23.750    597
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.46 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.36), residues: 523
  helix: -1.22 (0.78), residues: 28
  sheet: -1.59 (0.41), residues: 136
  loop : -0.74 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 618 
 HIS   0.006   0.001   HIS A 774 
 PHE   0.008   0.001   PHE A 747 
 TYR   0.019   0.002   TYR B 626 
 ARG   0.005   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03115 (   94)
  hydrogen bonds       : angle       7.40962 (  249)
  SS BOND              : bond        0.00356 (   15)
  SS BOND              : angle       1.13058 (   30)
  covalent geometry    : bond        0.00273 ( 4429)
  covalent geometry    : angle       0.55441 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7946 (pt) cc_final: 0.7714 (mp)
REVERT: B   25 ILE cc_start: 0.6771 (mp) cc_final: 0.6391 (mt)
REVERT: B  136 ASN cc_start: 0.8501 (t0) cc_final: 0.8218 (t0)
REVERT: B  242 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8183 (mm-30)
REVERT: B  244 TRP cc_start: 0.7254 (p-90) cc_final: 0.6376 (p-90)
REVERT: B  601 TRP cc_start: 0.6859 (p90) cc_final: 0.5823 (p90)
REVERT: B  773 ILE cc_start: 0.7925 (mt) cc_final: 0.7621 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2620
  time to fit residues: 20.5918
Evaluate side-chains
  50 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.127223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.114500 restraints weight = 65794.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.117648 restraints weight = 35754.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.119957 restraints weight = 22712.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6040
moved from start:          0.5972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4444  Z= 0.135
  Angle     :  0.566   4.000   6040  Z= 0.305
  Chirality :  0.045   0.155    640
  Planarity :  0.004   0.036    787
  Dihedral  :  5.506  23.672    597
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.60 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.23 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.36), residues: 523
  helix: -1.32 (0.79), residues: 28
  sheet: -1.55 (0.42), residues: 135
  loop : -0.89 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 618 
 HIS   0.005   0.001   HIS A 774 
 PHE   0.011   0.001   PHE A 747 
 TYR   0.020   0.002   TYR B 626 
 ARG   0.002   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (   94)
  hydrogen bonds       : angle       7.43128 (  249)
  SS BOND              : bond        0.00254 (   15)
  SS BOND              : angle       1.07813 (   30)
  covalent geometry    : bond        0.00311 ( 4429)
  covalent geometry    : angle       0.56249 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7960 (pt) cc_final: 0.7723 (mp)
REVERT: B   25 ILE cc_start: 0.6627 (mp) cc_final: 0.6189 (mt)
REVERT: B  136 ASN cc_start: 0.8563 (t0) cc_final: 0.8340 (t0)
REVERT: B  601 TRP cc_start: 0.6913 (p90) cc_final: 0.5887 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2551
  time to fit residues: 20.6447
Evaluate side-chains
  48 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0040
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.127054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.114478 restraints weight = 66490.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.117667 restraints weight = 35719.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.119853 restraints weight = 22569.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6016
moved from start:          0.6116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4444  Z= 0.112
  Angle     :  0.543   4.066   6040  Z= 0.292
  Chirality :  0.045   0.151    640
  Planarity :  0.004   0.034    787
  Dihedral  :  5.327  22.174    597
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.22 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.36), residues: 523
  helix: -1.51 (0.81), residues: 28
  sheet: -1.51 (0.42), residues: 134
  loop : -0.95 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 618 
 HIS   0.006   0.001   HIS A 774 
 PHE   0.007   0.001   PHE A 747 
 TYR   0.019   0.002   TYR B 626 
 ARG   0.004   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02911 (   94)
  hydrogen bonds       : angle       7.21003 (  249)
  SS BOND              : bond        0.00293 (   15)
  SS BOND              : angle       1.09472 (   30)
  covalent geometry    : bond        0.00259 ( 4429)
  covalent geometry    : angle       0.53843 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7924 (pt) cc_final: 0.7668 (mp)
REVERT: B  136 ASN cc_start: 0.8469 (t0) cc_final: 0.8236 (t0)
REVERT: B  601 TRP cc_start: 0.6741 (p90) cc_final: 0.5757 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2402
  time to fit residues: 19.6485
Evaluate side-chains
  48 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.119862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.104123 restraints weight = 57661.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.107923 restraints weight = 29659.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.110415 restraints weight = 18340.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.6530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   4444  Z= 0.194
  Angle     :  0.640   5.409   6040  Z= 0.345
  Chirality :  0.047   0.139    640
  Planarity :  0.005   0.036    787
  Dihedral  :  5.804  24.559    597
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 11.47 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.36), residues: 523
  helix: -2.21 (0.76), residues: 35
  sheet: -1.93 (0.43), residues: 125
  loop : -1.17 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 618 
 HIS   0.004   0.001   HIS B 774 
 PHE   0.013   0.002   PHE B  82 
 TYR   0.023   0.002   TYR B 745 
 ARG   0.005   0.001   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (   94)
  hydrogen bonds       : angle       7.66155 (  249)
  SS BOND              : bond        0.00384 (   15)
  SS BOND              : angle       1.45413 (   30)
  covalent geometry    : bond        0.00446 ( 4429)
  covalent geometry    : angle       0.63361 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 ASN cc_start: 0.8698 (t0) cc_final: 0.8408 (t0)
REVERT: B  601 TRP cc_start: 0.7216 (p90) cc_final: 0.6267 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.3050
  time to fit residues: 26.1009
Evaluate side-chains
  53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.121672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.105669 restraints weight = 58820.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.109648 restraints weight = 30067.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.112356 restraints weight = 18304.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.6698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4444  Z= 0.127
  Angle     :  0.564   4.971   6040  Z= 0.303
  Chirality :  0.045   0.140    640
  Planarity :  0.004   0.036    787
  Dihedral  :  5.486  22.233    597
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.22 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.36), residues: 523
  helix: -1.30 (0.88), residues: 28
  sheet: -1.61 (0.46), residues: 121
  loop : -1.24 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 618 
 HIS   0.006   0.001   HIS A 774 
 PHE   0.008   0.001   PHE A 747 
 TYR   0.015   0.001   TYR B 626 
 ARG   0.006   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03122 (   94)
  hydrogen bonds       : angle       7.39080 (  249)
  SS BOND              : bond        0.00302 (   15)
  SS BOND              : angle       1.25289 (   30)
  covalent geometry    : bond        0.00290 ( 4429)
  covalent geometry    : angle       0.55828 ( 6010)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.8210 (pt) cc_final: 0.8007 (mp)
REVERT: B  136 ASN cc_start: 0.8752 (t0) cc_final: 0.8432 (t0)
REVERT: B  287 GLN cc_start: 0.7247 (pt0) cc_final: 0.7002 (pp30)
REVERT: B  586 ASP cc_start: 0.6937 (t0) cc_final: 0.6603 (t0)
REVERT: B  601 TRP cc_start: 0.6897 (p90) cc_final: 0.6081 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.3189
  time to fit residues: 26.9664
Evaluate side-chains
  56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.121356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.105294 restraints weight = 58278.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.109213 restraints weight = 29642.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.111916 restraints weight = 18125.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6181
moved from start:          0.6924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4444  Z= 0.146
  Angle     :  0.578   4.501   6040  Z= 0.310
  Chirality :  0.045   0.145    640
  Planarity :  0.004   0.036    787
  Dihedral  :  5.497  22.814    597
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.13 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.36), residues: 523
  helix: -1.23 (0.89), residues: 28
  sheet: -1.67 (0.44), residues: 127
  loop : -1.33 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 618 
 HIS   0.004   0.001   HIS B 774 
 PHE   0.009   0.001   PHE B  82 
 TYR   0.017   0.002   TYR B 745 
 ARG   0.008   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (   94)
  hydrogen bonds       : angle       7.29288 (  249)
  SS BOND              : bond        0.00304 (   15)
  SS BOND              : angle       1.38818 (   30)
  covalent geometry    : bond        0.00338 ( 4429)
  covalent geometry    : angle       0.57102 ( 6010)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.8298 (pt) cc_final: 0.8034 (mp)
REVERT: A  757 ARG cc_start: 0.5369 (ttt180) cc_final: 0.5002 (ttt180)
REVERT: B   25 ILE cc_start: 0.6535 (mp) cc_final: 0.5881 (mt)
REVERT: B   53 GLU cc_start: 0.7947 (mp0) cc_final: 0.7725 (mp0)
REVERT: B  136 ASN cc_start: 0.8753 (t0) cc_final: 0.8462 (t0)
REVERT: B  287 GLN cc_start: 0.7325 (pt0) cc_final: 0.7103 (pp30)
REVERT: B  586 ASP cc_start: 0.6935 (t0) cc_final: 0.6691 (t0)
REVERT: B  601 TRP cc_start: 0.7084 (p90) cc_final: 0.6202 (p90)
REVERT: B  602 ASN cc_start: 0.7675 (m110) cc_final: 0.7152 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.3046
  time to fit residues: 25.5680
Evaluate side-chains
  54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0770
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.125845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.113022 restraints weight = 66269.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.116401 restraints weight = 35766.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.118576 restraints weight = 22569.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6094
moved from start:          0.7052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4444  Z= 0.108
  Angle     :  0.538   4.040   6040  Z= 0.288
  Chirality :  0.045   0.148    640
  Planarity :  0.004   0.035    787
  Dihedral  :  5.247  21.115    597
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.22 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.36), residues: 523
  helix: -1.12 (0.92), residues: 28
  sheet: -1.61 (0.44), residues: 131
  loop : -1.25 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 618 
 HIS   0.006   0.001   HIS A 774 
 PHE   0.008   0.001   PHE A 747 
 TYR   0.015   0.001   TYR B 628 
 ARG   0.006   0.000   ARG B 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02947 (   94)
  hydrogen bonds       : angle       6.97210 (  249)
  SS BOND              : bond        0.00265 (   15)
  SS BOND              : angle       1.12557 (   30)
  covalent geometry    : bond        0.00254 ( 4429)
  covalent geometry    : angle       0.53316 ( 6010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4378.07 seconds
wall clock time: 76 minutes 0.06 seconds (4560.06 seconds total)