Starting phenix.real_space_refine
on Thu Jul 31 00:45:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kld_0707/07_2025/6kld_0707.cif"
  }
  resolution = 3.58
  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=   0.000 sd=   0.011
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: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     Zn      1      6.06       5
     S      86      5.16       5
     C    8159      2.51       5
     N    2148      2.21       5
     O    2399      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12794
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1617, 12792
          Classifications: {'peptide': 1617}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 48, 'TRANS': 1568}
          Chain breaks: 16
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 201
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 129
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2171  SG  CYS A 284      40.315  69.743  28.123  1.00 52.57           S
  ATOM   2195  SG  CYS A 287      43.390  69.962  25.837  1.00 53.80           S
  ATOM   3474  SG  CYS A 470      39.712  71.589  24.834  1.00 87.91           S

  Time building chain proxies: 7.89, per 1000 atoms: 0.62
  Number of scatterers: 12794
  At special positions: 0
  Unit cell: (114.24, 114.24, 119.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Mn      1     24.99
     S      86     16.00
     O    2399      8.00
     N    2148      7.00
     C    8159      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1691 " - pdb=" SG  CYS A1776 " distance=2.03

  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: 3.28
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" ND1 HIS A 472 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 470 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 284 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 287 "
      Number of angles added : 3


  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3080

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 10 sheets defined
      54.1% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
      removed outlier: 3.768A  pdb=" N   GLU A   7 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A  10 " --> pdb=" O   GLN A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.547A  pdb=" N   GLY A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR A  28 " --> pdb=" O   HIS A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 57
      removed outlier: 4.515A  pdb=" N   LEU A  39 " --> pdb=" O   PRO A  35 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   THR A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 76
      removed outlier: 3.638A  pdb=" N   ILE A  72 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 133
      removed outlier: 3.510A  pdb=" N   LYS A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   HIS A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ASP A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 132 " --> pdb=" O   HIS A 128 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   SER A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 171
      removed outlier: 3.965A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 3.742A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.961A  pdb=" N   VAL A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 274
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.545A  pdb=" N   ASN A 288 " --> pdb=" O   CYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 303
    Processing helix  chain 'A' and resid 322 through 340
      removed outlier: 3.693A  pdb=" N   LEU A 340 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 396 through 405
    Processing helix  chain 'A' and resid 412 through 421
      removed outlier: 3.584A  pdb=" N   ASN A 416 " --> pdb=" O   ASN A 412 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 417 " --> pdb=" O   TRP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.979A  pdb=" N   LEU A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 478
      removed outlier: 3.541A  pdb=" N   MET A 478 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 501
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'A' and resid 579 through 583
      removed outlier: 4.440A  pdb=" N   PHE A 583 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 598
    Processing helix  chain 'A' and resid 605 through 623
      Proline residue:  A 611  - end of helix
    Processing helix  chain 'A' and resid 625 through 644
      removed outlier: 3.639A  pdb=" N   GLN A 629 " --> pdb=" O   SER A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.556A  pdb=" N   LEU A 655 " --> pdb=" O   THR A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 4.266A  pdb=" N   VAL A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 701
    Processing helix  chain 'A' and resid 702 through 705
    Processing helix  chain 'A' and resid 712 through 732
      Proline residue:  A 727  - end of helix
    Processing helix  chain 'A' and resid 745 through 760
    Processing helix  chain 'A' and resid 776 through 789
      removed outlier: 3.535A  pdb=" N   ARG A 789 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 852
    Processing helix  chain 'A' and resid 864 through 874
      removed outlier: 3.618A  pdb=" N   LEU A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 869 " --> pdb=" O   THR A 865 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASN A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   THR A 874 " --> pdb=" O   LEU A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 895
    Processing helix  chain 'A' and resid 898 through 921
      removed outlier: 3.652A  pdb=" N   ASP A 921 " --> pdb=" O   ALA A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 967
      removed outlier: 3.626A  pdb=" N   VAL A 967 " --> pdb=" O   SER A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 975
    Processing helix  chain 'A' and resid 981 through 989
    Processing helix  chain 'A' and resid 1009 through 1021
    Processing helix  chain 'A' and resid 1024 through 1035
    Processing helix  chain 'A' and resid 1135 through 1156
    Processing helix  chain 'A' and resid 1163 through 1181
    Processing helix  chain 'A' and resid 1197 through 1208
      removed outlier: 3.728A  pdb=" N   PHE A1201 " --> pdb=" O   SER A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1233
      removed outlier: 3.527A  pdb=" N   LYS A1225 " --> pdb=" O   LEU A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1249
    Processing helix  chain 'A' and resid 1264 through 1273
    Processing helix  chain 'A' and resid 1295 through 1319
    Processing helix  chain 'A' and resid 1351 through 1365
    Processing helix  chain 'A' and resid 1395 through 1405
      removed outlier: 3.835A  pdb=" N   PHE A1399 " --> pdb=" O   LEU A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1429
      removed outlier: 3.668A  pdb=" N   ASN A1429 " --> pdb=" O   GLN A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1435 through 1450
    Processing helix  chain 'A' and resid 1472 through 1485
    Processing helix  chain 'A' and resid 1488 through 1507
    Processing helix  chain 'A' and resid 1513 through 1520
      removed outlier: 3.778A  pdb=" N   ASN A1517 " --> pdb=" O   GLU A1513 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A1518 " --> pdb=" O   ASN A1514 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY A1520 " --> pdb=" O   ILE A1516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1535
    Processing helix  chain 'A' and resid 1537 through 1545
    Processing helix  chain 'A' and resid 1579 through 1590
      removed outlier: 3.913A  pdb=" N   LYS A1583 " --> pdb=" O   PRO A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1614 through 1625
    Processing helix  chain 'A' and resid 1639 through 1645
      removed outlier: 3.733A  pdb=" N   VAL A1643 " --> pdb=" O   TYR A1639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1664 through 1669
      removed outlier: 3.659A  pdb=" N   ASN A1669 " --> pdb=" O   ASN A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1678 through 1694
      removed outlier: 3.638A  pdb=" N   GLY A1694 " --> pdb=" O   ALA A1690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1699
      removed outlier: 3.861A  pdb=" N   SER A1699 " --> pdb=" O   TRP A1696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1735 through 1744
    Processing helix  chain 'A' and resid 1744 through 1750
    Processing helix  chain 'A' and resid 1758 through 1764
      removed outlier: 3.775A  pdb=" N   SER A1762 " --> pdb=" O   ASP A1758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1777 through 1783
      removed outlier: 3.535A  pdb=" N   MET A1782 " --> pdb=" O   ALA A1778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1787 through 1793
      removed outlier: 3.677A  pdb=" N   HIS A1791 " --> pdb=" O   GLY A1787 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A1793 " --> pdb=" O   ILE A1789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1805 through 1809
      removed outlier: 3.549A  pdb=" N   ALA A1809 " --> pdb=" O   GLN A1805 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1805 through 1809'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.506A  pdb=" N   LEU A  98 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE A 140 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ASP A 142 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU A 102 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ARG A 144 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   PHE A 104 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387
    Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534
      removed outlier: 6.167A  pdb=" N   LEU A 559 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   GLU A 567 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1116 through 1117
      removed outlier: 3.744A  pdb=" N   GLU A1237 " --> pdb=" O   PHE A1117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1119 through 1122
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1379 through 1380
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1719

    612 hydrogen bonds defined for protein.
    1758 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: 5.02

  Time building geometry restraints manager: 3.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4135
        1.34 -     1.46: 2880
        1.46 -     1.58: 5874
        1.58 -     1.70: 0
        1.70 -     1.82: 124
  Bond restraints: 13013
  Sorted by residual:
  bond pdb=" CG  GLU A 220 "
       pdb=" CD  GLU A 220 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.22e+00
  bond pdb=" CB  ASP A1488 "
       pdb=" CG  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" CA  SER A 950 "
       pdb=" C   SER A 950 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.10e-02 2.27e+03 8.79e-01
  bond pdb=" CA  ASP A1488 "
       pdb=" CB  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.36e-01
  bond pdb=" N   ASP A1488 "
       pdb=" CA  ASP A1488 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.66e-01
  ... (remaining 13008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 17229
        2.00 -     4.00: 271
        4.00 -     6.00: 45
        6.00 -     8.00: 7
        8.00 -    10.00: 2
  Bond angle restraints: 17554
  Sorted by residual:
  angle pdb=" C   ASN A 219 "
        pdb=" N   GLU A 220 "
        pdb=" CA  GLU A 220 "
      ideal   model   delta    sigma   weight residual
     122.38  114.97    7.41 1.81e+00 3.05e-01 1.68e+01
  angle pdb=" C   ASP A 248 "
        pdb=" N   GLU A 249 "
        pdb=" CA  GLU A 249 "
      ideal   model   delta    sigma   weight residual
     122.08  116.53    5.55 1.53e+00 4.27e-01 1.32e+01
  angle pdb=" N   GLU A 220 "
        pdb=" CA  GLU A 220 "
        pdb=" CB  GLU A 220 "
      ideal   model   delta    sigma   weight residual
     110.44  115.30   -4.86 1.53e+00 4.27e-01 1.01e+01
  angle pdb=" N   ILE A1435 "
        pdb=" CA  ILE A1435 "
        pdb=" C   ILE A1435 "
      ideal   model   delta    sigma   weight residual
     111.81  109.12    2.69 8.60e-01 1.35e+00 9.80e+00
  angle pdb=" N   GLU A 249 "
        pdb=" CA  GLU A 249 "
        pdb=" C   GLU A 249 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.59e+00
  ... (remaining 17549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.25: 7171
       18.25 -    36.51: 619
       36.51 -    54.76: 105
       54.76 -    73.01: 12
       73.01 -    91.27: 14
  Dihedral angle restraints: 7921
    sinusoidal: 3195
      harmonic: 4726
  Sorted by residual:
  dihedral pdb=" CB  CYS A  55 "
           pdb=" SG  CYS A  55 "
           pdb=" SG  CYS A  60 "
           pdb=" CB  CYS A  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    4.33   88.67     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CA  ASP A1467 "
           pdb=" C   ASP A1467 "
           pdb=" N   TRP A1468 "
           pdb=" CA  TRP A1468 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.14   22.86     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASP A 826 "
           pdb=" C   ASP A 826 "
           pdb=" N   GLU A 827 "
           pdb=" CA  GLU A 827 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 7918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1454
       0.041 -    0.082: 454
       0.082 -    0.123: 100
       0.123 -    0.163: 17
       0.163 -    0.204: 2
  Chirality restraints: 2027
  Sorted by residual:
  chirality pdb=" CB  VAL A1465 "
            pdb=" CA  VAL A1465 "
            pdb=" CG1 VAL A1465 "
            pdb=" CG2 VAL A1465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CG  LEU A 618 "
            pdb=" CB  LEU A 618 "
            pdb=" CD1 LEU A 618 "
            pdb=" CD2 LEU A 618 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CA  ASP A1488 "
            pdb=" N   ASP A1488 "
            pdb=" C   ASP A1488 "
            pdb=" CB  ASP A1488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.55e-01
  ... (remaining 2024 not shown)

  Planarity restraints: 2219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1753 "   -0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO A1754 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A1754 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1754 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  36 "    0.029 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  37 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  37 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  37 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1488 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   ASP A1488 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A1488 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A1489 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2216 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1115
        2.74 -     3.28: 13252
        3.28 -     3.82: 19806
        3.82 -     4.36: 22620
        4.36 -     4.90: 39718
  Nonbonded interactions: 96511
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1188 "
            pdb="MN    MN A2301 "
     model   vdw
     2.199 2.320
  nonbonded pdb=" ND2 ASN A 788 "
            pdb=" OE1 GLU A1209 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OE2 GLU A 102 "
            pdb=" NZ  LYS A 122 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NH1 ARG A 553 "
            pdb=" OH  TYR A 555 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   LYS A 757 "
            pdb=" OG  SER A 761 "
     model   vdw
     2.249 3.040
  ... (remaining 96506 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     36.000
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
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      :  0.004   0.083  13019  Z= 0.154
  Angle     :  0.641  10.003  17561  Z= 0.324
  Chirality :  0.041   0.204   2027
  Planarity :  0.004   0.044   2219
  Dihedral  : 14.001  91.266   4835
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.22 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.76 (0.21), residues: 1583
  helix:  1.10 (0.19), residues: 821
  sheet: -0.84 (0.51), residues: 95
  loop : -2.65 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1717 
 HIS   0.004   0.001   HIS A 472 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.023   0.001   TYR A 701 
 ARG   0.006   0.000   ARG A1473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14091 (  612)
  hydrogen bonds       : angle       4.98167 ( 1758)
  metal coordination   : bond        0.07086 (    4)
  metal coordination   : angle       6.68476 (    3)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       1.28882 (    4)
  covalent geometry    : bond        0.00336 (13013)
  covalent geometry    : angle       0.63485 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.495 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8554 (p0) cc_final: 0.8195 (p0)
REVERT: A  189 HIS cc_start: 0.8212 (t-90) cc_final: 0.7974 (t70)
REVERT: A  300 PHE cc_start: 0.8810 (m-10) cc_final: 0.8580 (m-10)
REVERT: A  478 MET cc_start: 0.8340 (mtm) cc_final: 0.8126 (mtm)
REVERT: A  639 LEU cc_start: 0.9120 (tp) cc_final: 0.8780 (tp)
REVERT: A  658 GLU cc_start: 0.7516 (pp20) cc_final: 0.7310 (pp20)
REVERT: A  860 LEU cc_start: 0.7457 (pt) cc_final: 0.7200 (pp)
REVERT: A  892 LEU cc_start: 0.8019 (mm) cc_final: 0.7566 (mm)
REVERT: A  958 ILE cc_start: 0.8084 (mt) cc_final: 0.7836 (mt)
REVERT: A  999 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6855 (pm20)
REVERT: A 1097 TYR cc_start: 0.7591 (t80) cc_final: 0.7331 (t80)
REVERT: A 1352 LEU cc_start: 0.9309 (tp) cc_final: 0.9091 (tp)
REVERT: A 1655 CYS cc_start: 0.8117 (m) cc_final: 0.7665 (t)
REVERT: A 1695 GLU cc_start: 0.7313 (pp20) cc_final: 0.7044 (pp20)
REVERT: A 1733 MET cc_start: 0.3958 (tpt) cc_final: 0.3738 (tpt)
REVERT: A 1780 ASP cc_start: 0.7815 (t70) cc_final: 0.7507 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2386
  time to fit residues: 93.1625
Evaluate side-chains
  207 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 135 optimal weight:    8.9990
   chunk 122 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0030
   chunk 93 optimal weight:    0.7980
   chunk 146 optimal weight:    6.9990
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
A 788 ASN
A1496 ASN
A1514 ASN
A1791 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.154171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.119120 restraints weight = 18541.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120586 restraints weight = 11916.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.121979 restraints weight = 8626.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13019  Z= 0.140
  Angle     :  0.613   9.449  17561  Z= 0.309
  Chirality :  0.040   0.184   2027
  Planarity :  0.004   0.039   2219
  Dihedral  :  4.253  21.893   1715
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.53 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.72 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.64 (0.21), residues: 1583
  helix:  1.19 (0.18), residues: 832
  sheet: -0.81 (0.51), residues: 95
  loop : -2.62 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1717 
 HIS   0.011   0.001   HIS A 472 
 PHE   0.021   0.001   PHE A1621 
 TYR   0.013   0.001   TYR A 572 
 ARG   0.007   0.000   ARG A1769 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04439 (  612)
  hydrogen bonds       : angle       4.12970 ( 1758)
  metal coordination   : bond        0.00915 (    4)
  metal coordination   : angle       2.27847 (    3)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.48573 (    4)
  covalent geometry    : bond        0.00322 (13013)
  covalent geometry    : angle       0.61173 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 238
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 ASN cc_start: 0.8533 (p0) cc_final: 0.8126 (p0)
REVERT: A  189 HIS cc_start: 0.8379 (t-90) cc_final: 0.8055 (t70)
REVERT: A  300 PHE cc_start: 0.8723 (m-10) cc_final: 0.8522 (m-10)
REVERT: A  639 LEU cc_start: 0.8987 (tp) cc_final: 0.8634 (tp)
REVERT: A  640 MET cc_start: 0.8837 (mmm) cc_final: 0.8618 (mmm)
REVERT: A  650 ASP cc_start: 0.8308 (t0) cc_final: 0.8106 (t0)
REVERT: A  658 GLU cc_start: 0.7690 (pp20) cc_final: 0.7381 (pp20)
REVERT: A  860 LEU cc_start: 0.7495 (pt) cc_final: 0.7278 (pp)
REVERT: A  888 GLU cc_start: 0.7480 (pm20) cc_final: 0.7172 (pm20)
REVERT: A  892 LEU cc_start: 0.8073 (mm) cc_final: 0.7417 (mm)
REVERT: A  999 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6936 (pm20)
REVERT: A 1097 TYR cc_start: 0.7527 (t80) cc_final: 0.7251 (t80)
REVERT: A 1393 THR cc_start: 0.8962 (p) cc_final: 0.8720 (p)
REVERT: A 1533 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6389 (t80)
REVERT: A 1540 GLU cc_start: 0.6791 (mp0) cc_final: 0.6470 (mp0)
REVERT: A 1655 CYS cc_start: 0.8240 (m) cc_final: 0.7800 (t)
REVERT: A 1771 LYS cc_start: 0.6163 (tptt) cc_final: 0.5859 (tptt)
REVERT: A 1780 ASP cc_start: 0.8247 (t70) cc_final: 0.7971 (t70)
  outliers start: 16
  outliers final: 10
  residues processed: 251
  average time/residue: 0.2273
  time to fit residues: 85.6502
Evaluate side-chains
  217 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 206
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1484 ILE
Chi-restraints excluded: chain A residue 1533 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0060
   chunk 25 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 143 optimal weight:    0.0470
   chunk 13 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 135 optimal weight:    0.8980
   overall best weight:    0.5094

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 HIS
A 800 ASN
A1034 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115576 restraints weight = 18521.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.117828 restraints weight = 13010.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118998 restraints weight = 9715.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13019  Z= 0.111
  Angle     :  0.565  10.075  17561  Z= 0.284
  Chirality :  0.039   0.181   2027
  Planarity :  0.003   0.035   2219
  Dihedral  :  4.081  20.712   1715
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.77 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.16 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.21), residues: 1583
  helix:  1.37 (0.19), residues: 831
  sheet: -0.50 (0.53), residues: 85
  loop : -2.52 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1717 
 HIS   0.007   0.001   HIS A 472 
 PHE   0.024   0.001   PHE A1025 
 TYR   0.012   0.001   TYR A1097 
 ARG   0.004   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  612)
  hydrogen bonds       : angle       3.85321 ( 1758)
  metal coordination   : bond        0.00287 (    4)
  metal coordination   : angle       1.07160 (    3)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       1.40746 (    4)
  covalent geometry    : bond        0.00243 (13013)
  covalent geometry    : angle       0.56483 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 239
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 ASN cc_start: 0.8519 (p0) cc_final: 0.8076 (p0)
REVERT: A  189 HIS cc_start: 0.8235 (t-90) cc_final: 0.7922 (t70)
REVERT: A  639 LEU cc_start: 0.8990 (tp) cc_final: 0.8669 (tp)
REVERT: A  640 MET cc_start: 0.8707 (mmm) cc_final: 0.8370 (mmm)
REVERT: A  650 ASP cc_start: 0.8189 (t0) cc_final: 0.7863 (t0)
REVERT: A  654 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8058 (mtpp)
REVERT: A  658 GLU cc_start: 0.7609 (pp20) cc_final: 0.7326 (pp20)
REVERT: A  750 ASP cc_start: 0.8599 (t0) cc_final: 0.8366 (t0)
REVERT: A  782 TYR cc_start: 0.8125 (m-10) cc_final: 0.7780 (m-80)
REVERT: A  785 SER cc_start: 0.8607 (m) cc_final: 0.8172 (p)
REVERT: A  888 GLU cc_start: 0.7579 (pm20) cc_final: 0.7219 (pm20)
REVERT: A  892 LEU cc_start: 0.8026 (mm) cc_final: 0.7264 (mm)
REVERT: A  999 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6915 (pm20)
REVERT: A 1393 THR cc_start: 0.8847 (p) cc_final: 0.8603 (p)
REVERT: A 1466 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7582 (tmtt)
REVERT: A 1540 GLU cc_start: 0.6930 (mp0) cc_final: 0.6594 (mp0)
REVERT: A 1655 CYS cc_start: 0.8188 (m) cc_final: 0.7774 (t)
REVERT: A 1717 TRP cc_start: 0.7968 (p-90) cc_final: 0.7668 (p-90)
REVERT: A 1780 ASP cc_start: 0.8133 (t70) cc_final: 0.7832 (t70)
REVERT: A 1782 MET cc_start: 0.7488 (mmm) cc_final: 0.7243 (mmm)
  outliers start: 29
  outliers final: 18
  residues processed: 259
  average time/residue: 0.2197
  time to fit residues: 87.3242
Evaluate side-chains
  228 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  989 LYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1460 ILE
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0570
   chunk 135 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 140 optimal weight:    5.9990
   overall best weight:    1.2106

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

Flipped N/Q/H residues before XYZ refinement:
A1088 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.147363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113122 restraints weight = 18342.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.113596 restraints weight = 13247.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.114884 restraints weight = 10287.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13019  Z= 0.156
  Angle     :  0.601   8.295  17561  Z= 0.304
  Chirality :  0.041   0.181   2027
  Planarity :  0.004   0.034   2219
  Dihedral  :  4.144  22.263   1715
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.97 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.09 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.44 (0.22), residues: 1583
  helix:  1.36 (0.19), residues: 836
  sheet: -0.71 (0.51), residues: 95
  loop : -2.58 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1549 
 HIS   0.008   0.001   HIS A1751 
 PHE   0.023   0.001   PHE A1621 
 TYR   0.019   0.001   TYR A 558 
 ARG   0.007   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  612)
  hydrogen bonds       : angle       3.94762 ( 1758)
  metal coordination   : bond        0.00622 (    4)
  metal coordination   : angle       1.30779 (    3)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       1.47426 (    4)
  covalent geometry    : bond        0.00367 (13013)
  covalent geometry    : angle       0.60092 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8521 (p0) cc_final: 0.8060 (p0)
REVERT: A  189 HIS cc_start: 0.8268 (t-90) cc_final: 0.7940 (t70)
REVERT: A  215 ASP cc_start: 0.7908 (p0) cc_final: 0.7642 (p0)
REVERT: A  640 MET cc_start: 0.8783 (mmm) cc_final: 0.8562 (mmm)
REVERT: A  650 ASP cc_start: 0.8285 (t0) cc_final: 0.7945 (t0)
REVERT: A  654 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8187 (mtpp)
REVERT: A  658 GLU cc_start: 0.7719 (pp20) cc_final: 0.7340 (pp20)
REVERT: A  785 SER cc_start: 0.8645 (m) cc_final: 0.8235 (p)
REVERT: A  827 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7592 (pm20)
REVERT: A  867 TYR cc_start: 0.8770 (t80) cc_final: 0.8499 (t80)
REVERT: A  888 GLU cc_start: 0.7658 (pm20) cc_final: 0.7266 (pm20)
REVERT: A  892 LEU cc_start: 0.8070 (mm) cc_final: 0.7321 (mm)
REVERT: A  999 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6974 (pm20)
REVERT: A 1097 TYR cc_start: 0.7471 (t80) cc_final: 0.7183 (t80)
REVERT: A 1393 THR cc_start: 0.8931 (p) cc_final: 0.8706 (p)
REVERT: A 1540 GLU cc_start: 0.7235 (mp0) cc_final: 0.6819 (mp0)
REVERT: A 1655 CYS cc_start: 0.8298 (m) cc_final: 0.7753 (t)
REVERT: A 1780 ASP cc_start: 0.8151 (t70) cc_final: 0.7914 (t70)
REVERT: A 1782 MET cc_start: 0.7628 (mmm) cc_final: 0.7389 (mmm)
  outliers start: 44
  outliers final: 34
  residues processed: 250
  average time/residue: 0.2127
  time to fit residues: 81.4987
Evaluate side-chains
  238 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 203
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 HIS
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  989 LYS
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1356 CYS
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 134 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 143 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 10 optimal weight:    0.4980
   chunk 21 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1743 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 = 0.3707 r_free = 0.3707 target = 0.150547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.115665 restraints weight = 18370.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.117755 restraints weight = 11962.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118991 restraints weight = 8660.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  13019  Z= 0.110
  Angle     :  0.568   9.986  17561  Z= 0.285
  Chirality :  0.039   0.224   2027
  Planarity :  0.003   0.031   2219
  Dihedral  :  4.049  19.845   1715
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.83 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.44 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.26 (0.22), residues: 1583
  helix:  1.46 (0.19), residues: 842
  sheet: -0.32 (0.54), residues: 85
  loop : -2.48 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1549 
 HIS   0.007   0.001   HIS A1751 
 PHE   0.021   0.001   PHE A  91 
 TYR   0.016   0.001   TYR A 558 
 ARG   0.004   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  612)
  hydrogen bonds       : angle       3.73584 ( 1758)
  metal coordination   : bond        0.00551 (    4)
  metal coordination   : angle       0.77146 (    3)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       1.23256 (    4)
  covalent geometry    : bond        0.00242 (13013)
  covalent geometry    : angle       0.56761 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 238
  time to evaluate  : 1.393 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8533 (p0) cc_final: 0.8064 (p0)
REVERT: A  189 HIS cc_start: 0.8282 (t-90) cc_final: 0.7967 (t70)
REVERT: A  215 ASP cc_start: 0.7857 (p0) cc_final: 0.7121 (t0)
REVERT: A  640 MET cc_start: 0.8674 (mmm) cc_final: 0.8391 (mmm)
REVERT: A  650 ASP cc_start: 0.8242 (t0) cc_final: 0.7917 (t0)
REVERT: A  658 GLU cc_start: 0.7557 (pp20) cc_final: 0.7267 (pp20)
REVERT: A  782 TYR cc_start: 0.8256 (m-10) cc_final: 0.8041 (m-80)
REVERT: A  827 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7646 (pm20)
REVERT: A  867 TYR cc_start: 0.8707 (t80) cc_final: 0.8450 (t80)
REVERT: A  888 GLU cc_start: 0.7651 (pm20) cc_final: 0.7284 (pm20)
REVERT: A  892 LEU cc_start: 0.8096 (mm) cc_final: 0.7329 (mm)
REVERT: A  999 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6987 (pm20)
REVERT: A 1018 SER cc_start: 0.8810 (p) cc_final: 0.8572 (p)
REVERT: A 1393 THR cc_start: 0.8716 (p) cc_final: 0.8502 (p)
REVERT: A 1466 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7443 (tmtt)
REVERT: A 1540 GLU cc_start: 0.7154 (mp0) cc_final: 0.6767 (mp0)
REVERT: A 1549 TRP cc_start: 0.7774 (p-90) cc_final: 0.7204 (p-90)
REVERT: A 1782 MET cc_start: 0.7428 (mmm) cc_final: 0.7226 (mmm)
REVERT: A 1813 ILE cc_start: 0.8250 (mp) cc_final: 0.8010 (tt)
  outliers start: 36
  outliers final: 26
  residues processed: 259
  average time/residue: 0.2253
  time to fit residues: 88.4975
Evaluate side-chains
  238 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 211
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1034 GLN
A1296 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.116552 restraints weight = 18817.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118078 restraints weight = 12681.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.120011 restraints weight = 9215.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13019  Z= 0.136
  Angle     :  0.591   8.775  17561  Z= 0.296
  Chirality :  0.040   0.199   2027
  Planarity :  0.003   0.033   2219
  Dihedral  :  4.046  20.830   1715
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.28 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.68 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.22), residues: 1583
  helix:  1.54 (0.19), residues: 834
  sheet: -0.61 (0.53), residues: 95
  loop : -2.51 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1549 
 HIS   0.006   0.001   HIS A1751 
 PHE   0.020   0.001   PHE A  91 
 TYR   0.015   0.001   TYR A1097 
 ARG   0.003   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  612)
  hydrogen bonds       : angle       3.79331 ( 1758)
  metal coordination   : bond        0.00754 (    4)
  metal coordination   : angle       0.96772 (    3)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       1.34498 (    4)
  covalent geometry    : bond        0.00316 (13013)
  covalent geometry    : angle       0.59078 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 218
  time to evaluate  : 1.559 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8541 (p0) cc_final: 0.8075 (p0)
REVERT: A  189 HIS cc_start: 0.8384 (t70) cc_final: 0.8009 (t70)
REVERT: A  215 ASP cc_start: 0.7894 (p0) cc_final: 0.7104 (t0)
REVERT: A  485 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7777 (mmm160)
REVERT: A  640 MET cc_start: 0.8752 (mmm) cc_final: 0.8478 (mmm)
REVERT: A  650 ASP cc_start: 0.8323 (t0) cc_final: 0.7965 (t0)
REVERT: A  658 GLU cc_start: 0.7675 (pp20) cc_final: 0.7247 (pp20)
REVERT: A  785 SER cc_start: 0.8693 (m) cc_final: 0.8240 (p)
REVERT: A  827 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7541 (pm20)
REVERT: A  867 TYR cc_start: 0.8786 (t80) cc_final: 0.8500 (t80)
REVERT: A  888 GLU cc_start: 0.7719 (pm20) cc_final: 0.7327 (pm20)
REVERT: A  892 LEU cc_start: 0.8112 (mm) cc_final: 0.7362 (mm)
REVERT: A  999 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6987 (pm20)
REVERT: A 1018 SER cc_start: 0.8827 (p) cc_final: 0.8560 (p)
REVERT: A 1393 THR cc_start: 0.8821 (p) cc_final: 0.8576 (p)
REVERT: A 1466 LYS cc_start: 0.7872 (tmtt) cc_final: 0.7440 (tmtt)
REVERT: A 1549 TRP cc_start: 0.7956 (p-90) cc_final: 0.7140 (p-90)
REVERT: A 1782 MET cc_start: 0.7674 (mmm) cc_final: 0.7454 (mmm)
REVERT: A 1813 ILE cc_start: 0.8264 (mp) cc_final: 0.8026 (tt)
  outliers start: 48
  outliers final: 35
  residues processed: 250
  average time/residue: 0.2083
  time to fit residues: 80.0247
Evaluate side-chains
  245 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 209
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 ASN
A1034 GLN
** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.111937 restraints weight = 18511.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.113815 restraints weight = 12447.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115271 restraints weight = 8973.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13019  Z= 0.161
  Angle     :  0.623   9.839  17561  Z= 0.310
  Chirality :  0.041   0.201   2027
  Planarity :  0.003   0.035   2219
  Dihedral  :  4.151  21.629   1715
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.85 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.31 (0.22), residues: 1583
  helix:  1.51 (0.19), residues: 833
  sheet: -0.77 (0.52), residues: 97
  loop : -2.55 (0.22), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1549 
 HIS   0.007   0.001   HIS A1751 
 PHE   0.022   0.001   PHE A1025 
 TYR   0.014   0.001   TYR A1801 
 ARG   0.003   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  612)
  hydrogen bonds       : angle       3.88581 ( 1758)
  metal coordination   : bond        0.00795 (    4)
  metal coordination   : angle       1.38679 (    3)
  SS BOND              : bond        0.00380 (    2)
  SS BOND              : angle       1.36999 (    4)
  covalent geometry    : bond        0.00379 (13013)
  covalent geometry    : angle       0.62206 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 208
  time to evaluate  : 1.488 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8558 (p0) cc_final: 0.8067 (p0)
REVERT: A  189 HIS cc_start: 0.8399 (t70) cc_final: 0.8027 (t70)
REVERT: A  215 ASP cc_start: 0.7930 (p0) cc_final: 0.7684 (p0)
REVERT: A  485 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7769 (mmm160)
REVERT: A  640 MET cc_start: 0.8752 (mmm) cc_final: 0.8518 (mmm)
REVERT: A  650 ASP cc_start: 0.8326 (t0) cc_final: 0.7932 (t0)
REVERT: A  658 GLU cc_start: 0.7712 (pp20) cc_final: 0.7307 (pp20)
REVERT: A  785 SER cc_start: 0.8699 (m) cc_final: 0.8273 (p)
REVERT: A  827 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7537 (pm20)
REVERT: A  867 TYR cc_start: 0.8847 (t80) cc_final: 0.8557 (t80)
REVERT: A  888 GLU cc_start: 0.7788 (pm20) cc_final: 0.7416 (pm20)
REVERT: A  892 LEU cc_start: 0.8167 (mm) cc_final: 0.7405 (mm)
REVERT: A  999 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6929 (pm20)
REVERT: A 1018 SER cc_start: 0.8857 (p) cc_final: 0.8580 (p)
REVERT: A 1393 THR cc_start: 0.8923 (p) cc_final: 0.8697 (p)
REVERT: A 1466 LYS cc_start: 0.7848 (tmtt) cc_final: 0.7404 (tmtt)
REVERT: A 1813 ILE cc_start: 0.8266 (mp) cc_final: 0.8060 (tt)
  outliers start: 47
  outliers final: 43
  residues processed: 242
  average time/residue: 0.2076
  time to fit residues: 77.8211
Evaluate side-chains
  248 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 204
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  800 ASN
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1324 SER
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1751 HIS
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 148 optimal weight:    0.6980
   chunk 102 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 142 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 80 optimal weight:    0.2980
   chunk 118 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1743 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 = 0.3682 r_free = 0.3682 target = 0.148465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113014 restraints weight = 18609.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115100 restraints weight = 12106.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.116456 restraints weight = 8377.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13019  Z= 0.118
  Angle     :  0.600  11.574  17561  Z= 0.297
  Chirality :  0.040   0.244   2027
  Planarity :  0.003   0.033   2219
  Dihedral  :  4.070  20.353   1715
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.28 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.47 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.22 (0.22), residues: 1583
  helix:  1.57 (0.19), residues: 837
  sheet: -0.71 (0.52), residues: 97
  loop : -2.50 (0.22), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1549 
 HIS   0.004   0.001   HIS A 472 
 PHE   0.022   0.001   PHE A  91 
 TYR   0.014   0.001   TYR A 558 
 ARG   0.003   0.000   ARG A 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  612)
  hydrogen bonds       : angle       3.74793 ( 1758)
  metal coordination   : bond        0.00603 (    4)
  metal coordination   : angle       0.86154 (    3)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       1.30223 (    4)
  covalent geometry    : bond        0.00266 (13013)
  covalent geometry    : angle       0.59958 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 217
  time to evaluate  : 1.323 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8568 (p0) cc_final: 0.8078 (p0)
REVERT: A  189 HIS cc_start: 0.8370 (t70) cc_final: 0.8018 (t70)
REVERT: A  215 ASP cc_start: 0.7861 (p0) cc_final: 0.7126 (t0)
REVERT: A  485 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7722 (mmm160)
REVERT: A  640 MET cc_start: 0.8737 (mmm) cc_final: 0.8492 (mmm)
REVERT: A  650 ASP cc_start: 0.8238 (t0) cc_final: 0.7881 (t0)
REVERT: A  658 GLU cc_start: 0.7634 (pp20) cc_final: 0.7231 (pp20)
REVERT: A  785 SER cc_start: 0.8712 (m) cc_final: 0.8248 (p)
REVERT: A  827 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7513 (pm20)
REVERT: A  867 TYR cc_start: 0.8819 (t80) cc_final: 0.8539 (t80)
REVERT: A  888 GLU cc_start: 0.7764 (pm20) cc_final: 0.7401 (pm20)
REVERT: A  892 LEU cc_start: 0.8162 (mm) cc_final: 0.7396 (mm)
REVERT: A  999 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6934 (pm20)
REVERT: A 1018 SER cc_start: 0.8793 (p) cc_final: 0.8526 (p)
REVERT: A 1393 THR cc_start: 0.8815 (p) cc_final: 0.8574 (p)
REVERT: A 1466 LYS cc_start: 0.7861 (tmtt) cc_final: 0.7430 (tmtt)
REVERT: A 1517 ASN cc_start: 0.7944 (t0) cc_final: 0.7720 (t0)
REVERT: A 1533 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6439 (t80)
REVERT: A 1549 TRP cc_start: 0.7967 (p-90) cc_final: 0.7149 (p-90)
REVERT: A 1625 MET cc_start: 0.8731 (ttm) cc_final: 0.8501 (ttm)
REVERT: A 1771 LYS cc_start: 0.6039 (tptt) cc_final: 0.5817 (tptt)
  outliers start: 45
  outliers final: 40
  residues processed: 250
  average time/residue: 0.2048
  time to fit residues: 79.4633
Evaluate side-chains
  251 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 209
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 129 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 118 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 145 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 901 GLN
** A1743 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 = 0.3683 r_free = 0.3683 target = 0.148236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.113708 restraints weight = 18499.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.115740 restraints weight = 12730.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.116831 restraints weight = 9958.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13019  Z= 0.129
  Angle     :  0.616  12.033  17561  Z= 0.305
  Chirality :  0.040   0.244   2027
  Planarity :  0.003   0.034   2219
  Dihedral  :  4.042  20.988   1715
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.16 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.22), residues: 1583
  helix:  1.57 (0.19), residues: 836
  sheet: -0.74 (0.52), residues: 97
  loop : -2.50 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1549 
 HIS   0.005   0.001   HIS A 472 
 PHE   0.023   0.001   PHE A  91 
 TYR   0.014   0.001   TYR A1097 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  612)
  hydrogen bonds       : angle       3.76264 ( 1758)
  metal coordination   : bond        0.00690 (    4)
  metal coordination   : angle       0.82225 (    3)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       1.30195 (    4)
  covalent geometry    : bond        0.00297 (13013)
  covalent geometry    : angle       0.61579 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 214
  time to evaluate  : 1.610 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8567 (p0) cc_final: 0.8070 (p0)
REVERT: A  189 HIS cc_start: 0.8314 (t70) cc_final: 0.7963 (t70)
REVERT: A  215 ASP cc_start: 0.7893 (p0) cc_final: 0.7148 (t0)
REVERT: A  485 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7739 (mmm160)
REVERT: A  640 MET cc_start: 0.8732 (mmm) cc_final: 0.8491 (mmm)
REVERT: A  650 ASP cc_start: 0.8228 (t0) cc_final: 0.7869 (t0)
REVERT: A  658 GLU cc_start: 0.7682 (pp20) cc_final: 0.7283 (pp20)
REVERT: A  785 SER cc_start: 0.8755 (m) cc_final: 0.8334 (p)
REVERT: A  827 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7360 (pm20)
REVERT: A  867 TYR cc_start: 0.8841 (t80) cc_final: 0.8583 (t80)
REVERT: A  888 GLU cc_start: 0.7770 (pm20) cc_final: 0.7417 (pm20)
REVERT: A  892 LEU cc_start: 0.8197 (mm) cc_final: 0.7427 (mm)
REVERT: A  999 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6942 (pm20)
REVERT: A 1018 SER cc_start: 0.8819 (p) cc_final: 0.8547 (p)
REVERT: A 1393 THR cc_start: 0.8815 (p) cc_final: 0.8580 (p)
REVERT: A 1466 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7420 (tmtt)
REVERT: A 1771 LYS cc_start: 0.6191 (tptt) cc_final: 0.5978 (tptt)
  outliers start: 41
  outliers final: 38
  residues processed: 243
  average time/residue: 0.2175
  time to fit residues: 81.7644
Evaluate side-chains
  250 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 211
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  799 LYS
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1773 LEU
Chi-restraints excluded: chain A residue 1793 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 146 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 108 optimal weight:    0.5980
   chunk 137 optimal weight:    7.9990
   chunk 90 optimal weight:    0.1980
   chunk 109 optimal weight:    0.7980
   chunk 129 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1034 GLN
** A1743 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 = 0.3793 r_free = 0.3793 target = 0.156413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.122399 restraints weight = 18483.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.122972 restraints weight = 11113.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124605 restraints weight = 8505.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13019  Z= 0.117
  Angle     :  0.613  12.367  17561  Z= 0.302
  Chirality :  0.040   0.233   2027
  Planarity :  0.003   0.061   2219
  Dihedral  :  4.015  19.872   1715
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.50 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.16 (0.22), residues: 1583
  helix:  1.62 (0.19), residues: 836
  sheet: -0.73 (0.52), residues: 97
  loop : -2.47 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1717 
 HIS   0.006   0.001   HIS A1751 
 PHE   0.023   0.001   PHE A  91 
 TYR   0.014   0.001   TYR A 558 
 ARG   0.002   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  612)
  hydrogen bonds       : angle       3.68283 ( 1758)
  metal coordination   : bond        0.00504 (    4)
  metal coordination   : angle       0.71515 (    3)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       1.25896 (    4)
  covalent geometry    : bond        0.00265 (13013)
  covalent geometry    : angle       0.61280 (17554)

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

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

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3166 Ramachandran restraints generated.
    1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 223
  time to evaluate  : 1.451 
Fit side-chains
REVERT: A  146 ASN cc_start: 0.8580 (p0) cc_final: 0.8087 (p0)
REVERT: A  189 HIS cc_start: 0.8418 (t70) cc_final: 0.8044 (t70)
REVERT: A  215 ASP cc_start: 0.7937 (p0) cc_final: 0.7242 (t0)
REVERT: A  300 PHE cc_start: 0.8794 (m-10) cc_final: 0.8593 (m-10)
REVERT: A  485 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7715 (mmm160)
REVERT: A  640 MET cc_start: 0.8723 (mmm) cc_final: 0.8473 (mmm)
REVERT: A  650 ASP cc_start: 0.8253 (t0) cc_final: 0.7941 (t0)
REVERT: A  658 GLU cc_start: 0.7615 (pp20) cc_final: 0.7185 (pp20)
REVERT: A  785 SER cc_start: 0.8733 (m) cc_final: 0.8309 (p)
REVERT: A  827 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7337 (pm20)
REVERT: A  867 TYR cc_start: 0.8836 (t80) cc_final: 0.8573 (t80)
REVERT: A  888 GLU cc_start: 0.7778 (pm20) cc_final: 0.7409 (pm20)
REVERT: A  892 LEU cc_start: 0.8141 (mm) cc_final: 0.7385 (mm)
REVERT: A  999 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6915 (pm20)
REVERT: A 1018 SER cc_start: 0.8716 (p) cc_final: 0.8462 (p)
REVERT: A 1393 THR cc_start: 0.8689 (p) cc_final: 0.8482 (p)
REVERT: A 1466 LYS cc_start: 0.7865 (tmtt) cc_final: 0.7444 (tmtt)
REVERT: A 1549 TRP cc_start: 0.7978 (p-90) cc_final: 0.7135 (p-90)
  outliers start: 38
  outliers final: 36
  residues processed: 249
  average time/residue: 0.2269
  time to fit residues: 86.8242
Evaluate side-chains
  247 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  193 ASN
Chi-restraints excluded: chain A residue  292 MET
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  737 ASN
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  827 GLU
Chi-restraints excluded: chain A residue  842 SER
Chi-restraints excluded: chain A residue  866 ASP
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1160 CYS
Chi-restraints excluded: chain A residue 1176 MET
Chi-restraints excluded: chain A residue 1212 THR
Chi-restraints excluded: chain A residue 1242 VAL
Chi-restraints excluded: chain A residue 1273 THR
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1472 SER
Chi-restraints excluded: chain A residue 1533 TYR
Chi-restraints excluded: chain A residue 1679 LEU
Chi-restraints excluded: chain A residue 1770 LEU
Chi-restraints excluded: chain A residue 1773 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 145 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 149 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9980
   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 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1743 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 = 0.3794 r_free = 0.3794 target = 0.156376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.121740 restraints weight = 18490.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124057 restraints weight = 11045.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.125350 restraints weight = 7718.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13019  Z= 0.125
  Angle     :  0.626  12.409  17561  Z= 0.309
  Chirality :  0.041   0.242   2027
  Planarity :  0.003   0.060   2219
  Dihedral  :  4.042  20.373   1715
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.85 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.15 (0.22), residues: 1583
  helix:  1.62 (0.19), residues: 834
  sheet: -0.66 (0.53), residues: 95
  loop : -2.44 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1717 
 HIS   0.006   0.001   HIS A1751 
 PHE   0.022   0.001   PHE A  91 
 TYR   0.014   0.001   TYR A 558 
 ARG   0.002   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  612)
  hydrogen bonds       : angle       3.72321 ( 1758)
  metal coordination   : bond        0.00563 (    4)
  metal coordination   : angle       0.70177 (    3)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       1.27950 (    4)
  covalent geometry    : bond        0.00286 (13013)
  covalent geometry    : angle       0.62593 (17554)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3943.92 seconds
wall clock time: 69 minutes 33.49 seconds (4173.49 seconds total)