Starting phenix.real_space_refine
on Mon Dec 30 10:53:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mxo_24074/12_2024/7mxo_24074.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
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
     K       2      8.98       5
     S      80      5.16       5
     Cl      2      4.86       5
     C    8370      2.51       5
     N    2111      2.21       5
     O    2267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 12832
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 825, 6443
          Classifications: {'peptide': 825}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 795}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 6385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 819, 6385
          Classifications: {'peptide': 819}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 29, 'TRANS': 789}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 1, ' CL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 1, ' CL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.21, per 1000 atoms: 0.64
  Number of scatterers: 12832
  At special positions: 0
  Unit cell: (112.32, 88.56, 158.76, 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)
     K       2     19.00
     Cl      2     17.00
     S      80     16.00
     O    2267      8.00
     N    2111      7.00
     C    8370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 577 " - pdb=" SG  CYS B 582 " 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: 3.71
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3048

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 4 sheets defined
      64.8% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 285 through 291
      removed outlier: 4.263A  pdb=" N   LYS A 289 " --> pdb=" O   PHE A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 300
    Processing helix  chain 'A' and resid 307 through 315
    Processing helix  chain 'A' and resid 316 through 343
    Processing helix  chain 'A' and resid 351 through 360
    Processing helix  chain 'A' and resid 361 through 398
      removed outlier: 3.785A  pdb=" N   ALA A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 427
      removed outlier: 3.752A  pdb=" N   VAL A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 454
      removed outlier: 3.562A  pdb=" N   ALA A 434 " --> pdb=" O   TRP A 430 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ILE A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 464
      Proline residue:  A 462  - end of helix
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 500 through 506
      removed outlier: 3.552A  pdb=" N   GLY A 504 " --> pdb=" O   GLY A 500 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ALA A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 542
      Proline residue:  A 519  - end of helix
      removed outlier: 3.876A  pdb=" N   LEU A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 580
      removed outlier: 4.331A  pdb=" N   SER A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 575 through 580'
    Processing helix  chain 'A' and resid 592 through 597
      removed outlier: 3.676A  pdb=" N   SER A 597 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 633
      removed outlier: 3.708A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 639 through 643
    Processing helix  chain 'A' and resid 653 through 667
      removed outlier: 3.801A  pdb=" N   LEU A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 699
    Processing helix  chain 'A' and resid 712 through 730
      removed outlier: 3.599A  pdb=" N   ILE A 730 " --> pdb=" O   VAL A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 751
    Processing helix  chain 'A' and resid 763 through 780
      removed outlier: 4.303A  pdb=" N   TYR A 767 " --> pdb=" O   GLN A 763 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A 780 " --> pdb=" O   ARG A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 811
      removed outlier: 4.000A  pdb=" N   LEU A 805 " --> pdb=" O   ARG A 801 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE A 811 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 849
      removed outlier: 3.539A  pdb=" N   GLU A 834 " --> pdb=" O   GLN A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 873
    Processing helix  chain 'A' and resid 896 through 914
      removed outlier: 3.665A  pdb=" N   VAL A 900 " --> pdb=" O   ASP A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1046
      Proline residue:  A1040  - end of helix
      removed outlier: 3.687A  pdb=" N   LYS A1046 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1050
    Processing helix  chain 'A' and resid 1064 through 1080
    Processing helix  chain 'A' and resid 1097 through 1109
    Processing helix  chain 'A' and resid 1110 through 1112
      No H-bonds generated for 'chain 'A' and resid 1110 through 1112'
    Processing helix  chain 'A' and resid 1119 through 1130
    Processing helix  chain 'A' and resid 1135 through 1142
    Processing helix  chain 'A' and resid 1142 through 1160
    Processing helix  chain 'A' and resid 1179 through 1191
    Processing helix  chain 'B' and resid 291 through 300
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.336A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 343
    Processing helix  chain 'B' and resid 351 through 360
    Processing helix  chain 'B' and resid 361 through 398
      removed outlier: 3.905A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 3.579A  pdb=" N   VAL B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA B 426 " --> pdb=" O   GLY B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 454
      removed outlier: 4.271A  pdb=" N   ILE B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL B 437 " --> pdb=" O   LYS B 433 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 469 through 477
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 500 through 506
      removed outlier: 4.074A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 544
      removed outlier: 3.834A  pdb=" N   ILE B 518 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
      Proline residue:  B 519  - end of helix
      removed outlier: 3.586A  pdb=" N   LEU B 523 " --> pdb=" O   PRO B 519 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 4.048A  pdb=" N   CYS B 577 " --> pdb=" O   ASP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 597
      removed outlier: 3.591A  pdb=" N   MET B 595 " --> pdb=" O   GLN B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 633
      removed outlier: 3.525A  pdb=" N   ILE B 603 " --> pdb=" O   PHE B 599 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER B 614 " --> pdb=" O   ALA B 610 " (cutoff:3.500A)
      Proline residue:  B 623  - end of helix
    Processing helix  chain 'B' and resid 635 through 639
    Processing helix  chain 'B' and resid 652 through 667
    Processing helix  chain 'B' and resid 674 through 699
      removed outlier: 3.552A  pdb=" N   ILE B 678 " --> pdb=" O   ILE B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 731
    Processing helix  chain 'B' and resid 731 through 752
    Processing helix  chain 'B' and resid 762 through 780
    Processing helix  chain 'B' and resid 801 through 811
      removed outlier: 3.898A  pdb=" N   LEU B 805 " --> pdb=" O   ARG B 801 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 827 through 849
      removed outlier: 4.269A  pdb=" N   LYS B 833 " --> pdb=" O   ARG B 829 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ALA B 840 " --> pdb=" O   SER B 836 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN B 849 " --> pdb=" O   TRP B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 862 through 873
    Processing helix  chain 'B' and resid 896 through 913
      removed outlier: 3.840A  pdb=" N   VAL B 900 " --> pdb=" O   ASP B 896 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   PHE B 907 " --> pdb=" O   TYR B 903 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS B 908 " --> pdb=" O   ILE B 904 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE B 913 " --> pdb=" O   ASP B 909 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1034 through 1046
      Proline residue:  B1040  - end of helix
      removed outlier: 3.962A  pdb=" N   LYS B1046 " --> pdb=" O   LEU B1042 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1064 through 1079
    Processing helix  chain 'B' and resid 1090 through 1094
      removed outlier: 4.402A  pdb=" N   ASN B1093 " --> pdb=" O   GLY B1090 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1097 through 1109
      removed outlier: 3.591A  pdb=" N   ILE B1101 " --> pdb=" O   LYS B1097 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1110 through 1112
      No H-bonds generated for 'chain 'B' and resid 1110 through 1112'
    Processing helix  chain 'B' and resid 1119 through 1128
      removed outlier: 3.710A  pdb=" N   LYS B1125 " --> pdb=" O   ASP B1121 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   MET B1126 " --> pdb=" O   ILE B1122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1135 through 1142
    Processing helix  chain 'B' and resid 1142 through 1160
    Processing helix  chain 'B' and resid 1179 through 1191
    Processing sheet with id=AA1, first strand: chain 'A' and resid 817 through 819
      removed outlier: 6.398A  pdb=" N   GLN A 790 " --> pdb=" O   THR A 883 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 885 " --> pdb=" O   GLN A 790 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   LEU A 792 " --> pdb=" O   VAL A 885 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   GLY A 887 " --> pdb=" O   LEU A 792 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   MET A 794 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 920 " --> pdb=" O   LEU A 886 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ILE A1166 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   VAL A1200 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   MET A1168 " --> pdb=" O   VAL A1200 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER A1169 " --> pdb=" O   TRP A1027 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   MET A1087 " --> pdb=" O   VAL A1056 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819
      removed outlier: 6.375A  pdb=" N   CYS B 791 " --> pdb=" O   ILE B 819 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 920 " --> pdb=" O   LEU B 886 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE B1166 " --> pdb=" O   LEU B1198 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL B1200 " --> pdb=" O   ILE B1166 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   MET B1168 " --> pdb=" O   VAL B1200 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824

    761 hydrogen bonds defined for protein.
    2247 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.70

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4003
        1.34 -     1.46: 1933
        1.46 -     1.57: 7039
        1.57 -     1.69: 0
        1.69 -     1.81: 136
  Bond restraints: 13111
  Sorted by residual:
  bond pdb=" CG1 ILE A 415 "
       pdb=" CD1 ILE A 415 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.87e+00
  bond pdb=" CG  ARG B 844 "
       pdb=" CD  ARG B 844 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.71e+00
  bond pdb=" CG  LEU A 586 "
       pdb=" CD2 LEU A 586 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" CB  MET B 296 "
       pdb=" CG  MET B 296 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.24e+00
  bond pdb=" CB  ILE B 603 "
       pdb=" CG2 ILE B 603 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.94e-01
  ... (remaining 13106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 17261
        1.49 -     2.98: 411
        2.98 -     4.47: 89
        4.47 -     5.96: 9
        5.96 -     7.45: 2
  Bond angle restraints: 17772
  Sorted by residual:
  angle pdb=" C   GLN B 843 "
        pdb=" N   ARG B 844 "
        pdb=" CA  ARG B 844 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.07e+01
  angle pdb=" N   GLU A1106 "
        pdb=" CA  GLU A1106 "
        pdb=" CB  GLU A1106 "
      ideal   model   delta    sigma   weight residual
     110.28  114.20   -3.92 1.55e+00 4.16e-01 6.38e+00
  angle pdb=" CA  ARG B 844 "
        pdb=" CB  ARG B 844 "
        pdb=" CG  ARG B 844 "
      ideal   model   delta    sigma   weight residual
     114.10  119.13   -5.03 2.00e+00 2.50e-01 6.34e+00
  angle pdb=" N   MET B 835 "
        pdb=" CA  MET B 835 "
        pdb=" CB  MET B 835 "
      ideal   model   delta    sigma   weight residual
     110.28  114.13   -3.85 1.55e+00 4.16e-01 6.18e+00
  angle pdb=" CB  MET B 835 "
        pdb=" CG  MET B 835 "
        pdb=" SD  MET B 835 "
      ideal   model   delta    sigma   weight residual
     112.70  120.15   -7.45 3.00e+00 1.11e-01 6.16e+00
  ... (remaining 17767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 6925
       17.37 -    34.75: 711
       34.75 -    52.12: 104
       52.12 -    69.50: 13
       69.50 -    86.87: 8
  Dihedral angle restraints: 7761
    sinusoidal: 3024
      harmonic: 4737
  Sorted by residual:
  dihedral pdb=" CB  CYS A 577 "
           pdb=" SG  CYS A 577 "
           pdb=" SG  CYS A 582 "
           pdb=" CB  CYS A 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.43  -56.43     1      1.00e+01 1.00e-02 4.29e+01
  dihedral pdb=" CB  CYS B 577 "
           pdb=" SG  CYS B 577 "
           pdb=" SG  CYS B 582 "
           pdb=" CB  CYS B 582 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.48   38.52     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CA  PRO B 754 "
           pdb=" C   PRO B 754 "
           pdb=" N   ASP B 755 "
           pdb=" CA  ASP B 755 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.84  -19.16     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 7758 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1357
       0.034 -    0.068: 493
       0.068 -    0.102: 151
       0.102 -    0.136: 55
       0.136 -    0.170: 3
  Chirality restraints: 2059
  Sorted by residual:
  chirality pdb=" CA  ILE A 730 "
            pdb=" N   ILE A 730 "
            pdb=" C   ILE A 730 "
            pdb=" CB  ILE A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.26e-01
  chirality pdb=" CA  ILE B 668 "
            pdb=" N   ILE B 668 "
            pdb=" C   ILE B 668 "
            pdb=" CB  ILE B 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  ILE A 668 "
            pdb=" N   ILE A 668 "
            pdb=" C   ILE A 668 "
            pdb=" CB  ILE A 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 2056 not shown)

  Planarity restraints: 2207
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 801 "    0.240 9.50e-02 1.11e+02   1.07e-01 7.15e+00
        pdb=" NE  ARG A 801 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 801 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 801 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 801 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B1102 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.55e+00
        pdb=" C   ILE B1102 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ILE B1102 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B1103 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 495 "    0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO B 496 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 496 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 496 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2204 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.70: 334
        2.70 -     3.31: 15948
        3.31 -     3.92: 24452
        3.92 -     4.53: 32872
        4.53 -     5.14: 50920
  Nonbonded interactions: 124526
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B1094 "
            pdb=" NH1 ARG B1151 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" O   GLY B 313 "
            pdb=" NH1 ARG B 546 "
     model   vdw
     2.088 3.120
  nonbonded pdb=" O   GLY A 313 "
            pdb=" NH1 ARG A 546 "
     model   vdw
     2.118 3.120
  nonbonded pdb=" O   ASP B1091 "
            pdb=" NH1 ARG B1151 "
     model   vdw
     2.133 3.120
  nonbonded pdb=" OG1 THR B 328 "
            pdb=" OG1 THR B 530 "
     model   vdw
     2.144 3.040
  ... (remaining 124521 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 284 through 644 or resid 651 through 836 or (resid 837 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 838 through 922 o \ 
r resid 1020 through 1079 or resid 1081 through 1206 or resid 1301 through 1302) \ 
)
  selection = chain 'B'
}

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 individual isotropic
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:             3.500
  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:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.620
  Find NCS groups from input model:        0.800
  Set up NCS constraints:                  0.050
  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:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
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   0.053  13111  Z= 0.285
  Angle     :  0.584   7.448  17772  Z= 0.319
  Chirality :  0.041   0.170   2059
  Planarity :  0.004   0.107   2207
  Dihedral  : 13.623  86.874   4707
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  0.60 (0.21), residues: 1630
  helix:  1.53 (0.17), residues: 973
  sheet: -0.00 (0.52), residues: 110
  loop : -1.65 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 287 
 HIS   0.004   0.001   HIS A 809 
 PHE   0.024   0.002   PHE A 907 
 TYR   0.023   0.002   TYR B 915 
 ARG   0.005   0.000   ARG A 801 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 LEU cc_start: 0.8597 (tp) cc_final: 0.8394 (tp)
REVERT: A  852 LYS cc_start: 0.7570 (mptt) cc_final: 0.7150 (mptt)
REVERT: A  902 MET cc_start: 0.7534 (ttp) cc_final: 0.7071 (ttm)
REVERT: A 1205 GLN cc_start: 0.7462 (tm-30) cc_final: 0.7117 (tm-30)
REVERT: B  354 TYR cc_start: 0.7125 (t80) cc_final: 0.6898 (t80)
REVERT: B  433 LYS cc_start: 0.7802 (tptp) cc_final: 0.7146 (pptt)
REVERT: B  818 MET cc_start: 0.7821 (tmm) cc_final: 0.7328 (tmm)
REVERT: B  835 MET cc_start: 0.7882 (mpp) cc_final: 0.7599 (mtm)
REVERT: B  903 TYR cc_start: 0.7734 (m-80) cc_final: 0.7094 (m-80)
REVERT: B 1112 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6916 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2595
  time to fit residues: 68.9557
Evaluate side-chains
  156 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 68 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 66 optimal weight:    7.9990
   chunk 127 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 148 optimal weight:    8.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13111  Z= 0.339
  Angle     :  0.623   6.373  17772  Z= 0.329
  Chirality :  0.045   0.170   2059
  Planarity :  0.004   0.075   2207
  Dihedral  :  4.502  18.938   1748
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.28 %
    Favored  : 89.78 %
  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:  0.56 (0.21), residues: 1630
  helix:  1.44 (0.17), residues: 980
  sheet:  0.17 (0.52), residues: 104
  loop : -1.60 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 892 
 HIS   0.003   0.001   HIS A 824 
 PHE   0.025   0.002   PHE A 387 
 TYR   0.009   0.001   TYR A 751 
 ARG   0.004   0.001   ARG A1133 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.7506 (tpp) cc_final: 0.7132 (tpp)
REVERT: A  852 LYS cc_start: 0.7657 (mptt) cc_final: 0.7254 (mptt)
REVERT: A  886 LEU cc_start: 0.8543 (mt) cc_final: 0.8301 (mt)
REVERT: A  902 MET cc_start: 0.7526 (ttp) cc_final: 0.6996 (ttm)
REVERT: A 1205 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7172 (tm-30)
REVERT: B  354 TYR cc_start: 0.7211 (t80) cc_final: 0.6922 (t80)
REVERT: B  433 LYS cc_start: 0.7859 (tptp) cc_final: 0.7210 (pptt)
REVERT: B  818 MET cc_start: 0.8012 (tmm) cc_final: 0.7309 (tmm)
REVERT: B  835 MET cc_start: 0.7567 (mpp) cc_final: 0.7037 (mpp)
REVERT: B  843 GLN cc_start: 0.8420 (tt0) cc_final: 0.8139 (tt0)
REVERT: B  903 TYR cc_start: 0.7855 (m-80) cc_final: 0.7485 (m-80)
REVERT: B 1168 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.5037 (ptm)
REVERT: B 1186 TRP cc_start: 0.8776 (m-10) cc_final: 0.8521 (m-10)
  outliers start: 13
  outliers final: 7
  residues processed: 186
  average time/residue: 0.2800
  time to fit residues: 74.9987
Evaluate side-chains
  163 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  786 ASN
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  578 GLU
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue 1168 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 123 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 148 optimal weight:   10.0000
   chunk 160 optimal weight:    3.9990
   chunk 132 optimal weight:    6.9990
   chunk 147 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 118 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 763 GLN
B 908 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  13111  Z= 0.399
  Angle     :  0.656   8.650  17772  Z= 0.344
  Chirality :  0.046   0.172   2059
  Planarity :  0.004   0.047   2207
  Dihedral  :  4.654  20.261   1748
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.78 %
    Favored  : 84.12 %
  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 (0.21), residues: 1630
  helix:  1.12 (0.16), residues: 996
  sheet:  0.21 (0.52), residues: 105
  loop : -1.73 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 892 
 HIS   0.003   0.001   HIS B 824 
 PHE   0.025   0.002   PHE B 811 
 TYR   0.012   0.002   TYR B 915 
 ARG   0.004   0.000   ARG B 546 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.7437 (tpp) cc_final: 0.6864 (tpt)
REVERT: A  852 LYS cc_start: 0.7807 (mptt) cc_final: 0.7420 (mptt)
REVERT: A  886 LEU cc_start: 0.8646 (mt) cc_final: 0.8423 (mt)
REVERT: A  902 MET cc_start: 0.7457 (ttp) cc_final: 0.6807 (ttm)
REVERT: A 1205 GLN cc_start: 0.7373 (tm-30) cc_final: 0.7135 (tm-30)
REVERT: B  354 TYR cc_start: 0.7280 (t80) cc_final: 0.6944 (t80)
REVERT: B  402 MET cc_start: 0.6512 (ptp) cc_final: 0.6080 (ptp)
REVERT: B  818 MET cc_start: 0.8249 (tmm) cc_final: 0.7503 (tmm)
REVERT: B  835 MET cc_start: 0.7494 (mpp) cc_final: 0.6964 (mtt)
REVERT: B  843 GLN cc_start: 0.8429 (tt0) cc_final: 0.8127 (tt0)
REVERT: B  892 TRP cc_start: 0.8377 (p-90) cc_final: 0.8145 (p-90)
REVERT: B 1168 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4907 (ptm)
REVERT: B 1186 TRP cc_start: 0.8819 (m-10) cc_final: 0.8583 (m-10)
  outliers start: 29
  outliers final: 16
  residues processed: 188
  average time/residue: 0.2737
  time to fit residues: 73.7051
Evaluate side-chains
  173 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  786 ASN
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1168 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 146 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 70 optimal weight:    0.4980
   chunk 99 optimal weight:    0.0010
   chunk 148 optimal weight:    5.9990
   chunk 157 optimal weight:    9.9990
   chunk 77 optimal weight:    6.9990
   chunk 141 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0050
   overall best weight:    0.6202

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

Flipped N/Q/H residues before XYZ refinement:
A 763 GLN
A 824 HIS
A1137 ASN
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13111  Z= 0.211
  Angle     :  0.552   8.271  17772  Z= 0.289
  Chirality :  0.041   0.154   2059
  Planarity :  0.004   0.046   2207
  Dihedral  :  4.394  19.093   1748
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.10 %
    Favored  : 82.16 %
  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:  0.61 (0.21), residues: 1630
  helix:  1.51 (0.16), residues: 985
  sheet: -0.07 (0.51), residues: 114
  loop : -1.63 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 733 
 HIS   0.005   0.001   HIS B 908 
 PHE   0.024   0.001   PHE B 811 
 TYR   0.009   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A1069 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 1.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 ILE cc_start: 0.8381 (pt) cc_final: 0.8034 (mt)
REVERT: A  852 LYS cc_start: 0.7834 (mptt) cc_final: 0.7418 (mptt)
REVERT: A  886 LEU cc_start: 0.8720 (mt) cc_final: 0.8498 (mt)
REVERT: A  902 MET cc_start: 0.7424 (ttp) cc_final: 0.6767 (ttm)
REVERT: A 1205 GLN cc_start: 0.7302 (tm-30) cc_final: 0.7087 (tm-30)
REVERT: B  354 TYR cc_start: 0.7185 (t80) cc_final: 0.6872 (t80)
REVERT: B  818 MET cc_start: 0.8283 (tmm) cc_final: 0.7355 (tmm)
REVERT: B  835 MET cc_start: 0.7516 (mpp) cc_final: 0.7223 (mtp)
REVERT: B  844 ARG cc_start: 0.8750 (pmt-80) cc_final: 0.8383 (pmt-80)
REVERT: B  892 TRP cc_start: 0.8343 (p-90) cc_final: 0.8099 (p-90)
  outliers start: 24
  outliers final: 13
  residues processed: 187
  average time/residue: 0.2649
  time to fit residues: 72.3724
Evaluate side-chains
  169 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  832 MET
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue 1094 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 131 optimal weight:    9.9990
   chunk 89 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 117 optimal weight:    0.0000
   chunk 65 optimal weight:    0.0980
   chunk 134 optimal weight:    7.9990
   chunk 108 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 141 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 843 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13111  Z= 0.174
  Angle     :  0.534   9.907  17772  Z= 0.279
  Chirality :  0.041   0.154   2059
  Planarity :  0.003   0.044   2207
  Dihedral  :  4.228  19.788   1748
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.53 %
    Favored  : 81.51 %
  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:  0.77 (0.21), residues: 1630
  helix:  1.66 (0.17), residues: 988
  sheet: -0.06 (0.50), residues: 114
  loop : -1.61 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 733 
 HIS   0.002   0.000   HIS B 908 
 PHE   0.024   0.001   PHE B 811 
 TYR   0.010   0.001   TYR B 915 
 ARG   0.003   0.000   ARG A1069 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 ILE cc_start: 0.8338 (pt) cc_final: 0.8046 (mt)
REVERT: A  835 MET cc_start: 0.5206 (mmm) cc_final: 0.4818 (mmm)
REVERT: A  852 LYS cc_start: 0.7768 (mptt) cc_final: 0.7358 (mptt)
REVERT: A  886 LEU cc_start: 0.8718 (mt) cc_final: 0.8475 (mt)
REVERT: A  902 MET cc_start: 0.7363 (ttp) cc_final: 0.6714 (ttm)
REVERT: A 1205 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7128 (tm-30)
REVERT: B  354 TYR cc_start: 0.7192 (t80) cc_final: 0.6906 (t80)
REVERT: B  433 LYS cc_start: 0.7760 (tptp) cc_final: 0.7254 (pptt)
REVERT: B  818 MET cc_start: 0.8271 (tmm) cc_final: 0.7399 (tmm)
REVERT: B  835 MET cc_start: 0.7494 (mpp) cc_final: 0.7154 (mtp)
REVERT: B  843 GLN cc_start: 0.8295 (tt0) cc_final: 0.8033 (tt0)
REVERT: B  844 ARG cc_start: 0.8769 (pmt-80) cc_final: 0.8481 (pmt-80)
REVERT: B  892 TRP cc_start: 0.8383 (p-90) cc_final: 0.8130 (p-90)
REVERT: B  903 TYR cc_start: 0.7822 (m-80) cc_final: 0.6770 (t80)
REVERT: B  914 GLN cc_start: 0.7690 (pp30) cc_final: 0.7345 (mm-40)
REVERT: B 1186 TRP cc_start: 0.8802 (m-10) cc_final: 0.8521 (m-10)
  outliers start: 27
  outliers final: 19
  residues processed: 187
  average time/residue: 0.2570
  time to fit residues: 70.1028
Evaluate side-chains
  176 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  595 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1128 GLU
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13111  Z= 0.245
  Angle     :  0.567   8.941  17772  Z= 0.294
  Chirality :  0.042   0.162   2059
  Planarity :  0.003   0.044   2207
  Dihedral  :  4.307  31.960   1748
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.04 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.65 (0.21), residues: 1630
  helix:  1.54 (0.16), residues: 998
  sheet: -0.09 (0.50), residues: 114
  loop : -1.67 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 758 
 HIS   0.002   0.001   HIS A 773 
 PHE   0.025   0.001   PHE B 811 
 TYR   0.011   0.001   TYR B 767 
 ARG   0.002   0.000   ARG A 546 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  835 MET cc_start: 0.5378 (mmm) cc_final: 0.4892 (mmm)
REVERT: A  852 LYS cc_start: 0.7845 (mptt) cc_final: 0.7438 (mptt)
REVERT: A  886 LEU cc_start: 0.8706 (mt) cc_final: 0.8477 (mt)
REVERT: A  902 MET cc_start: 0.7344 (ttp) cc_final: 0.6701 (ttm)
REVERT: A 1205 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7121 (tm-30)
REVERT: B  393 GLU cc_start: 0.7818 (tp30) cc_final: 0.7599 (tp30)
REVERT: B  433 LYS cc_start: 0.7786 (tptp) cc_final: 0.7268 (pptt)
REVERT: B  718 LEU cc_start: 0.8247 (mp) cc_final: 0.7793 (tt)
REVERT: B  818 MET cc_start: 0.8337 (tmm) cc_final: 0.7392 (tmm)
REVERT: B  892 TRP cc_start: 0.8397 (p-90) cc_final: 0.8148 (p-90)
REVERT: B  903 TYR cc_start: 0.7877 (m-80) cc_final: 0.6773 (t80)
REVERT: B  914 GLN cc_start: 0.7644 (pp30) cc_final: 0.7422 (mm-40)
REVERT: B 1186 TRP cc_start: 0.8846 (m-10) cc_final: 0.8553 (m-10)
  outliers start: 32
  outliers final: 24
  residues processed: 187
  average time/residue: 0.2670
  time to fit residues: 72.1112
Evaluate side-chains
  182 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  832 MET
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  595 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 152 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 132 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9990
   chunk 157 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 843 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13111  Z= 0.249
  Angle     :  0.579   8.586  17772  Z= 0.300
  Chirality :  0.042   0.257   2059
  Planarity :  0.004   0.044   2207
  Dihedral  :  4.338  36.637   1748
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.91 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: 1630
  helix:  1.54 (0.16), residues: 996
  sheet: -0.07 (0.51), residues: 114
  loop : -1.69 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 733 
 HIS   0.002   0.000   HIS B 908 
 PHE   0.025   0.001   PHE B 811 
 TYR   0.011   0.001   TYR B 354 
 ARG   0.002   0.000   ARG A 546 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  835 MET cc_start: 0.5448 (mmm) cc_final: 0.5094 (mmm)
REVERT: A  852 LYS cc_start: 0.7992 (mptt) cc_final: 0.7493 (mptt)
REVERT: A  886 LEU cc_start: 0.8700 (mt) cc_final: 0.8485 (mt)
REVERT: A 1205 GLN cc_start: 0.7318 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: B  433 LYS cc_start: 0.7797 (tptp) cc_final: 0.7278 (pptt)
REVERT: B  818 MET cc_start: 0.8332 (tmm) cc_final: 0.7341 (tmm)
REVERT: B  835 MET cc_start: 0.7373 (mpp) cc_final: 0.7083 (mmt)
REVERT: B  843 GLN cc_start: 0.8303 (tt0) cc_final: 0.8041 (tt0)
REVERT: B  892 TRP cc_start: 0.8398 (p-90) cc_final: 0.8126 (p-90)
REVERT: B  903 TYR cc_start: 0.7957 (m-80) cc_final: 0.6830 (t80)
REVERT: B 1186 TRP cc_start: 0.8879 (m-10) cc_final: 0.8626 (m-10)
  outliers start: 32
  outliers final: 27
  residues processed: 186
  average time/residue: 0.2654
  time to fit residues: 71.7461
Evaluate side-chains
  180 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  832 MET
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  595 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 99 optimal weight:    0.4980
   chunk 107 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 123 optimal weight:    0.7980
   chunk 142 optimal weight:   10.0000
   chunk 150 optimal weight:    0.8980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13111  Z= 0.202
  Angle     :  0.569  11.260  17772  Z= 0.295
  Chirality :  0.041   0.192   2059
  Planarity :  0.003   0.044   2207
  Dihedral  :  4.290  36.969   1748
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.35 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.72 (0.21), residues: 1630
  helix:  1.61 (0.16), residues: 993
  sheet: -0.03 (0.51), residues: 114
  loop : -1.68 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 733 
 HIS   0.003   0.000   HIS A 806 
 PHE   0.025   0.001   PHE B 811 
 TYR   0.010   0.001   TYR B 767 
 ARG   0.005   0.000   ARG A 801 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 1.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 ILE cc_start: 0.8368 (pt) cc_final: 0.8042 (mt)
REVERT: A  835 MET cc_start: 0.5393 (mmm) cc_final: 0.5048 (mmm)
REVERT: A  886 LEU cc_start: 0.8668 (mt) cc_final: 0.8449 (mt)
REVERT: A  902 MET cc_start: 0.7372 (ttp) cc_final: 0.6696 (ttm)
REVERT: B  433 LYS cc_start: 0.7853 (tptp) cc_final: 0.7361 (pptt)
REVERT: B  818 MET cc_start: 0.8345 (tmm) cc_final: 0.7356 (tmm)
REVERT: B  835 MET cc_start: 0.7405 (mpp) cc_final: 0.7066 (mmt)
REVERT: B  892 TRP cc_start: 0.8376 (p-90) cc_final: 0.8122 (p-90)
REVERT: B  903 TYR cc_start: 0.7987 (m-80) cc_final: 0.6833 (t80)
REVERT: B  914 GLN cc_start: 0.7573 (pp30) cc_final: 0.6941 (mm-40)
REVERT: B 1186 TRP cc_start: 0.8819 (m-10) cc_final: 0.8580 (m-10)
  outliers start: 28
  outliers final: 26
  residues processed: 179
  average time/residue: 0.2550
  time to fit residues: 66.8179
Evaluate side-chains
  181 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  832 MET
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  595 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    2.9990
   chunk 146 optimal weight:   10.0000
   chunk 150 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 138 optimal weight:    0.9990
   chunk 145 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 843 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  13111  Z= 0.385
  Angle     :  0.670  10.904  17772  Z= 0.345
  Chirality :  0.045   0.175   2059
  Planarity :  0.004   0.044   2207
  Dihedral  :  4.580  37.852   1748
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.35 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.36 (0.21), residues: 1630
  helix:  1.29 (0.16), residues: 994
  sheet:  0.05 (0.51), residues: 106
  loop : -1.79 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 758 
 HIS   0.003   0.001   HIS B 908 
 PHE   0.025   0.002   PHE B 811 
 TYR   0.013   0.002   TYR A 739 
 ARG   0.004   0.000   ARG A 546 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  835 MET cc_start: 0.5428 (mmm) cc_final: 0.5062 (mmm)
REVERT: A  902 MET cc_start: 0.7403 (ttp) cc_final: 0.6754 (ttm)
REVERT: B  433 LYS cc_start: 0.7861 (tptp) cc_final: 0.7470 (pptt)
REVERT: B  710 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6440 (m-80)
REVERT: B  818 MET cc_start: 0.8276 (tmm) cc_final: 0.7305 (tmm)
REVERT: B  835 MET cc_start: 0.7403 (mpp) cc_final: 0.7062 (mmt)
REVERT: B  843 GLN cc_start: 0.8252 (tt0) cc_final: 0.7928 (tt0)
REVERT: B  892 TRP cc_start: 0.8400 (p-90) cc_final: 0.8130 (p-90)
REVERT: B  903 TYR cc_start: 0.7952 (m-80) cc_final: 0.6754 (t80)
REVERT: B  914 GLN cc_start: 0.7707 (pp30) cc_final: 0.7111 (mm-40)
REVERT: B 1186 TRP cc_start: 0.8859 (m-10) cc_final: 0.8627 (m-10)
  outliers start: 33
  outliers final: 29
  residues processed: 180
  average time/residue: 0.2592
  time to fit residues: 68.3616
Evaluate side-chains
  179 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  408 ASP
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  832 MET
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  595 MET
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  697 SER
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 154 optimal weight:   10.0000
   chunk 94 optimal weight:    0.0870
   chunk 73 optimal weight:    7.9990
   chunk 107 optimal weight:    0.5980
   chunk 162 optimal weight:    0.7980
   chunk 149 optimal weight:    0.9990
   chunk 129 optimal weight:    0.0050
   chunk 13 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0870
   chunk 79 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.2750

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

Flipped N/Q/H residues before XYZ refinement:
** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13111  Z= 0.167
  Angle     :  0.580  11.108  17772  Z= 0.297
  Chirality :  0.041   0.187   2059
  Planarity :  0.003   0.047   2207
  Dihedral  :  4.306  38.887   1748
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.36 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.72 (0.21), residues: 1630
  helix:  1.62 (0.17), residues: 997
  sheet: -0.03 (0.51), residues: 113
  loop : -1.70 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 733 
 HIS   0.002   0.000   HIS A 859 
 PHE   0.025   0.001   PHE B 811 
 TYR   0.012   0.001   TYR B 767 
 ARG   0.002   0.000   ARG A 801 

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  666 ILE cc_start: 0.8286 (pt) cc_final: 0.8029 (mt)
REVERT: A  788 ARG cc_start: 0.7498 (mpt180) cc_final: 0.7141 (mpt180)
REVERT: A  835 MET cc_start: 0.5394 (mmm) cc_final: 0.5039 (mmm)
REVERT: A  846 LEU cc_start: 0.6408 (tp) cc_final: 0.6009 (mt)
REVERT: A  851 MET cc_start: 0.6053 (mmp) cc_final: 0.5801 (mmp)
REVERT: A  902 MET cc_start: 0.7318 (ttp) cc_final: 0.6644 (ttm)
REVERT: B  710 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6672 (m-80)
REVERT: B  818 MET cc_start: 0.8241 (tmm) cc_final: 0.7272 (tmm)
REVERT: B  835 MET cc_start: 0.7389 (mpp) cc_final: 0.7057 (mmt)
REVERT: B  892 TRP cc_start: 0.8271 (p-90) cc_final: 0.7959 (p-90)
REVERT: B  903 TYR cc_start: 0.7951 (m-80) cc_final: 0.6780 (t80)
REVERT: B  914 GLN cc_start: 0.7669 (pp30) cc_final: 0.7138 (mm-40)
REVERT: B 1186 TRP cc_start: 0.8803 (m-10) cc_final: 0.8573 (m-10)
  outliers start: 24
  outliers final: 20
  residues processed: 177
  average time/residue: 0.2610
  time to fit residues: 67.9019
Evaluate side-chains
  176 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 1.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  710 TYR
Chi-restraints excluded: chain B residue 1094 THR
Chi-restraints excluded: chain B residue 1140 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 119 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 129 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 132 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 843 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.201804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.134577 restraints weight = 16259.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.31
r_work: 0.3379 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13111  Z= 0.197
  Angle     :  0.578  10.653  17772  Z= 0.297
  Chirality :  0.041   0.183   2059
  Planarity :  0.003   0.047   2207
  Dihedral  :  4.267  38.634   1748
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.80 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: 1630
  helix:  1.64 (0.17), residues: 998
  sheet: -0.00 (0.51), residues: 113
  loop : -1.68 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 733 
 HIS   0.001   0.000   HIS A 859 
 PHE   0.024   0.001   PHE B 811 
 TYR   0.010   0.001   TYR B 767 
 ARG   0.002   0.000   ARG A 801 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2708.71 seconds
wall clock time: 50 minutes 29.65 seconds (3029.65 seconds total)