Starting phenix.real_space_refine
on Fri Mar 14 03:01:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dz2_47323/03_2025/9dz2_47323.cif"
  }
  resolution = 3.31
  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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6092      2.51       5
     N    1615      2.21       5
     O    1772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9523
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1723
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 14, 'TRANS': 197}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1198
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 12, 'TRANS': 144}
    Chain: "J"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 835
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 1230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1230
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 13, 'TRANS': 147}
    Chain: "B"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 812
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1701
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 13, 'TRANS': 195}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1189
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 12, 'TRANS': 143}
    Chain: "F"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 835
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
  Time building chain proxies: 6.74, per 1000 atoms: 0.71
  Number of scatterers: 9523
  At special positions: 0
  Unit cell: (118.635, 101.813, 141.653, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1772      8.00
     N    1615      7.00
     C    6092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 468 " - pdb=" SG  CYS C 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 516 " - pdb=" SG  CYS C 533 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I  53 " - pdb=" SG  CYS J 609 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I 108 " - pdb=" SG  CYS I 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 121 " - pdb=" SG  CYS I 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 511 " - pdb=" SG  CYS J 556 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J 601 " - pdb=" SG  CYS J 608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS B 609 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 556 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 601 " - pdb=" SG  CYS B 608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 468 " - pdb=" SG  CYS D 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 516 " - pdb=" SG  CYS D 533 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS F 609 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 108 " - pdb=" SG  CYS E 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 121 " - pdb=" SG  CYS E 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 511 " - pdb=" SG  CYS F 556 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 601 " - pdb=" SG  CYS F 608 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2230

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 23 sheets defined
      25.9% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 390 through 398
    Processing helix  chain 'C' and resid 432 through 435
    Processing helix  chain 'C' and resid 436 through 451
      removed outlier: 3.777A  pdb=" N   HIS C 441 " --> pdb=" O   ILE C 437 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLN C 442 " --> pdb=" O   GLN C 438 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL C 443 " --> pdb=" O   ILE C 439 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU C 444 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLN C 447 " --> pdb=" O   VAL C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 468
      removed outlier: 3.954A  pdb=" N   ILE C 467 " --> pdb=" O   THR C 463 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 489
    Processing helix  chain 'C' and resid 508 through 517
      removed outlier: 3.680A  pdb=" N   CYS C 516 " --> pdb=" O   HIS C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 542 through 546
      removed outlier: 3.503A  pdb=" N   VAL C 546 " --> pdb=" O   PHE C 542 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 542 through 546'
    Processing helix  chain 'C' and resid 554 through 558
    Processing helix  chain 'C' and resid 573 through 593
    Processing helix  chain 'I' and resid 59 through 61
      No H-bonds generated for 'chain 'I' and resid 59 through 61'
    Processing helix  chain 'I' and resid 71 through 74
    Processing helix  chain 'I' and resid 78 through 83
      removed outlier: 3.516A  pdb=" N   THR I  83 " --> pdb=" O   ILE I  79 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 551 through 559
      removed outlier: 3.552A  pdb=" N   VAL J 555 " --> pdb=" O   GLN J 551 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY J 557 " --> pdb=" O   ALA J 553 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 564 through 576
      removed outlier: 4.563A  pdb=" N   ALA J 568 " --> pdb=" O   GLU J 564 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 583 through 599
      removed outlier: 4.371A  pdb=" N   GLY J 599 " --> pdb=" O   ARG J 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 61
      No H-bonds generated for 'chain 'A' and resid 59 through 61'
    Processing helix  chain 'A' and resid 71 through 74
      removed outlier: 4.089A  pdb=" N   GLY A  74 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 74'
    Processing helix  chain 'B' and resid 554 through 576
      removed outlier: 3.619A  pdb=" N   LEU B 561 " --> pdb=" O   GLY B 557 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA B 562 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN B 563 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   GLU B 564 " --> pdb=" O   GLN B 560 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   GLN B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ALA B 568 " --> pdb=" O   GLU B 564 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG B 574 " --> pdb=" O   GLN B 570 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA B 575 " --> pdb=" O   LEU B 571 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 576 " --> pdb=" O   PHE B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 598
    Processing helix  chain 'D' and resid 391 through 398
      removed outlier: 3.552A  pdb=" N   PHE D 395 " --> pdb=" O   GLU D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 432 through 435
    Processing helix  chain 'D' and resid 436 through 452
      removed outlier: 3.829A  pdb=" N   HIS D 441 " --> pdb=" O   ILE D 437 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   GLN D 442 " --> pdb=" O   GLN D 438 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL D 443 " --> pdb=" O   ILE D 439 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU D 444 " --> pdb=" O   LEU D 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 463 through 468
      removed outlier: 3.929A  pdb=" N   ILE D 467 " --> pdb=" O   THR D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 483 through 489
    Processing helix  chain 'D' and resid 508 through 517
    Processing helix  chain 'D' and resid 542 through 546
      removed outlier: 3.653A  pdb=" N   VAL D 546 " --> pdb=" O   PHE D 542 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 542 through 546'
    Processing helix  chain 'D' and resid 554 through 558
    Processing helix  chain 'D' and resid 573 through 593
    Processing helix  chain 'E' and resid 59 through 61
      No H-bonds generated for 'chain 'E' and resid 59 through 61'
    Processing helix  chain 'E' and resid 71 through 74
      removed outlier: 4.052A  pdb=" N   GLY E  74 " --> pdb=" O   GLU E  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 71 through 74'
    Processing helix  chain 'E' and resid 82 through 84
      No H-bonds generated for 'chain 'E' and resid 82 through 84'
    Processing helix  chain 'F' and resid 554 through 563
      removed outlier: 3.512A  pdb=" N   GLN F 560 " --> pdb=" O   CYS F 556 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU F 561 " --> pdb=" O   GLY F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 564 through 576
      removed outlier: 4.504A  pdb=" N   ALA F 568 " --> pdb=" O   GLU F 564 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA F 575 " --> pdb=" O   LEU F 571 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 583 through 598
    Processing sheet with id=AA1, first strand: chain 'C' and resid 563 through 568
      removed outlier: 4.462A  pdb=" N   ILE C 563 " --> pdb=" O   LEU C 408 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C 408 " --> pdb=" O   ILE C 563 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER C 602 " --> pdb=" O   ILE C 409 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG C 411 " --> pdb=" O   THR C 600 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   THR C 600 " --> pdb=" O   ARG C 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 418 through 420
    Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 457
    Processing sheet with id=AA4, first strand: chain 'C' and resid 547 through 548
    Processing sheet with id=AA5, first strand: chain 'I' and resid 43 through 46
    Processing sheet with id=AA6, first strand: chain 'I' and resid 43 through 46
      removed outlier: 3.548A  pdb=" N   LEU I 165 " --> pdb=" O   TYR I 162 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL I  96 " --> pdb=" O   THR J 581 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 86 through 89
    Processing sheet with id=AA8, first strand: chain 'I' and resid 101 through 103
    Processing sheet with id=AA9, first strand: chain 'I' and resid 110 through 114
      removed outlier: 6.313A  pdb=" N   ASN I 110 " --> pdb=" O   ALA I 141 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   GLY I 143 " --> pdb=" O   ASN I 110 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   GLU I 112 " --> pdb=" O   GLY I 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 46
      removed outlier: 6.443A  pdb=" N   GLY A  36 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 43 through 46
      removed outlier: 6.443A  pdb=" N   GLY A  36 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   VAL A  96 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 86 through 89
    Processing sheet with id=AB4, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AB5, first strand: chain 'A' and resid 105 through 111
      removed outlier: 6.998A  pdb=" N   GLU A 106 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 563 through 567
      removed outlier: 4.501A  pdb=" N   ILE D 563 " --> pdb=" O   LEU D 408 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU D 408 " --> pdb=" O   ILE D 563 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG D 411 " --> pdb=" O   THR D 600 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR D 600 " --> pdb=" O   ARG D 411 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 418 through 420
    Processing sheet with id=AB8, first strand: chain 'D' and resid 455 through 457
    Processing sheet with id=AB9, first strand: chain 'D' and resid 547 through 548
    Processing sheet with id=AC1, first strand: chain 'E' and resid 43 through 46
      removed outlier: 6.253A  pdb=" N   GLY E  36 " --> pdb=" O   ILE E 185 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 43 through 46
      removed outlier: 6.253A  pdb=" N   GLY E  36 " --> pdb=" O   ILE E 185 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER E  98 " --> pdb=" O   THR F 581 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 86 through 89
    Processing sheet with id=AC4, first strand: chain 'E' and resid 101 through 103
    Processing sheet with id=AC5, first strand: chain 'E' and resid 105 through 114
      removed outlier: 7.061A  pdb=" N   GLU E 106 " --> pdb=" O   CYS E 135 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    762 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: 2.63

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3116
        1.35 -     1.47: 2397
        1.47 -     1.59: 4215
        1.59 -     1.71: 1
        1.71 -     1.84: 50
  Bond restraints: 9779
  Sorted by residual:
  bond pdb=" CG  PRO I 124 "
       pdb=" CD  PRO I 124 "
    ideal  model  delta    sigma   weight residual
    1.503  1.371  0.132 3.40e-02 8.65e+02 1.51e+01
  bond pdb=" C   PRO C 433 "
       pdb=" N   PRO C 434 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 8.40e-03 1.42e+04 1.03e+01
  bond pdb=" N   ILE J 603 "
       pdb=" CA  ILE J 603 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.54e+00
  bond pdb=" CB  PRO I 124 "
       pdb=" CG  PRO I 124 "
    ideal  model  delta    sigma   weight residual
    1.492  1.597 -0.105 5.00e-02 4.00e+02 4.40e+00
  bond pdb=" CA  ILE F 610 "
       pdb=" CB  ILE F 610 "
    ideal  model  delta    sigma   weight residual
    1.540  1.564 -0.024 1.36e-02 5.41e+03 3.16e+00
  ... (remaining 9774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 13086
        2.44 -     4.88: 201
        4.88 -     7.33: 33
        7.33 -     9.77: 4
        9.77 -    12.21: 2
  Bond angle restraints: 13326
  Sorted by residual:
  angle pdb=" CA  PRO I 124 "
        pdb=" N   PRO I 124 "
        pdb=" CD  PRO I 124 "
      ideal   model   delta    sigma   weight residual
     112.00   99.79   12.21 1.40e+00 5.10e-01 7.61e+01
  angle pdb=" N   PRO I 124 "
        pdb=" CD  PRO I 124 "
        pdb=" CG  PRO I 124 "
      ideal   model   delta    sigma   weight residual
     103.20   93.22    9.98 1.50e+00 4.44e-01 4.43e+01
  angle pdb=" CA  ILE F 610 "
        pdb=" CB  ILE F 610 "
        pdb=" CG2 ILE F 610 "
      ideal   model   delta    sigma   weight residual
     110.50  116.91   -6.41 1.70e+00 3.46e-01 1.42e+01
  angle pdb=" CA  ARG J 595 "
        pdb=" CB  ARG J 595 "
        pdb=" CG  ARG J 595 "
      ideal   model   delta    sigma   weight residual
     114.10  107.09    7.01 2.00e+00 2.50e-01 1.23e+01
  angle pdb=" CA  GLN E 142 "
        pdb=" CB  GLN E 142 "
        pdb=" CG  GLN E 142 "
      ideal   model   delta    sigma   weight residual
     114.10  120.84   -6.74 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 13321 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 5212
       17.95 -    35.90: 475
       35.90 -    53.85: 76
       53.85 -    71.80: 27
       71.80 -    89.76: 12
  Dihedral angle restraints: 5802
    sinusoidal: 2321
      harmonic: 3481
  Sorted by residual:
  dihedral pdb=" CB  CYS F 601 "
           pdb=" SG  CYS F 601 "
           pdb=" SG  CYS F 608 "
           pdb=" CB  CYS F 608 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.59   55.41     1      1.00e+01 1.00e-02 4.15e+01
  dihedral pdb=" CB  CYS I  53 "
           pdb=" SG  CYS I  53 "
           pdb=" SG  CYS J 609 "
           pdb=" CB  CYS J 609 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.54  -54.54     1      1.00e+01 1.00e-02 4.03e+01
  dihedral pdb=" CB  CYS C 516 "
           pdb=" SG  CYS C 516 "
           pdb=" SG  CYS C 533 "
           pdb=" CB  CYS C 533 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.89  -39.11     1      1.00e+01 1.00e-02 2.15e+01
  ... (remaining 5799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1117
       0.047 -    0.095: 248
       0.095 -    0.142: 85
       0.142 -    0.190: 3
       0.190 -    0.237: 2
  Chirality restraints: 1455
  Sorted by residual:
  chirality pdb=" CB  ILE F 610 "
            pdb=" CA  ILE F 610 "
            pdb=" CG1 ILE F 610 "
            pdb=" CG2 ILE F 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  ILE E  79 "
            pdb=" CA  ILE E  79 "
            pdb=" CG1 ILE E  79 "
            pdb=" CG2 ILE E  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CA  CYS C 516 "
            pdb=" N   CYS C 516 "
            pdb=" C   CYS C 516 "
            pdb=" CB  CYS C 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 1452 not shown)

  Planarity restraints: 1742
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO I 123 "    0.074 5.00e-02 4.00e+02   1.04e-01 1.72e+01
        pdb=" N   PRO I 124 "   -0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO I 124 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO I 124 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 611 "   -0.034 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO B 612 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 612 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 612 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E 142 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" C   GLN E 142 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLN E 142 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY E 143 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1739 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 376
        2.72 -     3.26: 9219
        3.26 -     3.81: 14545
        3.81 -     4.35: 18635
        4.35 -     4.90: 31351
  Nonbonded interactions: 74126
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E  64 "
            pdb=" OE1 GLU E 100 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" O   GLY J 598 "
            pdb=" NH1 ARG F 596 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   PRO D 430 "
            pdb=" ND2 ASN D 556 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   LEU D 472 "
            pdb=" N   ASN D 476 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OD1 ASP E  78 "
            pdb=" N   ILE E  79 "
     model   vdw
     2.291 3.120
  ... (remaining 74121 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 32 through 187)
  selection = chain 'E'
  selection = (chain 'I' and resid 32 through 187)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and (resid 510 through 523 or resid 527 through 614))
  selection = (chain 'J' and (resid 510 through 523 or resid 527 through 614))
}
ncs_group {
  reference = (chain 'C' and (resid 390 through 399 or resid 403 through 604))
  selection = chain 'D'
}

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:             22.720
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.920
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
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   0.132   9779  Z= 0.211
  Angle     :  0.739  12.211  13326  Z= 0.393
  Chirality :  0.046   0.237   1455
  Planarity :  0.005   0.104   1742
  Dihedral  : 14.552  89.756   3515
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  6.26 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.29 %
    Favored  : 92.23 %
  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: -2.10 (0.23), residues: 1183
  helix: -0.86 (0.33), residues: 226
  sheet: -0.94 (0.32), residues: 248
  loop : -1.80 (0.22), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  86 
 HIS   0.006   0.001   HIS C 512 
 PHE   0.022   0.002   PHE C 513 
 TYR   0.027   0.002   TYR C 509 
 ARG   0.007   0.001   ARG F 602 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 237
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   50 GLN cc_start: 0.7643 (tt0) cc_final: 0.7155 (tt0)
REVERT: D  514 LEU cc_start: 0.5846 (mt) cc_final: 0.5591 (tt)
REVERT: E  142 GLN cc_start: 0.7633 (pm20) cc_final: 0.7192 (pm20)
REVERT: F  612 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7925 (Cg_exo)
  outliers start: 5
  outliers final: 1
  residues processed: 240
  average time/residue: 0.2403
  time to fit residues: 77.5090
Evaluate side-chains
  163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  503 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:   20.0000
   chunk 35 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 478 ASN
** I  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 560 GLN
** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 596 ASN
E  50 GLN
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 524 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.166012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.110978 restraints weight = 21614.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 3.69
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9779  Z= 0.270
  Angle     :  0.715   8.074  13326  Z= 0.375
  Chirality :  0.046   0.220   1455
  Planarity :  0.005   0.049   1742
  Dihedral  :  5.403  59.045   1303
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  7.44 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.63 %
    Favored  : 85.13 %
  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: -1.87 (0.23), residues: 1183
  helix: -0.19 (0.34), residues: 223
  sheet: -1.07 (0.29), residues: 277
  loop : -1.71 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  86 
 HIS   0.008   0.001   HIS D 510 
 PHE   0.018   0.002   PHE C 395 
 TYR   0.019   0.001   TYR C 555 
 ARG   0.006   0.001   ARG E 164 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  437 ILE cc_start: 0.7868 (pt) cc_final: 0.7335 (tp)
REVERT: C  555 TYR cc_start: 0.8306 (m-80) cc_final: 0.8005 (m-10)
REVERT: I  142 GLN cc_start: 0.7639 (pp30) cc_final: 0.7283 (pp30)
REVERT: J  551 GLN cc_start: 0.8015 (tt0) cc_final: 0.7733 (mt0)
REVERT: A   64 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8211 (mmmm)
REVERT: E  120 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7629 (mt-10)
REVERT: E  142 GLN cc_start: 0.7381 (pm20) cc_final: 0.7144 (pm20)
REVERT: F  596 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7697 (mtp180)
  outliers start: 23
  outliers final: 15
  residues processed: 172
  average time/residue: 0.2042
  time to fit residues: 49.6877
Evaluate side-chains
  163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  503 PHE
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain J residue  583 THR
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain F residue  524 HIS
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  590 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 116 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 89 optimal weight:   40.0000
   chunk 60 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 83 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 465 GLN
C 492 HIS
** J 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 524 HIS
F 563 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.165176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.110318 restraints weight = 21855.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.70
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9779  Z= 0.287
  Angle     :  0.646   7.073  13326  Z= 0.341
  Chirality :  0.045   0.238   1455
  Planarity :  0.004   0.045   1742
  Dihedral  :  5.157  56.842   1303
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.78 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.09 %
    Favored  : 83.28 %
  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: -1.83 (0.23), residues: 1183
  helix: -0.00 (0.35), residues: 226
  sheet: -1.02 (0.31), residues: 260
  loop : -1.76 (0.23), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  86 
 HIS   0.016   0.001   HIS F 524 
 PHE   0.018   0.002   PHE F 592 
 TYR   0.012   0.001   TYR F 582 
 ARG   0.004   0.000   ARG B 596 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  437 ILE cc_start: 0.7850 (pt) cc_final: 0.7326 (tp)
REVERT: C  481 ILE cc_start: 0.1865 (mm) cc_final: 0.1299 (mm)
REVERT: I  100 GLU cc_start: 0.8281 (mp0) cc_final: 0.7715 (mp0)
REVERT: I  140 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8925 (mmtm)
REVERT: I  142 GLN cc_start: 0.7851 (pp30) cc_final: 0.7412 (pp30)
REVERT: J  551 GLN cc_start: 0.8055 (tt0) cc_final: 0.7715 (mt0)
REVERT: A   64 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8236 (mmmm)
REVERT: B  549 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8273 (t-90)
REVERT: B  611 GLU cc_start: 0.8179 (pm20) cc_final: 0.7977 (pm20)
REVERT: D  514 LEU cc_start: 0.7183 (mt) cc_final: 0.6896 (mt)
REVERT: E  120 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7787 (mt-10)
REVERT: E  142 GLN cc_start: 0.7540 (pm20) cc_final: 0.7313 (pm20)
REVERT: F  544 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8252 (p)
  outliers start: 27
  outliers final: 19
  residues processed: 174
  average time/residue: 0.2279
  time to fit residues: 56.1380
Evaluate side-chains
  171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  492 HIS
Chi-restraints excluded: chain C residue  503 PHE
Chi-restraints excluded: chain C residue  562 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  549 HIS
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0010
   chunk 115 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 70 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0670
   chunk 110 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.5124

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

Flipped N/Q/H residues before XYZ refinement:
** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
J 514 ASN
J 549 HIS
B 549 HIS
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 524 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.165645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109682 restraints weight = 21657.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.69
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9779  Z= 0.165
  Angle     :  0.600   7.375  13326  Z= 0.316
  Chirality :  0.043   0.242   1455
  Planarity :  0.004   0.041   1742
  Dihedral  :  4.899  54.660   1303
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.02 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.29 %
    Favored  : 83.28 %
  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: -1.79 (0.23), residues: 1183
  helix: -0.02 (0.34), residues: 238
  sheet: -0.92 (0.30), residues: 267
  loop : -1.77 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  86 
 HIS   0.006   0.001   HIS C 492 
 PHE   0.010   0.001   PHE C 395 
 TYR   0.010   0.001   TYR C 555 
 ARG   0.004   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  437 ILE cc_start: 0.7872 (pt) cc_final: 0.7354 (tp)
REVERT: C  481 ILE cc_start: 0.1829 (mm) cc_final: 0.1360 (mm)
REVERT: C  492 HIS cc_start: 0.8174 (t-90) cc_final: 0.7956 (t-90)
REVERT: C  555 TYR cc_start: 0.8182 (m-10) cc_final: 0.7885 (m-10)
REVERT: I  100 GLU cc_start: 0.8318 (mp0) cc_final: 0.7731 (mp0)
REVERT: I  142 GLN cc_start: 0.7909 (pp30) cc_final: 0.7213 (pp30)
REVERT: J  529 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8657 (tp)
REVERT: J  551 GLN cc_start: 0.8004 (tt0) cc_final: 0.7771 (mt0)
REVERT: A   64 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8260 (mmmm)
REVERT: A  115 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8628 (ptpp)
REVERT: D  514 LEU cc_start: 0.7251 (mt) cc_final: 0.6984 (mt)
REVERT: E   56 HIS cc_start: 0.8301 (m-70) cc_final: 0.8042 (m90)
REVERT: E  142 GLN cc_start: 0.7613 (pm20) cc_final: 0.7386 (pm20)
REVERT: F  544 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8271 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2057
  time to fit residues: 51.4720
Evaluate side-chains
  171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  503 PHE
Chi-restraints excluded: chain C residue  562 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain J residue  529 ILE
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain F residue  524 HIS
Chi-restraints excluded: chain F residue  544 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 549 HIS
** E  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 524 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.164763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.109940 restraints weight = 21647.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.67
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9779  Z= 0.227
  Angle     :  0.604   8.798  13326  Z= 0.318
  Chirality :  0.044   0.246   1455
  Planarity :  0.004   0.039   1742
  Dihedral  :  4.831  52.005   1303
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.27 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.97 %
    Favored  : 82.22 %
  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: -1.75 (0.23), residues: 1183
  helix:  0.03 (0.34), residues: 240
  sheet: -0.92 (0.31), residues: 263
  loop : -1.75 (0.23), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  86 
 HIS   0.005   0.001   HIS D 510 
 PHE   0.010   0.001   PHE C 504 
 TYR   0.010   0.001   TYR F 582 
 ARG   0.003   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  437 ILE cc_start: 0.7893 (pt) cc_final: 0.7369 (tp)
REVERT: C  481 ILE cc_start: 0.2012 (mm) cc_final: 0.1585 (mm)
REVERT: C  492 HIS cc_start: 0.8012 (t-90) cc_final: 0.7637 (t-90)
REVERT: I  100 GLU cc_start: 0.8343 (mp0) cc_final: 0.7799 (mp0)
REVERT: I  142 GLN cc_start: 0.7981 (pp30) cc_final: 0.7252 (pp30)
REVERT: J  529 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8643 (tp)
REVERT: J  551 GLN cc_start: 0.8132 (tt0) cc_final: 0.7822 (mt0)
REVERT: J  610 ILE cc_start: 0.8538 (mt) cc_final: 0.8229 (mm)
REVERT: A   64 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8300 (mmmm)
REVERT: A  115 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8634 (ptpp)
REVERT: B  603 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8166 (tp)
REVERT: D  514 LEU cc_start: 0.7291 (mt) cc_final: 0.7026 (mt)
REVERT: E  142 GLN cc_start: 0.7648 (pm20) cc_final: 0.7342 (pm20)
REVERT: E  172 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8177 (ttp80)
  outliers start: 29
  outliers final: 19
  residues processed: 176
  average time/residue: 0.2164
  time to fit residues: 53.3479
Evaluate side-chains
  171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  503 PHE
Chi-restraints excluded: chain C residue  562 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain J residue  529 ILE
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 8 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 ASN
B 613 HIS
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.161659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105502 restraints weight = 21771.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 3.66
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9779  Z= 0.350
  Angle     :  0.662   8.098  13326  Z= 0.346
  Chirality :  0.046   0.225   1455
  Planarity :  0.005   0.039   1742
  Dihedral  :  4.949  45.544   1303
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.86 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.72 %
    Favored  : 80.47 %
  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: -1.83 (0.23), residues: 1183
  helix:  0.03 (0.34), residues: 240
  sheet: -1.17 (0.31), residues: 254
  loop : -1.72 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 104 
 HIS   0.005   0.001   HIS D 510 
 PHE   0.014   0.002   PHE C 504 
 TYR   0.012   0.001   TYR F 582 
 ARG   0.007   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  481 ILE cc_start: 0.1932 (mm) cc_final: 0.1546 (mm)
REVERT: C  499 LYS cc_start: 0.8822 (tptt) cc_final: 0.8614 (tptt)
REVERT: C  569 ASN cc_start: 0.4563 (m-40) cc_final: 0.4295 (m-40)
REVERT: I  100 GLU cc_start: 0.8337 (mp0) cc_final: 0.7820 (mp0)
REVERT: I  142 GLN cc_start: 0.8065 (pp30) cc_final: 0.7314 (pp30)
REVERT: J  551 GLN cc_start: 0.8167 (tt0) cc_final: 0.7819 (mt0)
REVERT: J  600 THR cc_start: 0.7744 (p) cc_final: 0.7387 (p)
REVERT: A   64 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8331 (mmmm)
REVERT: D  514 LEU cc_start: 0.7333 (mt) cc_final: 0.7069 (mt)
REVERT: E   56 HIS cc_start: 0.8390 (m90) cc_final: 0.8019 (m90)
REVERT: E  142 GLN cc_start: 0.7604 (pm20) cc_final: 0.7174 (pm20)
REVERT: E  172 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8283 (ttp80)
  outliers start: 29
  outliers final: 21
  residues processed: 166
  average time/residue: 0.2156
  time to fit residues: 49.8897
Evaluate side-chains
  159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  562 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain J residue  544 THR
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    0.0020
   chunk 110 optimal weight:    0.4980
   chunk 93 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 61 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 90 optimal weight:   50.0000
   chunk 84 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 142 GLN ** 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 = 0.4254 r_free = 0.4254 target = 0.164590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.109449 restraints weight = 21730.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 3.72
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9779  Z= 0.163
  Angle     :  0.597   7.201  13326  Z= 0.313
  Chirality :  0.043   0.233   1455
  Planarity :  0.004   0.040   1742
  Dihedral  :  4.502  21.789   1301
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  6.93 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.08 %
    Favored  : 79.59 %
  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: -1.69 (0.23), residues: 1183
  helix:  0.05 (0.33), residues: 248
  sheet: -0.88 (0.32), residues: 241
  loop : -1.70 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 510 
 PHE   0.033   0.001   PHE F 592 
 TYR   0.009   0.001   TYR A 162 
 ARG   0.005   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
REVERT: C  481 ILE cc_start: 0.1840 (mm) cc_final: 0.1413 (mm)
REVERT: C  499 LYS cc_start: 0.8692 (tptt) cc_final: 0.8417 (tptt)
REVERT: C  569 ASN cc_start: 0.4530 (m-40) cc_final: 0.4225 (m-40)
REVERT: I   86 TRP cc_start: 0.7947 (p90) cc_final: 0.7676 (p90)
REVERT: I  100 GLU cc_start: 0.8425 (mp0) cc_final: 0.7908 (mp0)
REVERT: I  142 GLN cc_start: 0.8145 (pp30) cc_final: 0.7448 (pp30)
REVERT: J  551 GLN cc_start: 0.8063 (tt0) cc_final: 0.7827 (mt0)
REVERT: J  564 GLU cc_start: 0.8203 (mp0) cc_final: 0.7852 (mp0)
REVERT: J  610 ILE cc_start: 0.8564 (mt) cc_final: 0.8186 (mm)
REVERT: A   64 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8335 (mmmm)
REVERT: D  514 LEU cc_start: 0.7307 (mt) cc_final: 0.6915 (mt)
REVERT: D  556 ASN cc_start: 0.4857 (OUTLIER) cc_final: 0.4336 (p0)
REVERT: E  140 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8697 (mmmt)
REVERT: E  142 GLN cc_start: 0.7611 (pm20) cc_final: 0.7199 (pm20)
  outliers start: 24
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2841
  time to fit residues: 67.5042
Evaluate side-chains
  165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  515 TYR
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain D residue  556 ASN
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  610 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0570
   chunk 84 optimal weight:   30.0000
   chunk 116 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.4202

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

Flipped N/Q/H residues before XYZ refinement:
C 447 GLN
** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 GLN
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.162725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.107542 restraints weight = 21904.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 3.71
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9779  Z= 0.262
  Angle     :  0.614   7.114  13326  Z= 0.321
  Chirality :  0.044   0.211   1455
  Planarity :  0.004   0.041   1742
  Dihedral  :  4.504  19.959   1301
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.95 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.17 %
    Favored  : 79.20 %
  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: -1.71 (0.23), residues: 1183
  helix:  0.07 (0.33), residues: 249
  sheet: -0.97 (0.32), residues: 241
  loop : -1.69 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  86 
 HIS   0.004   0.001   HIS D 510 
 PHE   0.013   0.001   PHE C 542 
 TYR   0.012   0.001   TYR C 487 
 ARG   0.006   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  569 ASN cc_start: 0.4560 (m-40) cc_final: 0.4257 (m-40)
REVERT: I   86 TRP cc_start: 0.8017 (p90) cc_final: 0.7643 (p90)
REVERT: I  100 GLU cc_start: 0.8382 (mp0) cc_final: 0.7861 (mp0)
REVERT: I  142 GLN cc_start: 0.8167 (pp30) cc_final: 0.7396 (pp30)
REVERT: J  551 GLN cc_start: 0.8129 (tt0) cc_final: 0.7828 (mt0)
REVERT: J  564 GLU cc_start: 0.8195 (mp0) cc_final: 0.7806 (mp0)
REVERT: J  600 THR cc_start: 0.7743 (p) cc_final: 0.7465 (p)
REVERT: J  610 ILE cc_start: 0.8551 (mt) cc_final: 0.8199 (mm)
REVERT: A   64 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8351 (mmmm)
REVERT: A  115 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8727 (ptpp)
REVERT: E   56 HIS cc_start: 0.8415 (m90) cc_final: 0.8121 (m-70)
REVERT: E  142 GLN cc_start: 0.7609 (pm20) cc_final: 0.7162 (pm20)
  outliers start: 27
  outliers final: 24
  residues processed: 158
  average time/residue: 0.2450
  time to fit residues: 53.9844
Evaluate side-chains
  159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  488 PHE
Chi-restraints excluded: chain C residue  556 ASN
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  610 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 108 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 GLN
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.163111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.107787 restraints weight = 21646.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 3.72
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9779  Z= 0.238
  Angle     :  0.604   6.965  13326  Z= 0.316
  Chirality :  0.044   0.218   1455
  Planarity :  0.004   0.043   1742
  Dihedral  :  4.433  19.435   1301
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.35 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.08 %
    Favored  : 79.11 %
  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: -1.68 (0.23), residues: 1183
  helix:  0.08 (0.34), residues: 249
  sheet: -1.01 (0.32), residues: 244
  loop : -1.64 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  86 
 HIS   0.004   0.001   HIS C 510 
 PHE   0.010   0.001   PHE C 504 
 TYR   0.010   0.001   TYR C 394 
 ARG   0.004   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  547 LEU cc_start: 0.8465 (mt) cc_final: 0.8189 (mt)
REVERT: C  569 ASN cc_start: 0.4624 (m-40) cc_final: 0.4313 (m-40)
REVERT: I  100 GLU cc_start: 0.8420 (mp0) cc_final: 0.7907 (mp0)
REVERT: I  142 GLN cc_start: 0.8209 (pp30) cc_final: 0.7485 (pp30)
REVERT: J  551 GLN cc_start: 0.8168 (tt0) cc_final: 0.7868 (mt0)
REVERT: J  564 GLU cc_start: 0.8249 (mp0) cc_final: 0.7874 (mp0)
REVERT: J  610 ILE cc_start: 0.8509 (mt) cc_final: 0.8155 (mm)
REVERT: A   64 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8367 (mmmm)
REVERT: A  115 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8708 (ptpp)
REVERT: D  514 LEU cc_start: 0.7396 (mt) cc_final: 0.7022 (mt)
REVERT: D  556 ASN cc_start: 0.4908 (OUTLIER) cc_final: 0.4371 (p0)
REVERT: E  112 GLU cc_start: 0.7877 (tp30) cc_final: 0.7656 (tp30)
REVERT: E  120 GLU cc_start: 0.7486 (tp30) cc_final: 0.7044 (tp30)
REVERT: E  142 GLN cc_start: 0.7677 (pm20) cc_final: 0.7205 (pm20)
REVERT: E  172 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7762 (ttm110)
  outliers start: 29
  outliers final: 27
  residues processed: 166
  average time/residue: 0.2228
  time to fit residues: 50.9835
Evaluate side-chains
  167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  119 SER
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain J residue  511 CYS
Chi-restraints excluded: chain J residue  544 THR
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   86 TRP
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain D residue  556 ASN
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   59 SER
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  524 HIS
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  610 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0270
   chunk 2 optimal weight:    9.9990
   chunk 115 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 GLN
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** 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 = 0.4239 r_free = 0.4239 target = 0.163064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106726 restraints weight = 22048.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 3.86
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9779  Z= 0.174
  Angle     :  0.599   8.710  13326  Z= 0.311
  Chirality :  0.043   0.214   1455
  Planarity :  0.004   0.043   1742
  Dihedral  :  4.324  19.461   1301
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.02 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.76 %
    Favored  : 79.11 %
  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: -1.58 (0.23), residues: 1183
  helix:  0.19 (0.34), residues: 247
  sheet: -0.92 (0.32), residues: 244
  loop : -1.60 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  86 
 HIS   0.003   0.000   HIS D 510 
 PHE   0.009   0.001   PHE C 504 
 TYR   0.011   0.001   TYR I 137 
 ARG   0.007   0.000   ARG J 587 

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

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

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2366 Ramachandran restraints generated.
    1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 1.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  547 LEU cc_start: 0.8479 (mt) cc_final: 0.8192 (mt)
REVERT: C  569 ASN cc_start: 0.4751 (m-40) cc_final: 0.4436 (m-40)
REVERT: I   47 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8358 (tp30)
REVERT: I  100 GLU cc_start: 0.8414 (mp0) cc_final: 0.7978 (mp0)
REVERT: I  142 GLN cc_start: 0.8205 (pp30) cc_final: 0.7623 (pp30)
REVERT: J  551 GLN cc_start: 0.8168 (tt0) cc_final: 0.7892 (mt0)
REVERT: J  610 ILE cc_start: 0.8564 (mt) cc_final: 0.8157 (mm)
REVERT: A   64 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8477 (mmmm)
REVERT: B  545 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7670 (mp0)
REVERT: D  514 LEU cc_start: 0.7427 (mt) cc_final: 0.7061 (mt)
REVERT: D  556 ASN cc_start: 0.4810 (OUTLIER) cc_final: 0.4277 (p0)
REVERT: E  112 GLU cc_start: 0.7949 (tp30) cc_final: 0.7686 (tp30)
REVERT: E  120 GLU cc_start: 0.7459 (tp30) cc_final: 0.7073 (tp30)
REVERT: E  137 TYR cc_start: 0.7859 (t80) cc_final: 0.7659 (t80)
REVERT: E  142 GLN cc_start: 0.7666 (pm20) cc_final: 0.7250 (pm20)
REVERT: E  172 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7892 (ttm110)
  outliers start: 22
  outliers final: 20
  residues processed: 162
  average time/residue: 0.3531
  time to fit residues: 78.9978
Evaluate side-chains
  164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 SER
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  601 ILE
Chi-restraints excluded: chain I residue   51 LEU
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  112 GLU
Chi-restraints excluded: chain I residue  127 ASP
Chi-restraints excluded: chain I residue  168 THR
Chi-restraints excluded: chain J residue  511 CYS
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain D residue  556 ASN
Chi-restraints excluded: chain E residue   53 CYS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  610 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:   30.0000
   chunk 62 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0770
   chunk 8 optimal weight:   50.0000
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 139 HIS
E  56 HIS
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** 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 = 0.4234 r_free = 0.4234 target = 0.162362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.106510 restraints weight = 21963.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.79
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9779  Z= 0.205
  Angle     :  0.619   7.701  13326  Z= 0.322
  Chirality :  0.044   0.209   1455
  Planarity :  0.004   0.043   1742
  Dihedral  :  4.287  19.413   1301
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  7.10 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.56 %
    Favored  : 78.91 %
  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: -1.58 (0.23), residues: 1183
  helix:  0.17 (0.34), residues: 248
  sheet: -0.88 (0.33), residues: 244
  loop : -1.61 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  86 
 HIS   0.002   0.000   HIS D 510 
 PHE   0.009   0.001   PHE C 504 
 TYR   0.009   0.001   TYR A 162 
 ARG   0.007   0.000   ARG J 587 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5271.46 seconds
wall clock time: 95 minutes 25.81 seconds (5725.81 seconds total)