Starting phenix.real_space_refine
on Wed May 14 04:36:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wvx_37875/05_2025/8wvx_37875.cif"
  }
  resolution = 3.32
  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=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    7155      2.51       5
     N    2067      2.21       5
     O    2178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11460
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 725, 4931
          Classifications: {'peptide': 725}
          Incomplete info: {'truncation_to_alanine': 205}
          Link IDs: {'PTRANS': 35, 'TRANS': 689}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 783
          Unresolved non-hydrogen angles: 1014
          Unresolved non-hydrogen dihedrals: 684
          Unresolved non-hydrogen chiralities: 85
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 2, 'PHE:plan': 31, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 407
    Chain: "B"
      Number of atoms: 4964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 731, 4964
          Classifications: {'peptide': 731}
          Incomplete info: {'truncation_to_alanine': 207}
          Link IDs: {'PTRANS': 36, 'TRANS': 694}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 789
          Unresolved non-hydrogen angles: 1025
          Unresolved non-hydrogen dihedrals: 688
          Unresolved non-hydrogen chiralities: 87
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 2, 'PHE:plan': 31, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 414
    Chain: "C"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 783
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 782
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
  Time building chain proxies: 8.35, per 1000 atoms: 0.73
  Number of scatterers: 11460
  At special positions: 0
  Unit cell: (177.65, 113.05, 140.25, 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      60     16.00
     O    2178      8.00
     N    2067      7.00
     C    7155      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  35 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  43 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 364 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 618 " - pdb=" SG  CYS A 693 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  29 " - pdb=" SG  CYS B  35 " distance=1.21
    Simple disulfide: pdb=" SG  CYS B  33 " - pdb=" SG  CYS B  43 " distance=1.67
    Simple disulfide: pdb=" SG  CYS B 339 " - pdb=" SG  CYS B 364 " distance=2.34
    Simple disulfide: pdb=" SG  CYS B 470 " - pdb=" SG  CYS B 522 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 532 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 618 " - pdb=" SG  CYS B 693 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  39 " - pdb=" SG  CYS C  96 " distance=1.78
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 110 " distance=2.10
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C 126 " distance=1.88
    Simple disulfide: pdb=" SG  CYS C  69 " - pdb=" SG  CYS C 128 " distance=2.10
    Simple disulfide: pdb=" SG  CYS C  93 " - pdb=" SG  CYS D  95 " distance=2.20
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS D  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS D 131 " distance=1.48
    Simple disulfide: pdb=" SG  CYS D  39 " - pdb=" SG  CYS D  96 " distance=1.95
    Simple disulfide: pdb=" SG  CYS D  55 " - pdb=" SG  CYS D 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 126 " distance=2.00
    Simple disulfide: pdb=" SG  CYS D  69 " - pdb=" SG  CYS D 128 " distance=2.10

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.31
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3140

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 14 sheets defined
      29.8% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 4.148A  pdb=" N   GLY A 127 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 466 through 474
    Processing helix  chain 'A' and resid 538 through 566
      removed outlier: 3.876A  pdb=" N   PHE A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU A 558 " --> pdb=" O   PHE A 554 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 563 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 601
      removed outlier: 3.562A  pdb=" N   PHE A 586 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 614
    Processing helix  chain 'A' and resid 615 through 647
      removed outlier: 4.106A  pdb=" N   LYS A 619 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 638 " --> pdb=" O   PHE A 634 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA A 639 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   THR A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL A 641 " --> pdb=" O   MET A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 679
      removed outlier: 3.645A  pdb=" N   ARG A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL A 664 " --> pdb=" O   LYS A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 682
      No H-bonds generated for 'chain 'A' and resid 680 through 682'
    Processing helix  chain 'A' and resid 705 through 731
      removed outlier: 3.588A  pdb=" N   MET A 721 " --> pdb=" O   ALA A 717 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASN A 731 " --> pdb=" O   LYS A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 768
      removed outlier: 3.559A  pdb=" N   CYS A 761 " --> pdb=" O   CYS A 757 " (cutoff:3.500A)
      Proline residue:  A 762  - end of helix
      removed outlier: 3.798A  pdb=" N   PHE A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
      removed outlier: 4.062A  pdb=" N   ILE A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 776
      No H-bonds generated for 'chain 'A' and resid 774 through 776'
    Processing helix  chain 'A' and resid 780 through 790
    Processing helix  chain 'A' and resid 792 through 800
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 807 through 820
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 337 through 342
      removed outlier: 3.761A  pdb=" N   GLN B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 468
      No H-bonds generated for 'chain 'B' and resid 466 through 468'
    Processing helix  chain 'B' and resid 469 through 474
      removed outlier: 4.503A  pdb=" N   PHE B 473 " --> pdb=" O   GLN B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 564
      removed outlier: 3.729A  pdb=" N   ARG B 542 " --> pdb=" O   SER B 538 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU B 543 " --> pdb=" O   TRP B 539 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE B 554 " --> pdb=" O   LEU B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 601
      removed outlier: 3.528A  pdb=" N   GLY B 578 " --> pdb=" O   LYS B 574 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU B 579 " --> pdb=" O   LEU B 575 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER B 601 " --> pdb=" O   LEU B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 614
    Processing helix  chain 'B' and resid 615 through 647
      removed outlier: 4.046A  pdb=" N   LYS B 619 " --> pdb=" O   GLY B 615 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU B 638 " --> pdb=" O   PHE B 634 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA B 639 " --> pdb=" O   LEU B 635 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   THR B 640 " --> pdb=" O   LEU B 636 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL B 641 " --> pdb=" O   MET B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 679
      removed outlier: 3.777A  pdb=" N   ARG B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL B 664 " --> pdb=" O   LYS B 660 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 668 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 669 " --> pdb=" O   ALA B 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 731
      removed outlier: 3.778A  pdb=" N   ILE B 724 " --> pdb=" O   LEU B 720 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   TYR B 725 " --> pdb=" O   MET B 721 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 768
      Proline residue:  B 762  - end of helix
      removed outlier: 3.571A  pdb=" N   SER B 767 " --> pdb=" O   VAL B 763 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE B 768 " --> pdb=" O   ALA B 764 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 773
      removed outlier: 4.010A  pdb=" N   ILE B 772 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 774 through 776
      No H-bonds generated for 'chain 'B' and resid 774 through 776'
    Processing helix  chain 'B' and resid 778 through 790
    Processing helix  chain 'B' and resid 791 through 795
    Processing helix  chain 'B' and resid 796 through 804
      removed outlier: 3.725A  pdb=" N   TYR B 801 " --> pdb=" O   ASN B 797 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   VAL B 802 " --> pdb=" O   PRO B 798 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 805 through 820
      removed outlier: 3.913A  pdb=" N   LYS B 809 " --> pdb=" O   ASN B 805 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP B 811 " --> pdb=" O   LYS B 807 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41
      removed outlier: 7.177A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU A 110 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 183 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192
      removed outlier: 3.692A  pdb=" N   ILE A 192 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304
      removed outlier: 6.779A  pdb=" N   LEU A 348 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   LEU A 394 " --> pdb=" O   ASP A 419 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU A 418 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380
    Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42
      removed outlier: 7.335A  pdb=" N   VAL B  41 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   LEU B 110 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU B 182 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.726A  pdb=" N   ILE B 192 " --> pdb=" O   SER B 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 263
    Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 304
      removed outlier: 6.651A  pdb=" N   LEU B 348 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   LEU B 394 " --> pdb=" O   ASP B 419 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LEU B 418 " --> pdb=" O   LYS B 440 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 380
    Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 48
      removed outlier: 8.215A  pdb=" N   ALA C  63 " --> pdb=" O   PRO D  77 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   CYS C  65 " --> pdb=" O   SER D  75 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY C  67 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   SER D  73 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 92
      removed outlier: 3.665A  pdb=" N   ARG C  74 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER C  73 " --> pdb=" O   GLY D  67 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY D  67 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   ALA D  63 " --> pdb=" O   PRO C  77 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 106
      removed outlier: 6.760A  pdb=" N   SER C 125 " --> pdb=" O   GLN C  99 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER C 101 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   LEU C 103 " --> pdb=" O   ARG C 121 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ARG C 121 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA C 105 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C 119 " --> pdb=" O   ALA C 105 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 94 through 107
      removed outlier: 6.478A  pdb=" N   SER D 125 " --> pdb=" O   GLN D  99 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   SER D 101 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 101 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LEU D 103 " --> pdb=" O   ARG D 121 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ARG D 121 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA D 105 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   THR D 119 " --> pdb=" O   ALA D 105 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ARG D 107 " --> pdb=" O   THR D 117 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   THR D 117 " --> pdb=" O   ARG D 107 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1167 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: 3.65

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2635
        1.32 -     1.45: 2100
        1.45 -     1.57: 6844
        1.57 -     1.70: 3
        1.70 -     1.82: 71
  Bond restraints: 11653
  Sorted by residual:
  bond pdb=" C   ILE A 541 "
       pdb=" N   ARG A 542 "
    ideal  model  delta    sigma   weight residual
    1.334  1.577 -0.242 1.27e-02 6.20e+03 3.64e+02
  bond pdb=" C   SER B 601 "
       pdb=" N   TRP B 602 "
    ideal  model  delta    sigma   weight residual
    1.330  1.595 -0.265 1.40e-02 5.10e+03 3.59e+02
  bond pdb=" C   SER A 601 "
       pdb=" N   TRP A 602 "
    ideal  model  delta    sigma   weight residual
    1.330  1.588 -0.258 1.40e-02 5.10e+03 3.40e+02
  bond pdb=" C   ALA B 472 "
       pdb=" N   PHE B 473 "
    ideal  model  delta    sigma   weight residual
    1.334  1.561 -0.227 1.30e-02 5.92e+03 3.06e+02
  bond pdb=" C   GLN A 469 "
       pdb=" N   CYS A 470 "
    ideal  model  delta    sigma   weight residual
    1.335  1.543 -0.208 1.25e-02 6.40e+03 2.77e+02
  ... (remaining 11648 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.39: 15585
        6.39 -    12.78: 286
       12.78 -    19.17: 36
       19.17 -    25.55: 3
       25.55 -    31.94: 2
  Bond angle restraints: 15912
  Sorted by residual:
  angle pdb=" N   SER A 573 "
        pdb=" CA  SER A 573 "
        pdb=" C   SER A 573 "
      ideal   model   delta    sigma   weight residual
     114.62   82.68   31.94 1.14e+00 7.69e-01 7.85e+02
  angle pdb=" N   SER C  92 "
        pdb=" CA  SER C  92 "
        pdb=" C   SER C  92 "
      ideal   model   delta    sigma   weight residual
     108.76   79.38   29.38 1.58e+00 4.01e-01 3.46e+02
  angle pdb=" O   CYS A 471 "
        pdb=" C   CYS A 471 "
        pdb=" N   ALA A 472 "
      ideal   model   delta    sigma   weight residual
     122.08  140.74  -18.66 1.07e+00 8.73e-01 3.04e+02
  angle pdb=" N   GLN A 342 "
        pdb=" CA  GLN A 342 "
        pdb=" C   GLN A 342 "
      ideal   model   delta    sigma   weight residual
     109.15   85.11   24.04 1.44e+00 4.82e-01 2.79e+02
  angle pdb=" O   CYS A 470 "
        pdb=" C   CYS A 470 "
        pdb=" N   CYS A 471 "
      ideal   model   delta    sigma   weight residual
     122.09  138.17  -16.08 1.04e+00 9.25e-01 2.39e+02
  ... (remaining 15907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 6875
       17.67 -    35.34: 194
       35.34 -    53.01: 41
       53.01 -    70.69: 10
       70.69 -    88.36: 1
  Dihedral angle restraints: 7121
    sinusoidal: 2318
      harmonic: 4803
  Sorted by residual:
  dihedral pdb=" C   ALA B 185 "
           pdb=" N   ALA B 185 "
           pdb=" CA  ALA B 185 "
           pdb=" CB  ALA B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.26  -21.34     0      2.50e+00 1.60e-01 7.29e+01
  dihedral pdb=" CB  CYS A  29 "
           pdb=" SG  CYS A  29 "
           pdb=" SG  CYS A  35 "
           pdb=" CB  CYS A  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.50   56.50     1      1.00e+01 1.00e-02 4.30e+01
  dihedral pdb=" CB  CYS A  33 "
           pdb=" SG  CYS A  33 "
           pdb=" SG  CYS A  43 "
           pdb=" CB  CYS A  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -31.47  -54.53     1      1.00e+01 1.00e-02 4.03e+01
  ... (remaining 7118 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.178: 1873
       0.178 -    0.356: 43
       0.356 -    0.534: 2
       0.534 -    0.712: 0
       0.712 -    0.890: 1
  Chirality restraints: 1919
  Sorted by residual:
  chirality pdb=" CA  SER A 572 "
            pdb=" N   SER A 572 "
            pdb=" C   SER A 572 "
            pdb=" CB  SER A 572 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.62    0.89 2.00e-01 2.50e+01 1.98e+01
  chirality pdb=" CA  SER C  82 "
            pdb=" N   SER C  82 "
            pdb=" C   SER C  82 "
            pdb=" CB  SER C  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.96   -0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CA  ALA B 185 "
            pdb=" N   ALA B 185 "
            pdb=" C   ALA B 185 "
            pdb=" CB  ALA B 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.86   -0.37 2.00e-01 2.50e+01 3.51e+00
  ... (remaining 1916 not shown)

  Planarity restraints: 2118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 806 "   -0.042 2.00e-02 2.50e+03   8.38e-02 7.02e+01
        pdb=" C   PRO B 806 "    0.145 2.00e-02 2.50e+03
        pdb=" O   PRO B 806 "   -0.053 2.00e-02 2.50e+03
        pdb=" N   LYS B 807 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 703 "   -0.025 2.00e-02 2.50e+03   6.06e-02 3.67e+01
        pdb=" C   SER A 703 "    0.104 2.00e-02 2.50e+03
        pdb=" O   SER A 703 "   -0.042 2.00e-02 2.50e+03
        pdb=" N   LEU A 704 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 703 "    0.025 2.00e-02 2.50e+03   6.04e-02 3.65e+01
        pdb=" C   SER B 703 "   -0.104 2.00e-02 2.50e+03
        pdb=" O   SER B 703 "    0.042 2.00e-02 2.50e+03
        pdb=" N   LEU B 704 "    0.037 2.00e-02 2.50e+03
  ... (remaining 2115 not shown)

  Histogram of nonbonded interaction distances:
        1.18 -     1.92: 7
        1.92 -     2.67: 359
        2.67 -     3.41: 15167
        3.41 -     4.16: 25592
        4.16 -     4.90: 44871
  Nonbonded interactions: 85996
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 462 "
            pdb=" CZ  PHE A 473 "
     model   vdw
     1.179 3.760
  nonbonded pdb=" SG  CYS A 470 "
            pdb=" CG  PRO A 524 "
     model   vdw
     1.288 3.800
  nonbonded pdb=" CD2 LEU A 462 "
            pdb=" CE1 PHE A 473 "
     model   vdw
     1.369 3.760
  nonbonded pdb=" CD2 LEU A 462 "
            pdb=" CE2 PHE A 473 "
     model   vdw
     1.727 3.760
  nonbonded pdb=" O   VAL B 819 "
            pdb=" O   THR B 820 "
     model   vdw
     1.814 3.040
  ... (remaining 85991 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 29 through 467 or (resid 468 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 469 through 820))
  selection = (chain 'B' and (resid 29 through 45 or (resid 46 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 47 through 447 or (resid 448 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 449 through 474 or resid 519 t \ 
hrough 567 or resid 572 through 820))
}
ncs_group {
  reference = (chain 'C' and resid 35 through 133)
  selection = (chain 'D' and (resid 35 through 82 or (resid 83 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 84 through 113 or (resid 114 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 115 through 133))
}

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:             4.790
  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:          0.590
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.390
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5285
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      :  0.024   0.822  11675  Z= 1.689
  Angle     :  2.077  31.943  15954  Z= 1.580
  Chirality :  0.069   0.890   1919
  Planarity :  0.009   0.084   2118
  Dihedral  :  8.638  88.358   3918
  Min Nonbonded Distance : 1.179

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  4.96 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.38 %
  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: -2.44 (0.20), residues: 1629
  helix: -0.74 (0.23), residues: 426
  sheet: -1.88 (0.32), residues: 286
  loop : -1.99 (0.20), residues: 917

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 159 
 HIS   0.007   0.001   HIS D  50 
 PHE   0.021   0.001   PHE C  89 
 TYR   0.013   0.001   TYR C 122 
 ARG   0.006   0.000   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.33112 (  399)
  hydrogen bonds       : angle       9.51900 ( 1167)
  SS BOND              : bond        0.25337 (   21)
  SS BOND              : angle       5.08531 (   42)
  covalent geometry    : bond        0.02155 (11653)
  covalent geometry    : angle       2.06294 (15912)
  Misc. bond           : bond        0.08837 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 302
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 LYS cc_start: 0.7709 (ptmm) cc_final: 0.7459 (pttp)
REVERT: A   79 ASN cc_start: 0.5492 (m-40) cc_final: 0.5207 (t0)
REVERT: A   99 LYS cc_start: 0.7841 (mttt) cc_final: 0.7219 (mppt)
REVERT: A  252 GLU cc_start: 0.7501 (tt0) cc_final: 0.7141 (mt-10)
REVERT: A  286 PHE cc_start: 0.7842 (t80) cc_final: 0.7559 (t80)
REVERT: B   78 LYS cc_start: 0.7689 (ptmm) cc_final: 0.7477 (pttp)
REVERT: B   79 ASN cc_start: 0.5520 (m-40) cc_final: 0.5183 (t0)
REVERT: B  252 GLU cc_start: 0.7502 (tt0) cc_final: 0.7185 (mt-10)
REVERT: B  286 PHE cc_start: 0.7845 (t80) cc_final: 0.7530 (t80)
REVERT: C  109 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8239 (ptp-170)
REVERT: D  114 MET cc_start: 0.6263 (ptp) cc_final: 0.5984 (pmm)
  outliers start: 26
  outliers final: 7
  residues processed: 315
  average time/residue: 0.2866
  time to fit residues: 120.7648
Evaluate side-chains
  184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 176
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain C residue  109 ARG
Chi-restraints excluded: chain C residue  121 ARG
Chi-restraints excluded: chain D residue   54 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 138 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 83 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 148 optimal weight:    0.6980
   overall best weight:    2.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 ASN
A 294 ASN
A 311 GLN
A 386 GLN
A 417 ASN
B  71 GLN
B 218 GLN
B 219 HIS
B 294 ASN
B 311 GLN
B 337 ASN
B 342 GLN
B 386 GLN
B 417 ASN
C  87 GLN
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.239360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.207330 restraints weight = 14472.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.4450 rms_B_bonded: 3.10
r_work: 0.3745 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  11675  Z= 0.261
  Angle     :  0.814  11.812  15954  Z= 0.409
  Chirality :  0.050   0.222   1919
  Planarity :  0.006   0.069   2118
  Dihedral  :  5.679  54.575   1734
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 10.21 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.39 (0.21), residues: 1629
  helix:  1.39 (0.25), residues: 444
  sheet: -2.20 (0.27), residues: 313
  loop : -1.69 (0.21), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 159 
 HIS   0.015   0.002   HIS B 209 
 PHE   0.021   0.002   PHE D  89 
 TYR   0.015   0.002   TYR B 234 
 ARG   0.007   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05377 (  399)
  hydrogen bonds       : angle       5.23836 ( 1167)
  SS BOND              : bond        0.00923 (   21)
  SS BOND              : angle       2.28137 (   42)
  covalent geometry    : bond        0.00632 (11653)
  covalent geometry    : angle       0.80704 (15912)
  Misc. bond           : bond        0.00401 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 191
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8551 (mttt) cc_final: 0.8150 (mtmm)
REVERT: A  344 MET cc_start: 0.3968 (tpt) cc_final: 0.3054 (ptt)
REVERT: A  346 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.7017 (mmp80)
REVERT: A  368 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5552 (pt0)
REVERT: B  218 GLN cc_start: 0.7284 (tp40) cc_final: 0.6606 (tp-100)
REVERT: B  368 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5624 (pt0)
REVERT: B  369 GLU cc_start: 0.5787 (mm-30) cc_final: 0.5368 (mm-30)
REVERT: B  402 HIS cc_start: 0.7351 (p90) cc_final: 0.7139 (p90)
REVERT: B  529 PHE cc_start: 0.7465 (m-80) cc_final: 0.7251 (m-80)
REVERT: D   97 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7626 (mtt90)
  outliers start: 45
  outliers final: 28
  residues processed: 220
  average time/residue: 0.2224
  time to fit residues: 69.9015
Evaluate side-chains
  176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  311 GLN
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  225 ASP
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  311 GLN
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  690 SER
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain D residue  108 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 63 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   chunk 123 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
A 171 HIS
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 GLN
A 342 GLN
B 115 ASN
B 139 ASN
B 171 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 GLN
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.230713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.197672 restraints weight = 14871.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.4352 rms_B_bonded: 3.07
r_work: 0.3621 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.147  11675  Z= 0.505
  Angle     :  1.029  14.354  15954  Z= 0.518
  Chirality :  0.060   0.370   1919
  Planarity :  0.008   0.092   2118
  Dihedral  :  6.052  52.493   1720
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 11.07 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.21), residues: 1629
  helix:  2.29 (0.25), residues: 436
  sheet: -2.74 (0.26), residues: 300
  loop : -2.38 (0.19), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 159 
 HIS   0.018   0.003   HIS A 157 
 PHE   0.030   0.002   PHE D  89 
 TYR   0.019   0.003   TYR B 280 
 ARG   0.006   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06179 (  399)
  hydrogen bonds       : angle       4.88520 ( 1167)
  SS BOND              : bond        0.00710 (   21)
  SS BOND              : angle       3.08273 (   42)
  covalent geometry    : bond        0.01245 (11653)
  covalent geometry    : angle       1.01790 (15912)
  Misc. bond           : bond        0.01284 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 166
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8815 (mttt) cc_final: 0.8281 (mtmm)
REVERT: A  106 GLU cc_start: 0.8078 (tp30) cc_final: 0.7740 (tp30)
REVERT: B  106 GLU cc_start: 0.7994 (tp30) cc_final: 0.7761 (tp30)
REVERT: B  273 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6772 (tt)
  outliers start: 74
  outliers final: 44
  residues processed: 217
  average time/residue: 0.2277
  time to fit residues: 70.4189
Evaluate side-chains
  191 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 146
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  225 ASP
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  398 ARG
Chi-restraints excluded: chain B residue  690 SER
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 114 optimal weight:   30.0000
   chunk 137 optimal weight:   50.0000
   chunk 16 optimal weight:    0.6980
   chunk 52 optimal weight:   50.0000
   chunk 55 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 129 optimal weight:   50.0000
   chunk 23 optimal weight:    2.9990
   chunk 145 optimal weight:    0.2980
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
A 342 GLN
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.236410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.204176 restraints weight = 14446.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.4422 rms_B_bonded: 2.37
r_work: 0.3762 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  11675  Z= 0.154
  Angle     :  0.692  15.380  15954  Z= 0.345
  Chirality :  0.046   0.231   1919
  Planarity :  0.005   0.040   2118
  Dihedral  :  5.129  53.629   1720
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 15.27 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.21), residues: 1629
  helix:  2.53 (0.25), residues: 442
  sheet: -2.45 (0.27), residues: 305
  loop : -2.06 (0.20), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.014   0.001   HIS D  42 
 PHE   0.007   0.001   PHE A 312 
 TYR   0.014   0.002   TYR D  53 
 ARG   0.005   0.001   ARG B 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  399)
  hydrogen bonds       : angle       4.47556 ( 1167)
  SS BOND              : bond        0.00694 (   21)
  SS BOND              : angle       2.35879 (   42)
  covalent geometry    : bond        0.00372 (11653)
  covalent geometry    : angle       0.68229 (15912)
  Misc. bond           : bond        0.00651 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 151
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8783 (mttt) cc_final: 0.8356 (mtmm)
REVERT: A  346 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7500 (mmm160)
REVERT: A  369 GLU cc_start: 0.7043 (pm20) cc_final: 0.6447 (pm20)
REVERT: A  531 PRO cc_start: 0.7462 (Cg_exo) cc_final: 0.7227 (Cg_endo)
REVERT: D   87 GLN cc_start: 0.6493 (tp40) cc_final: 0.5979 (pt0)
  outliers start: 49
  outliers final: 34
  residues processed: 188
  average time/residue: 0.2294
  time to fit residues: 62.0367
Evaluate side-chains
  181 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  466 TYR
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  398 ARG
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    0.1980
   chunk 61 optimal weight:    0.5980
   chunk 37 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 127 optimal weight:    9.9990
   chunk 148 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
B 199 ASN
B 320 HIS
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.237535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.206710 restraints weight = 14575.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.4435 rms_B_bonded: 2.37
r_work: 0.3763 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  11675  Z= 0.134
  Angle     :  0.647  13.201  15954  Z= 0.323
  Chirality :  0.045   0.298   1919
  Planarity :  0.004   0.038   2118
  Dihedral  :  4.750  44.981   1720
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.26 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 15.17 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1629
  helix:  2.85 (0.25), residues: 438
  sheet: -2.33 (0.27), residues: 312
  loop : -1.88 (0.20), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 474 
 HIS   0.021   0.001   HIS D  42 
 PHE   0.010   0.001   PHE B 422 
 TYR   0.011   0.001   TYR D  53 
 ARG   0.006   0.000   ARG B 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  399)
  hydrogen bonds       : angle       4.19084 ( 1167)
  SS BOND              : bond        0.00682 (   21)
  SS BOND              : angle       1.98159 (   42)
  covalent geometry    : bond        0.00321 (11653)
  covalent geometry    : angle       0.64001 (15912)
  Misc. bond           : bond        0.00572 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8812 (mttt) cc_final: 0.8295 (mtmm)
REVERT: A  225 ASP cc_start: 0.7794 (m-30) cc_final: 0.7587 (m-30)
REVERT: A  231 ASP cc_start: 0.7980 (m-30) cc_final: 0.7658 (m-30)
REVERT: A  346 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7448 (tpt-90)
REVERT: A  424 GLU cc_start: 0.8139 (mp0) cc_final: 0.7932 (mp0)
REVERT: B   93 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7811 (tt)
  outliers start: 51
  outliers final: 34
  residues processed: 187
  average time/residue: 0.2344
  time to fit residues: 62.6790
Evaluate side-chains
  178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  466 TYR
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  398 ARG
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain B residue  690 SER
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 154 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 149 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 142 optimal weight:    0.0270
   chunk 59 optimal weight:   20.0000
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
B 199 ASN
B 342 GLN
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.238151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.214374 restraints weight = 14563.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.4495 rms_B_bonded: 1.69
r_work: 0.4013 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3901 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11675  Z= 0.134
  Angle     :  0.665  13.492  15954  Z= 0.327
  Chirality :  0.045   0.413   1919
  Planarity :  0.004   0.038   2118
  Dihedral  :  4.668  45.009   1720
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.22 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 14.79 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.22), residues: 1629
  helix:  2.97 (0.25), residues: 443
  sheet: -2.18 (0.28), residues: 307
  loop : -1.80 (0.20), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 474 
 HIS   0.008   0.001   HIS D  42 
 PHE   0.006   0.001   PHE A 255 
 TYR   0.010   0.001   TYR D  53 
 ARG   0.004   0.000   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (  399)
  hydrogen bonds       : angle       4.12286 ( 1167)
  SS BOND              : bond        0.00500 (   21)
  SS BOND              : angle       2.72655 (   42)
  covalent geometry    : bond        0.00320 (11653)
  covalent geometry    : angle       0.65143 (15912)
  Misc. bond           : bond        0.00765 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 142
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.7618 (m-30) cc_final: 0.7301 (m-30)
REVERT: B   93 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7932 (tt)
  outliers start: 56
  outliers final: 34
  residues processed: 184
  average time/residue: 0.2238
  time to fit residues: 59.9219
Evaluate side-chains
  170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  342 GLN
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 138 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 148 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:   20.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
B 199 ASN
B 218 GLN
B 242 GLN
C  42 HIS
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.237881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.214105 restraints weight = 14703.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.4495 rms_B_bonded: 1.74
r_work: 0.4023 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3955 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11675  Z= 0.144
  Angle     :  0.663  13.743  15954  Z= 0.326
  Chirality :  0.045   0.328   1919
  Planarity :  0.005   0.076   2118
  Dihedral  :  4.481  44.398   1718
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 14.50 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.22), residues: 1629
  helix:  3.11 (0.25), residues: 443
  sheet: -2.13 (0.28), residues: 312
  loop : -1.69 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 159 
 HIS   0.006   0.001   HIS D  68 
 PHE   0.007   0.001   PHE D  89 
 TYR   0.012   0.001   TYR D  53 
 ARG   0.004   0.000   ARG B 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  399)
  hydrogen bonds       : angle       3.96858 ( 1167)
  SS BOND              : bond        0.00565 (   21)
  SS BOND              : angle       2.73118 (   42)
  covalent geometry    : bond        0.00344 (11653)
  covalent geometry    : angle       0.64908 (15912)
  Misc. bond           : bond        0.00902 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 144
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7870 (tt)
  outliers start: 57
  outliers final: 35
  residues processed: 183
  average time/residue: 0.2275
  time to fit residues: 60.8618
Evaluate side-chains
  168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  466 TYR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  471 CYS
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain B residue  466 TYR
Chi-restraints excluded: chain B residue  690 SER
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 129 optimal weight:   50.0000
   chunk 42 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:   40.0000
   chunk 69 optimal weight:   20.0000
   chunk 57 optimal weight:    0.0270
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
B 199 ASN
B 218 GLN
B 242 GLN
B 342 GLN
** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.238118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.211902 restraints weight = 14515.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4472 rms_B_bonded: 1.85
r_work: 0.4013 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3925 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  11675  Z= 0.135
  Angle     :  0.667  15.984  15954  Z= 0.332
  Chirality :  0.046   0.364   1919
  Planarity :  0.005   0.069   2118
  Dihedral  :  4.509  48.588   1718
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.84 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.22), residues: 1629
  helix:  3.22 (0.25), residues: 444
  sheet: -1.98 (0.29), residues: 312
  loop : -1.61 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 474 
 HIS   0.010   0.001   HIS D  42 
 PHE   0.006   0.001   PHE A 312 
 TYR   0.024   0.002   TYR A 468 
 ARG   0.009   0.000   ARG B 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  399)
  hydrogen bonds       : angle       4.03461 ( 1167)
  SS BOND              : bond        0.00466 (   21)
  SS BOND              : angle       2.66673 (   42)
  covalent geometry    : bond        0.00321 (11653)
  covalent geometry    : angle       0.65328 (15912)
  Misc. bond           : bond        0.00980 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.7633 (m-30) cc_final: 0.7258 (m-30)
REVERT: B   93 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7893 (tt)
  outliers start: 45
  outliers final: 32
  residues processed: 168
  average time/residue: 0.2304
  time to fit residues: 56.3082
Evaluate side-chains
  157 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 CYS
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  466 TYR
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  293 HIS
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 67 optimal weight:   20.0000
   chunk 142 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 45 optimal weight:   20.0000
   chunk 14 optimal weight:    0.5980
   chunk 49 optimal weight:   50.0000
   chunk 15 optimal weight:    1.9990
   chunk 156 optimal weight:    0.0370
   chunk 147 optimal weight:    0.3980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 199 ASN
B 199 ASN
C 127 HIS
D  42 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.239584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.216842 restraints weight = 14553.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.4518 rms_B_bonded: 1.64
r_work: 0.3977 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3819 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11675  Z= 0.113
  Angle     :  0.656  14.075  15954  Z= 0.321
  Chirality :  0.044   0.327   1919
  Planarity :  0.004   0.075   2118
  Dihedral  :  4.335  50.655   1718
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.34 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.70 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.22), residues: 1629
  helix:  3.32 (0.25), residues: 443
  sheet: -1.91 (0.29), residues: 312
  loop : -1.52 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 474 
 HIS   0.010   0.001   HIS D  42 
 PHE   0.005   0.000   PHE A 255 
 TYR   0.035   0.001   TYR A 468 
 ARG   0.006   0.000   ARG B 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02946 (  399)
  hydrogen bonds       : angle       3.87883 ( 1167)
  SS BOND              : bond        0.00511 (   21)
  SS BOND              : angle       3.22742 (   42)
  covalent geometry    : bond        0.00260 (11653)
  covalent geometry    : angle       0.63528 (15912)
  Misc. bond           : bond        0.00800 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 2.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ASP cc_start: 0.7496 (t0) cc_final: 0.7049 (t0)
REVERT: A  231 ASP cc_start: 0.7555 (m-30) cc_final: 0.7161 (m-30)
REVERT: A  471 CYS cc_start: 0.6668 (m) cc_final: 0.6070 (m)
REVERT: B   93 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: D  109 ARG cc_start: 0.7646 (ptp-170) cc_final: 0.7386 (ptp-170)
  outliers start: 39
  outliers final: 29
  residues processed: 162
  average time/residue: 0.2279
  time to fit residues: 54.0883
Evaluate side-chains
  155 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  449 GLU
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 155 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 57 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 150 optimal weight:    0.0040
   chunk 60 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 124 optimal weight:   30.0000
   chunk 107 optimal weight:    6.9990
   chunk 129 optimal weight:   30.0000
   chunk 109 optimal weight:    8.9990
   overall best weight:    3.4000

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.230964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.202132 restraints weight = 14593.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.4410 rms_B_bonded: 2.77
r_work: 0.3714 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.097  11675  Z= 0.349
  Angle     :  0.864  16.653  15954  Z= 0.431
  Chirality :  0.053   0.359   1919
  Planarity :  0.006   0.074   2118
  Dihedral  :  5.273  59.515   1718
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.10 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.60 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.22), residues: 1629
  helix:  3.45 (0.25), residues: 443
  sheet: -2.22 (0.29), residues: 293
  loop : -1.89 (0.21), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 159 
 HIS   0.019   0.002   HIS D  42 
 PHE   0.017   0.002   PHE D  89 
 TYR   0.019   0.002   TYR A 468 
 ARG   0.009   0.001   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  399)
  hydrogen bonds       : angle       4.23595 ( 1167)
  SS BOND              : bond        0.00713 (   21)
  SS BOND              : angle       3.44416 (   42)
  covalent geometry    : bond        0.00864 (11653)
  covalent geometry    : angle       0.84697 (15912)
  Misc. bond           : bond        0.01472 (    1)

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

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

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3258 Ramachandran restraints generated.
    1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 133
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ASP cc_start: 0.7751 (t0) cc_final: 0.7271 (t0)
REVERT: A  106 GLU cc_start: 0.7978 (tp30) cc_final: 0.7688 (tp30)
REVERT: A  471 CYS cc_start: 0.6586 (m) cc_final: 0.6036 (m)
REVERT: B   92 ASP cc_start: 0.7683 (t0) cc_final: 0.7216 (t0)
REVERT: B  106 GLU cc_start: 0.7884 (tp30) cc_final: 0.7593 (tp30)
REVERT: B  273 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6643 (tt)
  outliers start: 37
  outliers final: 32
  residues processed: 164
  average time/residue: 0.2184
  time to fit residues: 52.9705
Evaluate side-chains
  162 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 CYS
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain B residue   35 CYS
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  378 TYR
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  101 SER
Chi-restraints excluded: chain D residue   42 HIS
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  132 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 116 optimal weight:    0.0370
   chunk 84 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 65 optimal weight:   30.0000
   chunk 128 optimal weight:   10.0000
   chunk 154 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 113 optimal weight:    0.0370
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 171 HIS
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 ASN
B  91 ASN
B 171 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.237890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.205145 restraints weight = 14482.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.4427 rms_B_bonded: 2.42
r_work: 0.3776 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11675  Z= 0.115
  Angle     :  0.670  17.889  15954  Z= 0.330
  Chirality :  0.045   0.306   1919
  Planarity :  0.005   0.074   2118
  Dihedral  :  4.507  54.880   1718
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.95 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.75 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.22), residues: 1629
  helix:  3.47 (0.25), residues: 443
  sheet: -2.01 (0.28), residues: 312
  loop : -1.60 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 474 
 HIS   0.010   0.001   HIS D  42 
 PHE   0.005   0.001   PHE B 255 
 TYR   0.016   0.001   TYR A 468 
 ARG   0.010   0.001   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02890 (  399)
  hydrogen bonds       : angle       3.79282 ( 1167)
  SS BOND              : bond        0.00503 (   21)
  SS BOND              : angle       3.14891 (   42)
  covalent geometry    : bond        0.00265 (11653)
  covalent geometry    : angle       0.65065 (15912)
  Misc. bond           : bond        0.00713 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6341.97 seconds
wall clock time: 110 minutes 27.83 seconds (6627.83 seconds total)