Starting phenix.real_space_refine
on Sat Aug 23 18:16:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iob_35614/08_2025/8iob_35614.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    9008      2.51       5
     N    2324      2.21       5
     O    2336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13736
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3434
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 412}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 3434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3434
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 412}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 3434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3434
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 412}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 3434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3434
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 18, 'TRANS': 412}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 3.41, per 1000 atoms: 0.25
  Number of scatterers: 13736
  At special positions: 0
  Unit cell: (116.313, 116.313, 125.652, 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      68     16.00
     O    2336      8.00
     N    2324      7.00
     C    9008      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 557.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3232

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 10 sheets defined
      64.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 404 through 431
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 451 through 473
      removed outlier: 3.642A  pdb=" N   ASP A 460 " --> pdb=" O   ASP A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 494
      removed outlier: 3.825A  pdb=" N   ILE A 489 " --> pdb=" O   HIS A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 506
      removed outlier: 3.562A  pdb=" N   ILE A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 4.333A  pdb=" N   LEU A 529 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 534 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 543
    Processing helix  chain 'A' and resid 545 through 576
      removed outlier: 3.899A  pdb=" N   VAL A 549 " --> pdb=" O   TYR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 593
    Processing helix  chain 'A' and resid 608 through 621
      removed outlier: 4.318A  pdb=" N   ALA A 614 " --> pdb=" O   LYS A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 687
      removed outlier: 5.002A  pdb=" N   GLY A 669 " --> pdb=" O   ARG A 665 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   THR A 670 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 708
      removed outlier: 3.711A  pdb=" N   TYR A 707 " --> pdb=" O   HIS A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 720
      removed outlier: 4.056A  pdb=" N   VAL A 716 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 720 " --> pdb=" O   VAL A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 731
      removed outlier: 3.540A  pdb=" N   LEU A 730 " --> pdb=" O   ALA A 726 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   HIS A 731 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 746
    Processing helix  chain 'A' and resid 747 through 757
    Processing helix  chain 'A' and resid 834 through 843
      removed outlier: 3.584A  pdb=" N   LEU A 839 " --> pdb=" O   ARG A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 855
    Processing helix  chain 'B' and resid 404 through 431
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 451 through 473
      removed outlier: 3.591A  pdb=" N   ASP B 460 " --> pdb=" O   ASP B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 494
      removed outlier: 3.875A  pdb=" N   ILE B 489 " --> pdb=" O   HIS B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 506
    Processing helix  chain 'B' and resid 525 through 538
      removed outlier: 4.160A  pdb=" N   LEU B 529 " --> pdb=" O   LYS B 525 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU B 532 " --> pdb=" O   ARG B 528 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL B 533 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ARG B 534 " --> pdb=" O   LEU B 530 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL B 535 " --> pdb=" O   ARG B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
    Processing helix  chain 'B' and resid 545 through 576
      removed outlier: 3.930A  pdb=" N   VAL B 549 " --> pdb=" O   TYR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 593
    Processing helix  chain 'B' and resid 608 through 621
      removed outlier: 4.269A  pdb=" N   ALA B 614 " --> pdb=" O   LYS B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 687
      removed outlier: 5.013A  pdb=" N   GLY B 669 " --> pdb=" O   ARG B 665 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   THR B 670 " --> pdb=" O   LEU B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 708
      removed outlier: 3.581A  pdb=" N   TYR B 707 " --> pdb=" O   HIS B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 720
      removed outlier: 4.019A  pdb=" N   VAL B 716 " --> pdb=" O   ASP B 712 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 720 " --> pdb=" O   VAL B 716 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 731
      removed outlier: 3.546A  pdb=" N   LEU B 730 " --> pdb=" O   ALA B 726 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   HIS B 731 " --> pdb=" O   ASP B 727 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 746
      removed outlier: 3.518A  pdb=" N   ARG B 744 " --> pdb=" O   LYS B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 757
    Processing helix  chain 'B' and resid 834 through 844
      removed outlier: 3.693A  pdb=" N   MET B 844 " --> pdb=" O   GLU B 840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 845 through 855
      removed outlier: 3.619A  pdb=" N   SER B 849 " --> pdb=" O   TYR B 845 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 431
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 451 through 473
      removed outlier: 3.607A  pdb=" N   ASP C 460 " --> pdb=" O   ASP C 456 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 494
      removed outlier: 3.870A  pdb=" N   ILE C 489 " --> pdb=" O   HIS C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 506
    Processing helix  chain 'C' and resid 525 through 538
      removed outlier: 4.168A  pdb=" N   LEU C 529 " --> pdb=" O   LYS C 525 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU C 532 " --> pdb=" O   ARG C 528 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   VAL C 533 " --> pdb=" O   LEU C 529 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ARG C 534 " --> pdb=" O   LEU C 530 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL C 535 " --> pdb=" O   ARG C 531 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 543
    Processing helix  chain 'C' and resid 545 through 576
      removed outlier: 3.907A  pdb=" N   VAL C 549 " --> pdb=" O   TYR C 545 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 593
    Processing helix  chain 'C' and resid 608 through 621
      removed outlier: 4.285A  pdb=" N   ALA C 614 " --> pdb=" O   LYS C 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 634 through 687
      removed outlier: 4.945A  pdb=" N   GLY C 669 " --> pdb=" O   ARG C 665 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   THR C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 690 through 708
      removed outlier: 3.594A  pdb=" N   TYR C 707 " --> pdb=" O   HIS C 703 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 712 through 720
      removed outlier: 4.000A  pdb=" N   VAL C 716 " --> pdb=" O   ASP C 712 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE C 720 " --> pdb=" O   VAL C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 722 through 731
      removed outlier: 3.566A  pdb=" N   LEU C 730 " --> pdb=" O   ALA C 726 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS C 731 " --> pdb=" O   ASP C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 741 through 746
    Processing helix  chain 'C' and resid 747 through 757
    Processing helix  chain 'C' and resid 834 through 844
      removed outlier: 3.698A  pdb=" N   MET C 844 " --> pdb=" O   GLU C 840 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 845 through 855
      removed outlier: 3.613A  pdb=" N   SER C 849 " --> pdb=" O   TYR C 845 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 431
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 451 through 473
      removed outlier: 3.609A  pdb=" N   ASP D 460 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 485 through 494
      removed outlier: 3.797A  pdb=" N   ILE D 489 " --> pdb=" O   HIS D 485 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 496 through 506
    Processing helix  chain 'D' and resid 525 through 538
      removed outlier: 4.211A  pdb=" N   LEU D 529 " --> pdb=" O   LYS D 525 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU D 532 " --> pdb=" O   ARG D 528 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   VAL D 533 " --> pdb=" O   LEU D 529 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ARG D 534 " --> pdb=" O   LEU D 530 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL D 535 " --> pdb=" O   ARG D 531 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
    Processing helix  chain 'D' and resid 545 through 576
      removed outlier: 3.897A  pdb=" N   VAL D 549 " --> pdb=" O   TYR D 545 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 593
    Processing helix  chain 'D' and resid 608 through 621
      removed outlier: 4.343A  pdb=" N   ALA D 614 " --> pdb=" O   LYS D 610 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 634 through 687
      removed outlier: 4.939A  pdb=" N   GLY D 669 " --> pdb=" O   ARG D 665 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   THR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 690 through 708
      removed outlier: 3.832A  pdb=" N   TYR D 707 " --> pdb=" O   HIS D 703 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 712 through 720
      removed outlier: 4.012A  pdb=" N   VAL D 716 " --> pdb=" O   ASP D 712 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE D 720 " --> pdb=" O   VAL D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 722 through 731
      removed outlier: 3.571A  pdb=" N   LEU D 730 " --> pdb=" O   ALA D 726 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS D 731 " --> pdb=" O   ASP D 727 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 741 through 746
    Processing helix  chain 'D' and resid 747 through 757
    Processing helix  chain 'D' and resid 834 through 844
      removed outlier: 3.773A  pdb=" N   MET D 844 " --> pdb=" O   GLU D 840 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 845 through 855
    Processing sheet with id=AA1, first strand: chain 'A' and resid 762 through 763
      removed outlier: 7.437A  pdb=" N   ASP A 829 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 795 through 796
      removed outlier: 3.799A  pdb=" N   GLU A 788 " --> pdb=" O   ARG A 823 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 759 through 763
      removed outlier: 7.468A  pdb=" N   ASP B 829 " --> pdb=" O   SER B 783 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 795 through 796
      removed outlier: 3.806A  pdb=" N   GLU B 788 " --> pdb=" O   ARG B 823 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 762 through 763
      removed outlier: 7.417A  pdb=" N   ASP C 829 " --> pdb=" O   SER C 783 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 795 through 796
      removed outlier: 3.804A  pdb=" N   GLU C 788 " --> pdb=" O   ARG C 823 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 805 through 806
      removed outlier: 4.214A  pdb=" N   GLY C 806 " --> pdb=" O   PHE C 860 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 762 through 763
      removed outlier: 7.355A  pdb=" N   ASP D 829 " --> pdb=" O   SER D 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 795 through 796
      removed outlier: 3.803A  pdb=" N   GLU D 788 " --> pdb=" O   ARG D 823 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 805 through 806
      removed outlier: 4.227A  pdb=" N   GLY D 806 " --> pdb=" O   PHE D 860 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    800 hydrogen bonds defined for protein.
    2352 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: 1.82

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4255
        1.34 -     1.46: 2719
        1.46 -     1.58: 7017
        1.58 -     1.70: 1
        1.70 -     1.82: 104
  Bond restraints: 14096
  Sorted by residual:
  bond pdb=" CB  PRO C 808 "
       pdb=" CG  PRO C 808 "
    ideal  model  delta    sigma   weight residual
    1.492  1.607 -0.115 5.00e-02 4.00e+02 5.33e+00
  bond pdb=" CG  GLN B 676 "
       pdb=" CD  GLN B 676 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.15e+00
  bond pdb=" CB  LYS A 718 "
       pdb=" CG  LYS A 718 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.13e+00
  bond pdb=" CB  LYS C 718 "
       pdb=" CG  LYS C 718 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.12e+00
  bond pdb=" CG  GLN C 676 "
       pdb=" CD  GLN C 676 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.11e+00
  ... (remaining 14091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 18364
        1.67 -     3.34: 618
        3.34 -     5.01: 130
        5.01 -     6.68: 26
        6.68 -     8.35: 14
  Bond angle restraints: 19152
  Sorted by residual:
  angle pdb=" CA  PRO C 808 "
        pdb=" N   PRO C 808 "
        pdb=" CD  PRO C 808 "
      ideal   model   delta    sigma   weight residual
     112.00  105.27    6.73 1.40e+00 5.10e-01 2.31e+01
  angle pdb=" N   GLY C 806 "
        pdb=" CA  GLY C 806 "
        pdb=" C   GLY C 806 "
      ideal   model   delta    sigma   weight residual
     110.29  115.37   -5.08 1.28e+00 6.10e-01 1.58e+01
  angle pdb=" N   PRO C 808 "
        pdb=" CD  PRO C 808 "
        pdb=" CG  PRO C 808 "
      ideal   model   delta    sigma   weight residual
     103.20   97.92    5.28 1.50e+00 4.44e-01 1.24e+01
  angle pdb=" N   GLY D 806 "
        pdb=" CA  GLY D 806 "
        pdb=" C   GLY D 806 "
      ideal   model   delta    sigma   weight residual
     110.29  114.78   -4.49 1.28e+00 6.10e-01 1.23e+01
  angle pdb=" C   VAL B 491 "
        pdb=" N   HIS B 492 "
        pdb=" CA  HIS B 492 "
      ideal   model   delta    sigma   weight residual
     120.68  114.75    5.93 1.70e+00 3.46e-01 1.22e+01
  ... (remaining 19147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 7313
       16.06 -    32.13: 733
       32.13 -    48.19: 137
       48.19 -    64.26: 17
       64.26 -    80.32: 8
  Dihedral angle restraints: 8208
    sinusoidal: 3192
      harmonic: 5016
  Sorted by residual:
  dihedral pdb=" CA  LYS C 757 "
           pdb=" C   LYS C 757 "
           pdb=" N   PHE C 758 "
           pdb=" CA  PHE C 758 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.64   23.36     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  LYS B 757 "
           pdb=" C   LYS B 757 "
           pdb=" N   PHE B 758 "
           pdb=" CA  PHE B 758 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.99   21.01     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  TYR C 780 "
           pdb=" C   TYR C 780 "
           pdb=" N   PHE C 781 "
           pdb=" CA  PHE C 781 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.99   19.01     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 8205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1380
       0.034 -    0.069: 533
       0.069 -    0.103: 176
       0.103 -    0.138: 69
       0.138 -    0.172: 18
  Chirality restraints: 2176
  Sorted by residual:
  chirality pdb=" CB  ILE D 521 "
            pdb=" CA  ILE D 521 "
            pdb=" CG1 ILE D 521 "
            pdb=" CG2 ILE D 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CB  ILE B 521 "
            pdb=" CA  ILE B 521 "
            pdb=" CG1 ILE B 521 "
            pdb=" CG2 ILE B 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CB  ILE A 521 "
            pdb=" CA  ILE A 521 "
            pdb=" CG1 ILE A 521 "
            pdb=" CG2 ILE A 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 2173 not shown)

  Planarity restraints: 2376
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 652 "    0.022 2.00e-02 2.50e+03   1.49e-02 4.45e+00
        pdb=" CG  TYR B 652 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 652 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 652 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 652 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 652 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 652 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR B 652 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 720 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO A 721 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 721 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 721 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 720 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO B 721 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 721 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 721 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2373 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 238
        2.68 -     3.23: 14387
        3.23 -     3.79: 22425
        3.79 -     4.34: 28236
        4.34 -     4.90: 45123
  Nonbonded interactions: 110409
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 672 "
            pdb=" OG1 THR B 675 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   ARG C 672 "
            pdb=" OG1 THR C 675 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OG  SER B 735 "
            pdb=" OD1 ASN B 802 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG  SER C 735 "
            pdb=" OD1 ASN C 802 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG  SER A 735 "
            pdb=" OD1 ASN A 802 "
     model   vdw
     2.129 3.040
  ... (remaining 110404 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.100
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.060
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
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      :  0.003   0.115  14096  Z= 0.155
  Angle     :  0.757   8.346  19152  Z= 0.428
  Chirality :  0.045   0.172   2176
  Planarity :  0.004   0.045   2376
  Dihedral  : 13.275  80.323   4976
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.77 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.21), residues: 1684
  helix:  1.38 (0.16), residues: 1048
  sheet: -3.71 (0.48), residues: 68
  loop : -2.52 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 679 
 TYR   0.035   0.002   TYR B 652 
 PHE   0.025   0.002   PHE B 656 
 TRP   0.013   0.001   TRP D 410 
 HIS   0.006   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (14096)
  covalent geometry    : angle       0.75711 (19152)
  hydrogen bonds       : bond        0.14031 (  800)
  hydrogen bonds       : angle       5.91064 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 347
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7191 (ttm170)
REVERT: A  586 LEU cc_start: 0.9051 (mt) cc_final: 0.8840 (mt)
REVERT: A  698 GLU cc_start: 0.8990 (pp20) cc_final: 0.8688 (pp20)
REVERT: A  728 ILE cc_start: 0.9364 (tp) cc_final: 0.9100 (tp)
REVERT: A  729 CYS cc_start: 0.8943 (m) cc_final: 0.8678 (p)
REVERT: A  731 HIS cc_start: 0.8320 (m-70) cc_final: 0.7878 (m-70)
REVERT: A  756 MET cc_start: 0.8917 (ttp) cc_final: 0.8602 (ttp)
REVERT: A  758 PHE cc_start: 0.7746 (m-80) cc_final: 0.7519 (m-80)
REVERT: B  541 ARG cc_start: 0.7804 (tpt90) cc_final: 0.7534 (ptm160)
REVERT: B  678 LEU cc_start: 0.9328 (mt) cc_final: 0.8829 (mt)
REVERT: B  705 TRP cc_start: 0.8753 (t-100) cc_final: 0.8534 (t-100)
REVERT: B  728 ILE cc_start: 0.9369 (tp) cc_final: 0.9109 (tp)
REVERT: B  729 CYS cc_start: 0.9031 (m) cc_final: 0.8754 (p)
REVERT: B  731 HIS cc_start: 0.8318 (m-70) cc_final: 0.7896 (m-70)
REVERT: B  759 LYS cc_start: 0.9110 (mptt) cc_final: 0.8895 (mmtm)
REVERT: C  541 ARG cc_start: 0.7793 (tpt90) cc_final: 0.7516 (ptm160)
REVERT: C  562 HIS cc_start: 0.8624 (t-90) cc_final: 0.8415 (t-170)
REVERT: C  586 LEU cc_start: 0.9041 (mt) cc_final: 0.8837 (mt)
REVERT: C  678 LEU cc_start: 0.9329 (mt) cc_final: 0.8826 (mt)
REVERT: C  728 ILE cc_start: 0.9345 (tp) cc_final: 0.9070 (tp)
REVERT: C  729 CYS cc_start: 0.8995 (m) cc_final: 0.8721 (p)
REVERT: C  731 HIS cc_start: 0.8326 (m-70) cc_final: 0.7917 (m-70)
REVERT: C  759 LYS cc_start: 0.9084 (mptt) cc_final: 0.8853 (mmtm)
REVERT: C  780 TYR cc_start: 0.7669 (m-10) cc_final: 0.7462 (m-10)
REVERT: C  819 ASN cc_start: 0.5623 (t0) cc_final: 0.5403 (t0)
REVERT: D  586 LEU cc_start: 0.9057 (mt) cc_final: 0.8844 (mt)
REVERT: D  676 GLN cc_start: 0.9403 (mt0) cc_final: 0.8888 (mt0)
REVERT: D  728 ILE cc_start: 0.9349 (tp) cc_final: 0.9095 (tp)
REVERT: D  729 CYS cc_start: 0.9009 (m) cc_final: 0.8672 (p)
REVERT: D  731 HIS cc_start: 0.8338 (m-70) cc_final: 0.7926 (m-70)
REVERT: D  756 MET cc_start: 0.8898 (ttp) cc_final: 0.8605 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1141
  time to fit residues: 59.2193
Evaluate side-chains
  276 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 562 HIS
A 633 ASN
A 714 ASN
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 HIS
** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
A 831 HIS
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 762 HIS
B 810 ASN
B 831 HIS
C 633 ASN
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 739 HIS
C 762 HIS
C 810 ASN
C 831 HIS
D 633 ASN
** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 831 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.150985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.108298 restraints weight = 42573.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.112074 restraints weight = 17892.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.114104 restraints weight = 10659.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.115126 restraints weight = 8135.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.115429 restraints weight = 7196.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  14096  Z= 0.267
  Angle     :  0.784  11.074  19152  Z= 0.405
  Chirality :  0.048   0.212   2176
  Planarity :  0.005   0.048   2376
  Dihedral  :  4.558  20.129   1876
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.14 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.12 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.21), residues: 1684
  helix:  1.20 (0.15), residues: 1068
  sheet: -4.12 (0.45), residues: 68
  loop : -2.50 (0.29), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 531 
 TYR   0.019   0.003   TYR D 673 
 PHE   0.024   0.003   PHE D 498 
 TRP   0.016   0.002   TRP B 497 
 HIS   0.010   0.002   HIS A 674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (14096)
  covalent geometry    : angle       0.78352 (19152)
  hydrogen bonds       : bond        0.05365 (  800)
  hydrogen bonds       : angle       5.48246 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 293
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7584 (ttm170)
REVERT: A  676 GLN cc_start: 0.9367 (mt0) cc_final: 0.8339 (mp10)
REVERT: A  702 GLN cc_start: 0.8852 (pm20) cc_final: 0.8596 (pm20)
REVERT: A  728 ILE cc_start: 0.9348 (tp) cc_final: 0.9042 (tp)
REVERT: A  729 CYS cc_start: 0.9078 (m) cc_final: 0.8720 (p)
REVERT: A  731 HIS cc_start: 0.8351 (m-70) cc_final: 0.7956 (m-70)
REVERT: A  748 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8600 (pttm)
REVERT: A  756 MET cc_start: 0.8928 (ttp) cc_final: 0.8668 (ttp)
REVERT: B  415 LEU cc_start: 0.8461 (tp) cc_final: 0.8232 (mt)
REVERT: B  541 ARG cc_start: 0.7757 (tpt90) cc_final: 0.7390 (tpt90)
REVERT: B  559 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9173 (tp)
REVERT: B  682 GLU cc_start: 0.8621 (pp20) cc_final: 0.8416 (pp20)
REVERT: B  844 MET cc_start: 0.7772 (tmm) cc_final: 0.6909 (tmm)
REVERT: C  541 ARG cc_start: 0.7737 (tpt90) cc_final: 0.7365 (tpt90)
REVERT: C  559 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9155 (tp)
REVERT: C  705 TRP cc_start: 0.8843 (t-100) cc_final: 0.8265 (t-100)
REVERT: C  844 MET cc_start: 0.7794 (tmm) cc_final: 0.6988 (tmm)
REVERT: D  541 ARG cc_start: 0.7792 (tpt90) cc_final: 0.7349 (tpt90)
REVERT: D  559 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9202 (tp)
REVERT: D  698 GLU cc_start: 0.9021 (pp20) cc_final: 0.8673 (pp20)
REVERT: D  729 CYS cc_start: 0.9132 (m) cc_final: 0.8676 (p)
REVERT: D  756 MET cc_start: 0.8889 (ttp) cc_final: 0.8650 (ttp)
REVERT: D  759 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8618 (mmtm)
REVERT: D  853 TRP cc_start: 0.7633 (m100) cc_final: 0.7432 (m100)
  outliers start: 38
  outliers final: 27
  residues processed: 313
  average time/residue: 0.1138
  time to fit residues: 53.5439
Evaluate side-chains
  288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 258
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  646 LEU
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 169 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0170
   chunk 73 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
A 674 HIS
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 762 HIS
B 831 HIS
C 664 GLN
C 762 HIS
C 831 HIS
D 573 ASN
D 592 GLN
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 831 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.152078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.109150 restraints weight = 42240.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.112906 restraints weight = 17875.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.114925 restraints weight = 10709.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.115893 restraints weight = 8253.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.116179 restraints weight = 7383.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14096  Z= 0.196
  Angle     :  0.711  10.479  19152  Z= 0.366
  Chirality :  0.046   0.180   2176
  Planarity :  0.004   0.032   2376
  Dihedral  :  4.429  17.959   1876
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.08 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.35 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.21), residues: 1684
  helix:  1.10 (0.16), residues: 1060
  sheet: -4.14 (0.47), residues: 68
  loop : -2.52 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 531 
 TYR   0.014   0.002   TYR C 673 
 PHE   0.024   0.002   PHE C 498 
 TRP   0.050   0.002   TRP A 705 
 HIS   0.010   0.001   HIS A 674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (14096)
  covalent geometry    : angle       0.71072 (19152)
  hydrogen bonds       : bond        0.05246 (  800)
  hydrogen bonds       : angle       5.21797 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 285
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.6449 (m100) cc_final: 0.5957 (m100)
REVERT: A  534 ARG cc_start: 0.8439 (mtp85) cc_final: 0.7690 (ttm170)
REVERT: A  541 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7554 (tpt90)
REVERT: A  629 ASN cc_start: 0.8402 (t0) cc_final: 0.8175 (t0)
REVERT: A  645 MET cc_start: 0.8696 (mtm) cc_final: 0.8355 (mtm)
REVERT: A  728 ILE cc_start: 0.9312 (tp) cc_final: 0.9035 (tp)
REVERT: A  731 HIS cc_start: 0.8280 (m-70) cc_final: 0.7836 (m-70)
REVERT: A  748 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8561 (pttm)
REVERT: A  759 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8617 (mmtm)
REVERT: A  831 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.7995 (m-70)
REVERT: B  415 LEU cc_start: 0.8427 (tp) cc_final: 0.8215 (mt)
REVERT: B  541 ARG cc_start: 0.7715 (tpt90) cc_final: 0.7367 (tpt90)
REVERT: B  559 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9175 (tp)
REVERT: B  645 MET cc_start: 0.8752 (mtm) cc_final: 0.8540 (mtm)
REVERT: B  729 CYS cc_start: 0.9133 (m) cc_final: 0.8773 (p)
REVERT: B  831 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7906 (m90)
REVERT: C  541 ARG cc_start: 0.7748 (tpt90) cc_final: 0.7400 (tpt90)
REVERT: C  559 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9152 (tp)
REVERT: C  645 MET cc_start: 0.8774 (mtm) cc_final: 0.8525 (mtm)
REVERT: C  729 CYS cc_start: 0.9157 (m) cc_final: 0.8763 (p)
REVERT: C  831 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8034 (m90)
REVERT: D  541 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7366 (tpt90)
REVERT: D  559 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9192 (tp)
REVERT: D  645 MET cc_start: 0.8693 (mtm) cc_final: 0.8429 (mtm)
REVERT: D  729 CYS cc_start: 0.9080 (m) cc_final: 0.8510 (p)
REVERT: D  748 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8557 (pttm)
REVERT: D  756 MET cc_start: 0.8887 (ttp) cc_final: 0.8598 (ttp)
REVERT: D  759 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8596 (mmtm)
REVERT: D  831 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8011 (m90)
  outliers start: 50
  outliers final: 35
  residues processed: 305
  average time/residue: 0.1134
  time to fit residues: 51.5011
Evaluate side-chains
  305 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  651 MET
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  777 THR
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain D residue  492 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  777 THR
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 136 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 150 optimal weight:    0.8980
   chunk 168 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 170 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 HIS
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 762 HIS
B 831 HIS
C 762 HIS
C 831 HIS
D 664 GLN
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.160290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113145 restraints weight = 42633.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.117163 restraints weight = 17671.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.119321 restraints weight = 10554.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.120189 restraints weight = 8102.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.120472 restraints weight = 7294.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14096  Z= 0.158
  Angle     :  0.685   9.363  19152  Z= 0.347
  Chirality :  0.045   0.171   2176
  Planarity :  0.004   0.052   2376
  Dihedral  :  4.381  18.748   1876
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.90 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.09 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.21), residues: 1684
  helix:  1.23 (0.16), residues: 1072
  sheet: -4.37 (0.41), residues: 44
  loop : -2.74 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 531 
 TYR   0.020   0.002   TYR D 700 
 PHE   0.022   0.002   PHE B 758 
 TRP   0.032   0.002   TRP A 705 
 HIS   0.006   0.001   HIS D 674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14096)
  covalent geometry    : angle       0.68460 (19152)
  hydrogen bonds       : bond        0.05062 (  800)
  hydrogen bonds       : angle       4.98920 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 282
  time to evaluate  : 0.568 
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  412 TRP cc_start: 0.6588 (m100) cc_final: 0.6127 (m100)
REVERT: A  534 ARG cc_start: 0.8410 (mtp85) cc_final: 0.7940 (ttm-80)
REVERT: A  541 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7536 (tpt90)
REVERT: A  645 MET cc_start: 0.8735 (mtm) cc_final: 0.8358 (mtm)
REVERT: A  729 CYS cc_start: 0.9176 (m) cc_final: 0.8671 (p)
REVERT: A  748 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8567 (pttm)
REVERT: A  756 MET cc_start: 0.8635 (ttp) cc_final: 0.8435 (ptm)
REVERT: A  759 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8721 (mmtm)
REVERT: A  823 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7849 (mmt-90)
REVERT: A  831 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8151 (m90)
REVERT: B  541 ARG cc_start: 0.7725 (tpt90) cc_final: 0.7365 (tpt90)
REVERT: B  729 CYS cc_start: 0.9191 (m) cc_final: 0.8758 (p)
REVERT: B  759 LYS cc_start: 0.9136 (mptt) cc_final: 0.8777 (mmtm)
REVERT: B  831 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7852 (m-70)
REVERT: C  541 ARG cc_start: 0.7717 (tpt90) cc_final: 0.7368 (tpt90)
REVERT: C  559 LEU cc_start: 0.9402 (mm) cc_final: 0.9163 (tp)
REVERT: C  729 CYS cc_start: 0.9207 (m) cc_final: 0.8759 (p)
REVERT: C  759 LYS cc_start: 0.9194 (mptt) cc_final: 0.8855 (mmtm)
REVERT: C  831 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8031 (m90)
REVERT: D  541 ARG cc_start: 0.7759 (tpt90) cc_final: 0.7363 (tpt90)
REVERT: D  559 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9168 (tp)
REVERT: D  645 MET cc_start: 0.8736 (mtm) cc_final: 0.8396 (mtm)
REVERT: D  705 TRP cc_start: 0.8688 (t-100) cc_final: 0.8217 (t-100)
REVERT: D  729 CYS cc_start: 0.9100 (m) cc_final: 0.8466 (p)
REVERT: D  748 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8508 (pttm)
REVERT: D  756 MET cc_start: 0.8874 (ttp) cc_final: 0.8619 (ttp)
REVERT: D  758 PHE cc_start: 0.8028 (m-80) cc_final: 0.7633 (m-80)
REVERT: D  759 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8877 (mmtt)
REVERT: D  831 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8134 (m-70)
REVERT: D  857 GLU cc_start: 0.8284 (mp0) cc_final: 0.7637 (pm20)
  outliers start: 47
  outliers final: 29
  residues processed: 303
  average time/residue: 0.1174
  time to fit residues: 53.0503
Evaluate side-chains
  296 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 262
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  664 GLN
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 131 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 160 optimal weight:    0.9990
   chunk 140 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9990
   chunk 161 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 674 HIS
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 HIS
B 762 HIS
B 831 HIS
C 762 HIS
C 831 HIS
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 834 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.151992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.108737 restraints weight = 43535.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.112616 restraints weight = 17671.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.114724 restraints weight = 10457.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.115790 restraints weight = 8054.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.116078 restraints weight = 7175.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14096  Z= 0.190
  Angle     :  0.708  11.370  19152  Z= 0.356
  Chirality :  0.045   0.169   2176
  Planarity :  0.004   0.035   2376
  Dihedral  :  4.387  19.339   1876
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.78 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.91 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.21), residues: 1684
  helix:  1.18 (0.16), residues: 1076
  sheet: -4.61 (0.38), residues: 44
  loop : -2.48 (0.28), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 531 
 TYR   0.015   0.002   TYR D 673 
 PHE   0.017   0.002   PHE C 758 
 TRP   0.026   0.002   TRP A 705 
 HIS   0.005   0.001   HIS A 674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (14096)
  covalent geometry    : angle       0.70753 (19152)
  hydrogen bonds       : bond        0.05053 (  800)
  hydrogen bonds       : angle       5.01547 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 267
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 TRP cc_start: 0.6619 (m100) cc_final: 0.6098 (m100)
REVERT: A  534 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8170 (ttm-80)
REVERT: A  541 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7622 (tpt90)
REVERT: A  676 GLN cc_start: 0.9283 (mt0) cc_final: 0.8938 (mp10)
REVERT: A  698 GLU cc_start: 0.9020 (pp20) cc_final: 0.8667 (pp20)
REVERT: A  729 CYS cc_start: 0.9126 (m) cc_final: 0.8736 (p)
REVERT: A  748 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8583 (pttm)
REVERT: A  756 MET cc_start: 0.8835 (ttp) cc_final: 0.8591 (ptm)
REVERT: A  759 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8813 (mmtm)
REVERT: B  415 LEU cc_start: 0.8331 (mt) cc_final: 0.8068 (mm)
REVERT: B  541 ARG cc_start: 0.7706 (tpt90) cc_final: 0.7365 (tpt90)
REVERT: B  645 MET cc_start: 0.8438 (mtp) cc_final: 0.8083 (mtm)
REVERT: B  729 CYS cc_start: 0.9135 (m) cc_final: 0.8742 (p)
REVERT: C  410 TRP cc_start: 0.6984 (t-100) cc_final: 0.6712 (t-100)
REVERT: C  541 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7368 (tpt90)
REVERT: C  629 ASN cc_start: 0.8391 (t0) cc_final: 0.8115 (t0)
REVERT: C  729 CYS cc_start: 0.9123 (m) cc_final: 0.8764 (p)
REVERT: D  541 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7390 (tpt90)
REVERT: D  559 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9204 (tp)
REVERT: D  705 TRP cc_start: 0.8624 (t-100) cc_final: 0.8239 (t-100)
REVERT: D  729 CYS cc_start: 0.9038 (m) cc_final: 0.8495 (p)
REVERT: D  748 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8568 (pttm)
REVERT: D  758 PHE cc_start: 0.7967 (m-80) cc_final: 0.7541 (m-80)
REVERT: D  823 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7886 (mmt-90)
REVERT: D  831 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8281 (m-70)
REVERT: D  834 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8084 (t70)
  outliers start: 55
  outliers final: 41
  residues processed: 296
  average time/residue: 0.1174
  time to fit residues: 51.6907
Evaluate side-chains
  299 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 254
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  759 LYS
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  634 THR
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  777 THR
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain C residue  845 TYR
Chi-restraints excluded: chain D residue  492 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  556 THR
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  777 THR
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 163 optimal weight:    5.9990
   chunk 81 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 82 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 HIS
B 664 GLN
B 762 HIS
B 810 ASN
** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 834 HIS
C 762 HIS
C 831 HIS
C 834 HIS
D 664 GLN
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 834 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.150513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.107252 restraints weight = 43281.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.111082 restraints weight = 17387.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.113149 restraints weight = 10351.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.114137 restraints weight = 8032.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.114412 restraints weight = 7216.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  14096  Z= 0.224
  Angle     :  0.750  13.665  19152  Z= 0.377
  Chirality :  0.046   0.170   2176
  Planarity :  0.004   0.035   2376
  Dihedral  :  4.433  19.134   1876
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.43 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.28 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.21), residues: 1684
  helix:  1.07 (0.16), residues: 1080
  sheet: -4.68 (0.39), residues: 44
  loop : -2.63 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 531 
 TYR   0.022   0.002   TYR D 700 
 PHE   0.021   0.002   PHE B 758 
 TRP   0.024   0.002   TRP A 705 
 HIS   0.013   0.001   HIS D 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (14096)
  covalent geometry    : angle       0.75009 (19152)
  hydrogen bonds       : bond        0.05211 (  800)
  hydrogen bonds       : angle       5.07239 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 268
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  459 VAL cc_start: 0.8254 (t) cc_final: 0.8008 (t)
REVERT: A  534 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8204 (ttm-80)
REVERT: A  651 MET cc_start: 0.8191 (ttt) cc_final: 0.7752 (ttt)
REVERT: A  676 GLN cc_start: 0.9306 (mt0) cc_final: 0.8925 (mp10)
REVERT: A  729 CYS cc_start: 0.9182 (m) cc_final: 0.8813 (p)
REVERT: A  748 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8562 (pttm)
REVERT: A  756 MET cc_start: 0.8889 (ttp) cc_final: 0.8658 (ptm)
REVERT: B  410 TRP cc_start: 0.7149 (t-100) cc_final: 0.6914 (t-100)
REVERT: B  415 LEU cc_start: 0.8323 (mt) cc_final: 0.8058 (mt)
REVERT: B  541 ARG cc_start: 0.7730 (tpt90) cc_final: 0.7384 (tpt90)
REVERT: B  645 MET cc_start: 0.8560 (mtp) cc_final: 0.8248 (mtm)
REVERT: B  759 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8764 (mmtm)
REVERT: B  834 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8341 (t70)
REVERT: C  410 TRP cc_start: 0.7014 (t-100) cc_final: 0.6764 (t-100)
REVERT: C  541 ARG cc_start: 0.7697 (tpt90) cc_final: 0.7336 (tpt90)
REVERT: C  645 MET cc_start: 0.8449 (mtp) cc_final: 0.8064 (mtm)
REVERT: C  651 MET cc_start: 0.8208 (ttt) cc_final: 0.7569 (ttt)
REVERT: C  729 CYS cc_start: 0.9132 (m) cc_final: 0.8781 (p)
REVERT: C  756 MET cc_start: 0.9079 (ptt) cc_final: 0.8681 (ptp)
REVERT: C  759 LYS cc_start: 0.9238 (mptt) cc_final: 0.9008 (mmtm)
REVERT: D  410 TRP cc_start: 0.7125 (t-100) cc_final: 0.6902 (t-100)
REVERT: D  541 ARG cc_start: 0.7787 (tpt90) cc_final: 0.7423 (tpt90)
REVERT: D  559 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9223 (tp)
REVERT: D  705 TRP cc_start: 0.8639 (t-100) cc_final: 0.8239 (t-100)
REVERT: D  748 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8566 (pttm)
REVERT: D  758 PHE cc_start: 0.8137 (m-80) cc_final: 0.7587 (m-80)
REVERT: D  759 LYS cc_start: 0.9328 (mptt) cc_final: 0.8959 (mmtm)
REVERT: D  831 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8271 (m-70)
REVERT: D  834 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8244 (t70)
  outliers start: 57
  outliers final: 44
  residues processed: 297
  average time/residue: 0.1127
  time to fit residues: 50.3390
Evaluate side-chains
  297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 249
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  709 ASN
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  556 THR
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  834 HIS
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  634 THR
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  777 THR
Chi-restraints excluded: chain C residue  782 ILE
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  834 HIS
Chi-restraints excluded: chain C residue  845 TYR
Chi-restraints excluded: chain D residue  492 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  556 THR
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  664 GLN
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  777 THR
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 135 optimal weight:   20.0000
   chunk 167 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 676 GLN
A 702 GLN
** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS
C 834 HIS
D 592 GLN
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 834 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.160777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.114576 restraints weight = 42581.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.118605 restraints weight = 17480.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.120779 restraints weight = 10453.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.121857 restraints weight = 8010.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.122153 restraints weight = 7122.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14096  Z= 0.150
  Angle     :  0.744  15.791  19152  Z= 0.367
  Chirality :  0.045   0.194   2176
  Planarity :  0.004   0.062   2376
  Dihedral  :  4.388  19.983   1876
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.30 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.27 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.21), residues: 1684
  helix:  1.18 (0.16), residues: 1080
  sheet: -4.47 (0.42), residues: 44
  loop : -2.59 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 665 
 TYR   0.024   0.002   TYR A 700 
 PHE   0.021   0.002   PHE C 781 
 TRP   0.018   0.002   TRP A 705 
 HIS   0.009   0.001   HIS D 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14096)
  covalent geometry    : angle       0.74361 (19152)
  hydrogen bonds       : bond        0.05099 (  800)
  hydrogen bonds       : angle       4.82431 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 275
  time to evaluate  : 0.547 
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: A  534 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8217 (ttm-80)
REVERT: A  676 GLN cc_start: 0.9318 (mt0) cc_final: 0.8904 (mp10)
REVERT: A  702 GLN cc_start: 0.9373 (mm110) cc_final: 0.9101 (pp30)
REVERT: A  729 CYS cc_start: 0.9192 (m) cc_final: 0.8790 (p)
REVERT: A  748 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8502 (pttp)
REVERT: A  756 MET cc_start: 0.8841 (ttp) cc_final: 0.8588 (ptm)
REVERT: A  758 PHE cc_start: 0.7791 (m-80) cc_final: 0.7526 (m-10)
REVERT: B  410 TRP cc_start: 0.7095 (t-100) cc_final: 0.6832 (t-100)
REVERT: B  415 LEU cc_start: 0.8292 (mt) cc_final: 0.8023 (mt)
REVERT: B  541 ARG cc_start: 0.7740 (tpt90) cc_final: 0.7388 (tpt90)
REVERT: B  645 MET cc_start: 0.8441 (mtp) cc_final: 0.8124 (mtm)
REVERT: B  677 MET cc_start: 0.8746 (tmm) cc_final: 0.8456 (tmm)
REVERT: B  705 TRP cc_start: 0.8570 (t-100) cc_final: 0.8226 (t-100)
REVERT: B  729 CYS cc_start: 0.9243 (m) cc_final: 0.8771 (p)
REVERT: B  759 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8748 (mmtm)
REVERT: C  410 TRP cc_start: 0.6955 (t-100) cc_final: 0.6676 (t-100)
REVERT: C  541 ARG cc_start: 0.7703 (tpt90) cc_final: 0.7351 (tpt90)
REVERT: C  645 MET cc_start: 0.8362 (mtp) cc_final: 0.7996 (mtm)
REVERT: C  677 MET cc_start: 0.8737 (tmm) cc_final: 0.8433 (tmm)
REVERT: C  729 CYS cc_start: 0.9166 (m) cc_final: 0.8758 (p)
REVERT: C  756 MET cc_start: 0.9020 (ptt) cc_final: 0.8622 (ptp)
REVERT: C  759 LYS cc_start: 0.9285 (mptt) cc_final: 0.9058 (mmtm)
REVERT: C  844 MET cc_start: 0.7940 (tmm) cc_final: 0.7603 (ppp)
REVERT: D  410 TRP cc_start: 0.7047 (t-100) cc_final: 0.6802 (t-100)
REVERT: D  541 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7390 (tpt90)
REVERT: D  645 MET cc_start: 0.8289 (mtp) cc_final: 0.7957 (mtm)
REVERT: D  705 TRP cc_start: 0.8556 (t-100) cc_final: 0.8171 (t-100)
REVERT: D  729 CYS cc_start: 0.9130 (m) cc_final: 0.8614 (p)
REVERT: D  735 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6110 (t)
REVERT: D  756 MET cc_start: 0.8967 (ptm) cc_final: 0.8615 (ptt)
REVERT: D  758 PHE cc_start: 0.8182 (m-80) cc_final: 0.7875 (m-80)
REVERT: D  759 LYS cc_start: 0.9393 (mptt) cc_final: 0.9061 (mmtm)
REVERT: D  831 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8416 (m-70)
REVERT: D  834 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8369 (t70)
REVERT: D  857 GLU cc_start: 0.8239 (mp0) cc_final: 0.7795 (pm20)
  outliers start: 52
  outliers final: 38
  residues processed: 301
  average time/residue: 0.1161
  time to fit residues: 52.1973
Evaluate side-chains
  292 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 251
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  556 THR
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  634 THR
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  782 ILE
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain C residue  834 HIS
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  831 HIS
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 129 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 154 optimal weight:    0.0870
   chunk 136 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 762 HIS
B 831 HIS
B 834 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS
C 834 HIS
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 810 ASN
D 834 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.160928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.115510 restraints weight = 41945.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.119515 restraints weight = 17296.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.121657 restraints weight = 10302.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.122711 restraints weight = 7880.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.123040 restraints weight = 6974.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  14096  Z= 0.156
  Angle     :  0.749  15.986  19152  Z= 0.368
  Chirality :  0.046   0.238   2176
  Planarity :  0.004   0.094   2376
  Dihedral  :  4.317  20.602   1876
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.60 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 25.48 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.21), residues: 1684
  helix:  1.25 (0.16), residues: 1076
  sheet: -4.23 (0.48), residues: 44
  loop : -2.57 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 541 
 TYR   0.030   0.002   TYR B 700 
 PHE   0.035   0.002   PHE B 758 
 TRP   0.017   0.001   TRP A 705 
 HIS   0.013   0.001   HIS D 687 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (14096)
  covalent geometry    : angle       0.74888 (19152)
  hydrogen bonds       : bond        0.04981 (  800)
  hydrogen bonds       : angle       4.77172 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 264
  time to evaluate  : 0.597 
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: A  412 TRP cc_start: 0.6273 (m100) cc_final: 0.5767 (m100)
REVERT: A  534 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8253 (ttm-80)
REVERT: A  541 ARG cc_start: 0.7832 (tpt90) cc_final: 0.7592 (tmt-80)
REVERT: A  676 GLN cc_start: 0.9419 (mt0) cc_final: 0.9068 (mp10)
REVERT: A  687 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8462 (m170)
REVERT: A  702 GLN cc_start: 0.9352 (mm110) cc_final: 0.9074 (pp30)
REVERT: A  705 TRP cc_start: 0.8659 (t-100) cc_final: 0.8061 (t-100)
REVERT: A  729 CYS cc_start: 0.9211 (m) cc_final: 0.8818 (p)
REVERT: A  748 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8498 (pttp)
REVERT: A  756 MET cc_start: 0.8853 (ttp) cc_final: 0.8601 (ptm)
REVERT: A  758 PHE cc_start: 0.7768 (m-80) cc_final: 0.7510 (m-10)
REVERT: B  410 TRP cc_start: 0.7134 (t-100) cc_final: 0.6863 (t-100)
REVERT: B  415 LEU cc_start: 0.8288 (mt) cc_final: 0.8017 (mt)
REVERT: B  541 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7363 (tpt90)
REVERT: B  645 MET cc_start: 0.8445 (mtp) cc_final: 0.8111 (mtm)
REVERT: B  677 MET cc_start: 0.8726 (tmm) cc_final: 0.8433 (tmm)
REVERT: B  687 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8472 (m170)
REVERT: B  705 TRP cc_start: 0.8557 (t-100) cc_final: 0.8246 (t-100)
REVERT: B  729 CYS cc_start: 0.9304 (m) cc_final: 0.8827 (p)
REVERT: B  759 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8725 (mmtm)
REVERT: B  834 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.8489 (t70)
REVERT: C  410 TRP cc_start: 0.7072 (t-100) cc_final: 0.6798 (t-100)
REVERT: C  541 ARG cc_start: 0.7706 (tpt90) cc_final: 0.7347 (tpt90)
REVERT: C  645 MET cc_start: 0.8422 (mtp) cc_final: 0.8103 (mtm)
REVERT: C  729 CYS cc_start: 0.9166 (m) cc_final: 0.8766 (p)
REVERT: C  756 MET cc_start: 0.9009 (ptt) cc_final: 0.8612 (ptp)
REVERT: C  759 LYS cc_start: 0.9262 (mptt) cc_final: 0.9051 (mmtm)
REVERT: D  410 TRP cc_start: 0.6982 (t-100) cc_final: 0.6744 (t-100)
REVERT: D  541 ARG cc_start: 0.7784 (tpt90) cc_final: 0.7380 (tpt90)
REVERT: D  645 MET cc_start: 0.8312 (mtp) cc_final: 0.7960 (mtm)
REVERT: D  705 TRP cc_start: 0.8526 (t-100) cc_final: 0.8184 (t-100)
REVERT: D  729 CYS cc_start: 0.9226 (m) cc_final: 0.8786 (p)
REVERT: D  735 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.6342 (t)
REVERT: D  748 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8538 (pttm)
REVERT: D  756 MET cc_start: 0.9007 (ptm) cc_final: 0.8580 (ptt)
REVERT: D  758 PHE cc_start: 0.8198 (m-80) cc_final: 0.7858 (m-80)
REVERT: D  759 LYS cc_start: 0.9414 (mptt) cc_final: 0.9078 (mmtm)
REVERT: D  834 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8447 (t70)
REVERT: D  857 GLU cc_start: 0.8223 (mp0) cc_final: 0.7776 (pm20)
  outliers start: 50
  outliers final: 39
  residues processed: 293
  average time/residue: 0.1111
  time to fit residues: 49.3650
Evaluate side-chains
  297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 253
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  687 HIS
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  492 HIS
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  687 HIS
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain B residue  834 HIS
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  492 HIS
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  634 THR
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  782 ILE
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain C residue  834 HIS
Chi-restraints excluded: chain D residue  555 CYS
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0020
   chunk 41 optimal weight:    1.9990
   chunk 156 optimal weight:    0.8980
   chunk 134 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 171 optimal weight:    7.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 688 GLN
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 688 GLN
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 831 HIS
B 834 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS
C 834 HIS
** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 834 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.162185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.115498 restraints weight = 42520.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.119602 restraints weight = 17506.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.121842 restraints weight = 10468.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.122922 restraints weight = 8013.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.123293 restraints weight = 7113.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14096  Z= 0.147
  Angle     :  0.756  15.168  19152  Z= 0.370
  Chirality :  0.046   0.246   2176
  Planarity :  0.004   0.049   2376
  Dihedral  :  4.319  22.944   1876
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.42 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.82 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.21), residues: 1684
  helix:  1.31 (0.16), residues: 1072
  sheet: -3.99 (0.51), residues: 44
  loop : -2.55 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 835 
 TYR   0.030   0.002   TYR C 700 
 PHE   0.039   0.002   PHE C 758 
 TRP   0.014   0.001   TRP D 563 
 HIS   0.009   0.001   HIS D 687 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (14096)
  covalent geometry    : angle       0.75630 (19152)
  hydrogen bonds       : bond        0.04892 (  800)
  hydrogen bonds       : angle       4.69494 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 268
  time to evaluate  : 0.713 
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: A  412 TRP cc_start: 0.6231 (m100) cc_final: 0.5660 (m100)
REVERT: A  534 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8227 (ttm-80)
REVERT: A  676 GLN cc_start: 0.9422 (mt0) cc_final: 0.8716 (mp10)
REVERT: A  677 MET cc_start: 0.8689 (tmm) cc_final: 0.8268 (tmm)
REVERT: A  687 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (m170)
REVERT: A  702 GLN cc_start: 0.9369 (mm110) cc_final: 0.9075 (pp30)
REVERT: A  729 CYS cc_start: 0.9204 (m) cc_final: 0.8768 (p)
REVERT: A  748 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8491 (pttp)
REVERT: A  756 MET cc_start: 0.8841 (ttp) cc_final: 0.8586 (ptm)
REVERT: A  758 PHE cc_start: 0.7807 (m-10) cc_final: 0.7309 (m-80)
REVERT: B  410 TRP cc_start: 0.7075 (t-100) cc_final: 0.6796 (t-100)
REVERT: B  415 LEU cc_start: 0.8270 (mt) cc_final: 0.8004 (mt)
REVERT: B  541 ARG cc_start: 0.7683 (tpt90) cc_final: 0.7328 (tpt90)
REVERT: B  645 MET cc_start: 0.8419 (mtp) cc_final: 0.8102 (mtm)
REVERT: B  677 MET cc_start: 0.8705 (tmm) cc_final: 0.8414 (tmm)
REVERT: B  687 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8495 (m170)
REVERT: B  705 TRP cc_start: 0.8599 (t-100) cc_final: 0.8308 (t-100)
REVERT: B  729 CYS cc_start: 0.9348 (m) cc_final: 0.8854 (p)
REVERT: B  759 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8757 (mmtm)
REVERT: B  834 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8559 (t70)
REVERT: C  410 TRP cc_start: 0.7028 (t-100) cc_final: 0.6737 (t-100)
REVERT: C  541 ARG cc_start: 0.7712 (tpt90) cc_final: 0.7353 (tpt90)
REVERT: C  645 MET cc_start: 0.8373 (mtp) cc_final: 0.8062 (mtm)
REVERT: C  677 MET cc_start: 0.8744 (tmm) cc_final: 0.8422 (tmm)
REVERT: C  705 TRP cc_start: 0.8570 (t-100) cc_final: 0.8247 (t-100)
REVERT: C  729 CYS cc_start: 0.9180 (m) cc_final: 0.8781 (p)
REVERT: C  756 MET cc_start: 0.9004 (ptt) cc_final: 0.8585 (ptp)
REVERT: C  759 LYS cc_start: 0.9270 (mptt) cc_final: 0.9061 (mmtm)
REVERT: C  834 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8607 (t70)
REVERT: D  410 TRP cc_start: 0.6890 (t-100) cc_final: 0.6631 (t-100)
REVERT: D  541 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7386 (tpt90)
REVERT: D  645 MET cc_start: 0.8284 (mtp) cc_final: 0.7965 (mtm)
REVERT: D  703 HIS cc_start: 0.8865 (t-170) cc_final: 0.8446 (t70)
REVERT: D  729 CYS cc_start: 0.9265 (m) cc_final: 0.8890 (p)
REVERT: D  735 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.6721 (p)
REVERT: D  748 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8547 (pttm)
REVERT: D  756 MET cc_start: 0.9005 (ptm) cc_final: 0.8605 (ptt)
REVERT: D  759 LYS cc_start: 0.9363 (mptt) cc_final: 0.9121 (mmtm)
REVERT: D  834 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8607 (t70)
REVERT: D  857 GLU cc_start: 0.8235 (mp0) cc_final: 0.7783 (pm20)
  outliers start: 42
  outliers final: 34
  residues processed: 293
  average time/residue: 0.1134
  time to fit residues: 50.4448
Evaluate side-chains
  297 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 257
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 HIS
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Chi-restraints excluded: chain A residue  687 HIS
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  492 HIS
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  687 HIS
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  831 HIS
Chi-restraints excluded: chain B residue  834 HIS
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  492 HIS
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  634 THR
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  782 ILE
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain C residue  834 HIS
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  647 ILE
Chi-restraints excluded: chain D residue  676 GLN
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 137 optimal weight:    0.9980
   chunk 149 optimal weight:    0.9990
   chunk 134 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 145 optimal weight:    0.1980
   chunk 105 optimal weight:    0.0370
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
A 676 GLN
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 762 HIS
** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 834 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 688 GLN
** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS
C 834 HIS
D 688 GLN
** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.162962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.114872 restraints weight = 42309.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.119053 restraints weight = 17463.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.121303 restraints weight = 10463.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.122426 restraints weight = 8055.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.122779 restraints weight = 7177.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14096  Z= 0.149
  Angle     :  0.764  15.787  19152  Z= 0.375
  Chirality :  0.047   0.254   2176
  Planarity :  0.004   0.034   2376
  Dihedral  :  4.365  25.537   1876
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.48 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 26.92 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.21), residues: 1684
  helix:  1.30 (0.16), residues: 1072
  sheet: -3.87 (0.54), residues: 44
  loop : -2.53 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 823 
 TYR   0.032   0.002   TYR D 700 
 PHE   0.026   0.002   PHE B 758 
 TRP   0.086   0.003   TRP D 705 
 HIS   0.022   0.002   HIS C 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (14096)
  covalent geometry    : angle       0.76425 (19152)
  hydrogen bonds       : bond        0.04753 (  800)
  hydrogen bonds       : angle       4.69094 ( 2352)

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

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

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3368 Ramachandran restraints generated.
    1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 266
  time to evaluate  : 0.582 
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  412 TRP cc_start: 0.6445 (m100) cc_final: 0.5931 (m100)
REVERT: A  534 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8197 (ttm-80)
REVERT: A  541 ARG cc_start: 0.7860 (tmt170) cc_final: 0.7524 (tmt170)
REVERT: A  687 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8431 (m170)
REVERT: A  702 GLN cc_start: 0.9366 (mm110) cc_final: 0.9014 (pp30)
REVERT: A  729 CYS cc_start: 0.9247 (m) cc_final: 0.8792 (p)
REVERT: A  748 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8453 (pttm)
REVERT: A  756 MET cc_start: 0.8842 (ttp) cc_final: 0.8583 (ptm)
REVERT: A  758 PHE cc_start: 0.7805 (m-10) cc_final: 0.7308 (m-80)
REVERT: B  410 TRP cc_start: 0.7038 (t-100) cc_final: 0.6771 (t-100)
REVERT: B  415 LEU cc_start: 0.8251 (mt) cc_final: 0.7990 (mt)
REVERT: B  541 ARG cc_start: 0.7724 (tpt90) cc_final: 0.7352 (tpt90)
REVERT: B  645 MET cc_start: 0.8425 (mtp) cc_final: 0.8096 (mtm)
REVERT: B  687 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (m170)
REVERT: B  705 TRP cc_start: 0.8622 (t-100) cc_final: 0.8334 (t-100)
REVERT: B  729 CYS cc_start: 0.9379 (m) cc_final: 0.8940 (p)
REVERT: B  759 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8759 (mmtm)
REVERT: B  838 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8575 (mm)
REVERT: C  410 TRP cc_start: 0.7056 (t-100) cc_final: 0.6801 (t-100)
REVERT: C  541 ARG cc_start: 0.7744 (tpt90) cc_final: 0.7360 (tpt90)
REVERT: C  645 MET cc_start: 0.8321 (mtp) cc_final: 0.8007 (mtm)
REVERT: C  677 MET cc_start: 0.8752 (tmm) cc_final: 0.8403 (tmm)
REVERT: C  705 TRP cc_start: 0.8586 (t-100) cc_final: 0.8269 (t-100)
REVERT: C  729 CYS cc_start: 0.9220 (m) cc_final: 0.8797 (p)
REVERT: C  735 SER cc_start: 0.7260 (OUTLIER) cc_final: 0.6214 (t)
REVERT: C  756 MET cc_start: 0.8947 (ptt) cc_final: 0.8457 (ptt)
REVERT: C  759 LYS cc_start: 0.9266 (mptt) cc_final: 0.9066 (mmtm)
REVERT: C  834 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8627 (t70)
REVERT: D  410 TRP cc_start: 0.6817 (t-100) cc_final: 0.6559 (t-100)
REVERT: D  541 ARG cc_start: 0.7805 (tpt90) cc_final: 0.7389 (tpt90)
REVERT: D  645 MET cc_start: 0.8239 (mtp) cc_final: 0.7915 (mtm)
REVERT: D  699 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8037 (tm-30)
REVERT: D  729 CYS cc_start: 0.9334 (m) cc_final: 0.8868 (p)
REVERT: D  735 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.6672 (p)
REVERT: D  748 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8550 (pttm)
REVERT: D  756 MET cc_start: 0.8903 (ptm) cc_final: 0.8514 (ptt)
REVERT: D  834 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8552 (t-90)
REVERT: D  857 GLU cc_start: 0.8245 (mp0) cc_final: 0.7821 (pm20)
  outliers start: 34
  outliers final: 24
  residues processed: 287
  average time/residue: 0.1146
  time to fit residues: 49.2637
Evaluate side-chains
  290 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 259
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  687 HIS
Chi-restraints excluded: chain A residue  735 SER
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue  831 HIS
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  619 PHE
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  687 HIS
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  830 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  845 TYR
Chi-restraints excluded: chain C residue  492 HIS
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  619 PHE
Chi-restraints excluded: chain C residue  647 ILE
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  735 SER
Chi-restraints excluded: chain C residue  782 ILE
Chi-restraints excluded: chain C residue  830 LEU
Chi-restraints excluded: chain C residue  831 HIS
Chi-restraints excluded: chain C residue  834 HIS
Chi-restraints excluded: chain D residue  619 PHE
Chi-restraints excluded: chain D residue  634 THR
Chi-restraints excluded: chain D residue  735 SER
Chi-restraints excluded: chain D residue  830 LEU
Chi-restraints excluded: chain D residue  834 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 155 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0770
   chunk 131 optimal weight:    2.9990
   chunk 145 optimal weight:    0.5980
   chunk 151 optimal weight:    3.9990
   chunk 135 optimal weight:    0.1980
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 160 optimal weight:    0.9990
   overall best weight:    0.7742

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

Flipped N/Q/H residues before XYZ refinement:
** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 831 HIS
C 687 HIS
** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS
C 834 HIS
** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 834 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.154317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.120679 restraints weight = 42888.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.119644 restraints weight = 16987.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.119516 restraints weight = 14160.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.119722 restraints weight = 11771.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.119934 restraints weight = 10825.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14096  Z= 0.147
  Angle     :  0.760  14.330  19152  Z= 0.376
  Chirality :  0.046   0.245   2176
  Planarity :  0.004   0.027   2376
  Dihedral  :  4.337  27.781   1876
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.42 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 26.99 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.22), residues: 1684
  helix:  1.32 (0.16), residues: 1072
  sheet: -3.75 (0.55), residues: 44
  loop : -2.48 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 823 
 TYR   0.024   0.002   TYR C 700 
 PHE   0.029   0.002   PHE C 758 
 TRP   0.071   0.002   TRP D 705 
 HIS   0.012   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (14096)
  covalent geometry    : angle       0.76047 (19152)
  hydrogen bonds       : bond        0.04645 (  800)
  hydrogen bonds       : angle       4.67290 ( 2352)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3725.02 seconds
wall clock time: 64 minutes 56.59 seconds (3896.59 seconds total)