Starting phenix.real_space_refine
on Wed Nov 19 06:11:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wta_32773/11_2025/7wta_32773.cif"
  }
  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=   0.001
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     148      5.16       5
     C   13396      2.51       5
     N    3616      2.21       5
     O    3920      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21080
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 5255
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 45, 'TRANS': 638}
    Chain: "B"
      Number of atoms: 5255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 5255
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 45, 'TRANS': 638}
    Chain: "C"
      Number of atoms: 5255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 5255
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 45, 'TRANS': 638}
    Chain: "D"
      Number of atoms: 5255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 5255
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 45, 'TRANS': 638}
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.52, per 1000 atoms: 0.26
  Number of scatterers: 21080
  At special positions: 0
  Unit cell: (161.7, 147.4, 127.6, 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     148     16.00
     O    3920      8.00
     N    3616      7.00
     C   13396      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 752 " - pdb=" SG  CYS A 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 752 " - pdb=" SG  CYS B 786 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 752 " - pdb=" SG  CYS C 786 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 752 " - pdb=" SG  CYS D 786 " distance=2.02

  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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 935.1 milliseconds
  

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5032

  Finding SS restraints...
    Secondary structure from input PDB file:
      114 helices and 16 sheets defined
      47.1% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 496 through 511
    Processing helix  chain 'A' and resid 540 through 560
      removed outlier: 4.208A  pdb=" N   ILE A 544 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      Proline residue:  A 550  - end of helix
    Processing helix  chain 'A' and resid 568 through 577
      removed outlier: 3.511A  pdb=" N   ALA A 573 " --> pdb=" O   THR A 569 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   HIS A 574 " --> pdb=" O   PHE A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 598
      removed outlier: 4.172A  pdb=" N   LEU A 587 " --> pdb=" O   ARG A 583 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS A 589 " --> pdb=" O   HIS A 585 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ILE A 590 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      Proline residue:  A 592  - end of helix
    Processing helix  chain 'A' and resid 608 through 618
      removed outlier: 3.728A  pdb=" N   ASP A 613 " --> pdb=" O   GLY A 609 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL A 614 " --> pdb=" O   ALA A 610 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A 616 " --> pdb=" O   PHE A 612 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 618 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 634
      removed outlier: 3.605A  pdb=" N   GLU A 632 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 670
      removed outlier: 3.711A  pdb=" N   VAL A 659 " --> pdb=" O   PRO A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 697
    Processing helix  chain 'A' and resid 719 through 734
    Processing helix  chain 'A' and resid 748 through 761
    Processing helix  chain 'A' and resid 778 through 789
      removed outlier: 3.535A  pdb=" N   ALA A 782 " --> pdb=" O   ALA A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 817
    Processing helix  chain 'A' and resid 828 through 843
    Processing helix  chain 'A' and resid 844 through 846
      No H-bonds generated for 'chain 'A' and resid 844 through 846'
    Processing helix  chain 'A' and resid 849 through 853
      removed outlier: 3.829A  pdb=" N   ALA A 852 " --> pdb=" O   ASP A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 865
    Processing helix  chain 'A' and resid 870 through 881
    Processing helix  chain 'A' and resid 886 through 901
      removed outlier: 4.002A  pdb=" N   LYS A 892 " --> pdb=" O   LYS A 888 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 894 " --> pdb=" O   VAL A 890 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   VAL A 895 " --> pdb=" O   LYS A 891 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   GLU A 896 " --> pdb=" O   LYS A 892 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU A 901 " --> pdb=" O   ALA A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 925
    Processing helix  chain 'A' and resid 927 through 934
    Processing helix  chain 'A' and resid 941 through 949
    Processing helix  chain 'A' and resid 960 through 969
    Processing helix  chain 'A' and resid 977 through 982
    Processing helix  chain 'A' and resid 986 through 998
      removed outlier: 3.735A  pdb=" N   LEU A 990 " --> pdb=" O   ASP A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1013
    Processing helix  chain 'A' and resid 1013 through 1028
      removed outlier: 3.667A  pdb=" N   PHE A1017 " --> pdb=" O   TYR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1040
    Processing helix  chain 'B' and resid 496 through 510
    Processing helix  chain 'B' and resid 541 through 548
    Processing helix  chain 'B' and resid 549 through 560
    Processing helix  chain 'B' and resid 571 through 578
      removed outlier: 4.195A  pdb=" N   GLN B 575 " --> pdb=" O   ARG B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 588
      removed outlier: 3.873A  pdb=" N   LEU B 587 " --> pdb=" O   ARG B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 598
    Processing helix  chain 'B' and resid 608 through 610
      No H-bonds generated for 'chain 'B' and resid 608 through 610'
    Processing helix  chain 'B' and resid 611 through 617
    Processing helix  chain 'B' and resid 622 through 634
      removed outlier: 3.661A  pdb=" N   ARG B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   GLU B 632 " --> pdb=" O   GLN B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 669
    Processing helix  chain 'B' and resid 682 through 697
      removed outlier: 3.614A  pdb=" N   MET B 686 " --> pdb=" O   TYR B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 734
    Processing helix  chain 'B' and resid 748 through 763
      removed outlier: 3.849A  pdb=" N   ARG B 762 " --> pdb=" O   SER B 758 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 778 through 790
      removed outlier: 3.678A  pdb=" N   ALA B 782 " --> pdb=" O   ALA B 778 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLY B 790 " --> pdb=" O   CYS B 786 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 817
      removed outlier: 3.701A  pdb=" N   LEU B 813 " --> pdb=" O   SER B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 827 through 843
      removed outlier: 3.966A  pdb=" N   VAL B 831 " --> pdb=" O   PRO B 827 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP B 833 " --> pdb=" O   GLU B 829 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLY B 843 " --> pdb=" O   GLU B 839 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 846
      No H-bonds generated for 'chain 'B' and resid 844 through 846'
    Processing helix  chain 'B' and resid 849 through 853
    Processing helix  chain 'B' and resid 860 through 865
    Processing helix  chain 'B' and resid 870 through 881
    Processing helix  chain 'B' and resid 886 through 893
      removed outlier: 3.699A  pdb=" N   VAL B 890 " --> pdb=" O   LYS B 886 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 891 " --> pdb=" O   PHE B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 893 through 902
    Processing helix  chain 'B' and resid 908 through 925
    Processing helix  chain 'B' and resid 927 through 934
      removed outlier: 3.820A  pdb=" N   GLN B 934 " --> pdb=" O   GLU B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 941 through 950
      removed outlier: 3.667A  pdb=" N   GLY B 950 " --> pdb=" O   GLU B 946 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 969
      removed outlier: 3.542A  pdb=" N   ARG B 964 " --> pdb=" O   PRO B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 977 through 982
    Processing helix  chain 'B' and resid 987 through 999
    Processing helix  chain 'B' and resid 1003 through 1013
    Processing helix  chain 'B' and resid 1013 through 1028
      removed outlier: 3.512A  pdb=" N   PHE B1017 " --> pdb=" O   TYR B1013 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1034 through 1040
    Processing helix  chain 'C' and resid 496 through 510
      removed outlier: 3.798A  pdb=" N   LEU C 500 " --> pdb=" O   ARG C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 541 through 548
    Processing helix  chain 'C' and resid 549 through 560
    Processing helix  chain 'C' and resid 571 through 578
      removed outlier: 4.048A  pdb=" N   GLN C 575 " --> pdb=" O   ARG C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 590 through 598
    Processing helix  chain 'C' and resid 608 through 610
      No H-bonds generated for 'chain 'C' and resid 608 through 610'
    Processing helix  chain 'C' and resid 611 through 616
    Processing helix  chain 'C' and resid 622 through 632
      removed outlier: 4.331A  pdb=" N   GLU C 632 " --> pdb=" O   GLN C 628 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 655 through 669
    Processing helix  chain 'C' and resid 682 through 697
    Processing helix  chain 'C' and resid 719 through 734
    Processing helix  chain 'C' and resid 748 through 763
      removed outlier: 3.541A  pdb=" N   ARG C 762 " --> pdb=" O   SER C 758 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 778 through 790
      removed outlier: 4.176A  pdb=" N   GLY C 790 " --> pdb=" O   CYS C 786 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 809 through 817
      removed outlier: 3.787A  pdb=" N   LEU C 813 " --> pdb=" O   SER C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 827 through 843
      removed outlier: 3.828A  pdb=" N   VAL C 831 " --> pdb=" O   PRO C 827 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY C 843 " --> pdb=" O   GLU C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 844 through 846
      No H-bonds generated for 'chain 'C' and resid 844 through 846'
    Processing helix  chain 'C' and resid 860 through 865
    Processing helix  chain 'C' and resid 867 through 869
      No H-bonds generated for 'chain 'C' and resid 867 through 869'
    Processing helix  chain 'C' and resid 870 through 882
    Processing helix  chain 'C' and resid 886 through 902
      removed outlier: 4.177A  pdb=" N   VAL C 895 " --> pdb=" O   LYS C 891 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   GLU C 896 " --> pdb=" O   LYS C 892 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 908 through 925
    Processing helix  chain 'C' and resid 927 through 934
    Processing helix  chain 'C' and resid 941 through 950
    Processing helix  chain 'C' and resid 960 through 969
      removed outlier: 3.981A  pdb=" N   ARG C 964 " --> pdb=" O   PRO C 960 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 977 through 982
    Processing helix  chain 'C' and resid 987 through 999
      removed outlier: 3.663A  pdb=" N   LYS C 992 " --> pdb=" O   GLN C 988 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1003 through 1013
    Processing helix  chain 'C' and resid 1013 through 1028
    Processing helix  chain 'C' and resid 1034 through 1040
    Processing helix  chain 'D' and resid 496 through 511
    Processing helix  chain 'D' and resid 541 through 548
      removed outlier: 3.582A  pdb=" N   LEU D 545 " --> pdb=" O   PHE D 541 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 549 through 560
    Processing helix  chain 'D' and resid 571 through 578
    Processing helix  chain 'D' and resid 584 through 598
      Proline residue:  D 592  - end of helix
    Processing helix  chain 'D' and resid 610 through 617
    Processing helix  chain 'D' and resid 622 through 634
      removed outlier: 3.515A  pdb=" N   ARG D 626 " --> pdb=" O   CYS D 622 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 655 through 670
    Processing helix  chain 'D' and resid 682 through 697
    Processing helix  chain 'D' and resid 719 through 733
    Processing helix  chain 'D' and resid 748 through 761
    Processing helix  chain 'D' and resid 778 through 790
      removed outlier: 3.655A  pdb=" N   ALA D 782 " --> pdb=" O   ALA D 778 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 809 through 817
      removed outlier: 4.047A  pdb=" N   LEU D 813 " --> pdb=" O   SER D 809 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 827 through 845
      removed outlier: 3.723A  pdb=" N   VAL D 831 " --> pdb=" O   PRO D 827 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU D 844 " --> pdb=" O   GLY D 840 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 846 through 853
      removed outlier: 3.911A  pdb=" N   ASP D 849 " --> pdb=" O   ALA D 846 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   CYS D 850 " --> pdb=" O   ALA D 847 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   THR D 851 " --> pdb=" O   PHE D 848 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA D 852 " --> pdb=" O   ASP D 849 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 870 through 882
    Processing helix  chain 'D' and resid 883 through 885
      No H-bonds generated for 'chain 'D' and resid 883 through 885'
    Processing helix  chain 'D' and resid 886 through 901
      removed outlier: 3.506A  pdb=" N   LYS D 892 " --> pdb=" O   LYS D 888 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR D 894 " --> pdb=" O   VAL D 890 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL D 895 " --> pdb=" O   LYS D 891 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLU D 896 " --> pdb=" O   LYS D 892 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU D 901 " --> pdb=" O   ALA D 897 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 907 through 925
    Processing helix  chain 'D' and resid 927 through 934
    Processing helix  chain 'D' and resid 941 through 950
      removed outlier: 3.705A  pdb=" N   VAL D 945 " --> pdb=" O   PRO D 941 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 960 through 969
    Processing helix  chain 'D' and resid 977 through 982
    Processing helix  chain 'D' and resid 988 through 998
    Processing helix  chain 'D' and resid 1003 through 1013
      removed outlier: 3.846A  pdb=" N   VAL D1007 " --> pdb=" O   THR D1003 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1013 through 1028
      removed outlier: 3.627A  pdb=" N   PHE D1017 " --> pdb=" O   TYR D1013 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1034 through 1040
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567
      removed outlier: 7.288A  pdb=" N   LEU A 565 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   GLU A 605 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ASP A 567 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   MET A 604 " --> pdb=" O   GLN A 640 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   LEU A 642 " --> pdb=" O   MET A 604 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   PHE A 639 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ARG A 675 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   MET A 641 " --> pdb=" O   ARG A 675 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   PHE A 677 " --> pdb=" O   MET A 641 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 643 " --> pdb=" O   PHE A 677 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE A 674 " --> pdb=" O   VAL A 699 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   CYS A 739 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ALA A 702 " --> pdb=" O   CYS A 739 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LYS A 741 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ILE A 704 " --> pdb=" O   LYS A 741 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU A 738 " --> pdb=" O   HIS A 769 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   HIS A 771 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ILE A 740 " --> pdb=" O   HIS A 771 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU A 768 " --> pdb=" O   VAL A 793 " (cutoff:3.500A)
      removed outlier: 8.587A  pdb=" N   ASP A 795 " --> pdb=" O   LEU A 768 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ILE A 770 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LEU A 564 " --> pdb=" O   VAL A 794 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   VAL A 796 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   MET A 566 " --> pdb=" O   VAL A 796 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1050
      removed outlier: 6.726A  pdb=" N   PHE A1077 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   VAL A1065 " --> pdb=" O   GLN A1075 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLN A1075 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113
      removed outlier: 4.010A  pdb=" N   LEU A1175 " --> pdb=" O   ILE A1112 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE A1174 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   VAL A1160 " --> pdb=" O   ILE A1174 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   GLU A1176 " --> pdb=" O   ARG A1158 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY A1155 " --> pdb=" O   VAL A1131 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1149
      removed outlier: 3.587A  pdb=" N   THR A1147 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS A1138 " --> pdb=" O   VAL A1149 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASP A1122 " --> pdb=" O   VAL A1139 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER A1141 " --> pdb=" O   VAL A1120 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   VAL A1120 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 567
      removed outlier: 7.009A  pdb=" N   LEU B 565 " --> pdb=" O   SER B 603 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   GLU B 605 " --> pdb=" O   LEU B 565 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ASP B 567 " --> pdb=" O   GLU B 605 " (cutoff:3.500A)
      removed outlier: 8.850A  pdb=" N   TRP B 607 " --> pdb=" O   ASP B 567 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   MET B 604 " --> pdb=" O   GLN B 640 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   LEU B 642 " --> pdb=" O   MET B 604 " (cutoff:3.500A)
      removed outlier: 9.395A  pdb=" N   ASN B 606 " --> pdb=" O   LEU B 642 " (cutoff:3.500A)
      removed outlier: 13.411A  pdb=" N   ARG B 644 " --> pdb=" O   ASN B 606 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE B 674 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   VAL B 700 " --> pdb=" O   ILE B 737 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   CYS B 739 " --> pdb=" O   VAL B 700 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ALA B 702 " --> pdb=" O   CYS B 739 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   LYS B 741 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ILE B 704 " --> pdb=" O   LYS B 741 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   LEU B 738 " --> pdb=" O   HIS B 769 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU B 768 " --> pdb=" O   VAL B 793 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ASP B 795 " --> pdb=" O   LEU B 768 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ILE B 770 " --> pdb=" O   ASP B 795 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1051
      removed outlier: 6.851A  pdb=" N   PHE B1077 " --> pdb=" O   LEU B1063 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   VAL B1065 " --> pdb=" O   GLN B1075 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLN B1075 " --> pdb=" O   VAL B1065 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1113
      removed outlier: 6.824A  pdb=" N   ILE B1112 " --> pdb=" O   ILE B1174 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE B1174 " --> pdb=" O   VAL B1160 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   VAL B1160 " --> pdb=" O   ILE B1174 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   GLU B1176 " --> pdb=" O   ARG B1158 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG B1158 " --> pdb=" O   GLU B1176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1119 through 1123
      removed outlier: 3.574A  pdb=" N   LYS B1119 " --> pdb=" O   SER B1141 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B1139 " --> pdb=" O   ILE B1121 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ILE B1123 " --> pdb=" O   LEU B1137 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU B1137 " --> pdb=" O   ILE B1123 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   CYS B1138 " --> pdb=" O   VAL B1149 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 699 through 702
      removed outlier: 6.689A  pdb=" N   MET C 604 " --> pdb=" O   GLN C 640 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   LEU C 642 " --> pdb=" O   MET C 604 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU C 565 " --> pdb=" O   SER C 603 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   GLU C 605 " --> pdb=" O   LEU C 565 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ASP C 567 " --> pdb=" O   GLU C 605 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP C 795 " --> pdb=" O   ILE C 770 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   THR C 772 " --> pdb=" O   ASP C 795 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ILE C 704 " --> pdb=" O   LYS C 741 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 1046 through 1051
      removed outlier: 3.934A  pdb=" N   GLU C1046 " --> pdb=" O   ALA C1062 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA C1062 " --> pdb=" O   GLU C1046 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   PHE C1077 " --> pdb=" O   LEU C1063 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   VAL C1065 " --> pdb=" O   GLN C1075 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLN C1075 " --> pdb=" O   VAL C1065 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 1111 through 1112
      removed outlier: 3.949A  pdb=" N   LEU C1175 " --> pdb=" O   ILE C1112 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   GLU C1176 " --> pdb=" O   ARG C1158 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG C1158 " --> pdb=" O   GLU C1176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1146 through 1151
      removed outlier: 6.751A  pdb=" N   THR C1147 " --> pdb=" O   VAL C1139 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL C1139 " --> pdb=" O   THR C1147 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL C1149 " --> pdb=" O   LEU C1137 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN C1135 " --> pdb=" O   SER C1151 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   LEU C1137 " --> pdb=" O   ILE C1123 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ILE C1123 " --> pdb=" O   LEU C1137 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   VAL C1139 " --> pdb=" O   ILE C1121 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER C1141 " --> pdb=" O   LYS C1119 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS C1119 " --> pdb=" O   SER C1141 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 564 through 567
      removed outlier: 7.045A  pdb=" N   LEU D 564 " --> pdb=" O   VAL D 794 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL D 796 " --> pdb=" O   LEU D 564 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   MET D 566 " --> pdb=" O   VAL D 796 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   LEU D 768 " --> pdb=" O   VAL D 793 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ASP D 795 " --> pdb=" O   LEU D 768 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   ILE D 770 " --> pdb=" O   ASP D 795 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL D 700 " --> pdb=" O   ILE D 737 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   CYS D 739 " --> pdb=" O   VAL D 700 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   ALA D 702 " --> pdb=" O   CYS D 739 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LYS D 741 " --> pdb=" O   ALA D 702 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ILE D 704 " --> pdb=" O   LYS D 741 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   PHE D 639 " --> pdb=" O   VAL D 673 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ARG D 675 " --> pdb=" O   PHE D 639 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   MET D 641 " --> pdb=" O   ARG D 675 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   PHE D 677 " --> pdb=" O   MET D 641 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   LEU D 643 " --> pdb=" O   PHE D 677 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   MET D 604 " --> pdb=" O   GLN D 640 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   LEU D 642 " --> pdb=" O   MET D 604 " (cutoff:3.500A)
      removed outlier: 9.304A  pdb=" N   ASN D 606 " --> pdb=" O   LEU D 642 " (cutoff:3.500A)
      removed outlier: 13.836A  pdb=" N   ARG D 644 " --> pdb=" O   ASN D 606 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 1047 through 1050
      removed outlier: 6.510A  pdb=" N   PHE D1077 " --> pdb=" O   LEU D1063 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 1111 through 1113
      removed outlier: 7.968A  pdb=" N   ILE D1112 " --> pdb=" O   ILE D1174 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE D1174 " --> pdb=" O   ILE D1112 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE D1174 " --> pdb=" O   VAL D1160 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL D1160 " --> pdb=" O   ILE D1174 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLU D1176 " --> pdb=" O   ARG D1158 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR D1156 " --> pdb=" O   GLU D1178 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 1119 through 1123
      removed outlier: 7.204A  pdb=" N   VAL D1139 " --> pdb=" O   ILE D1121 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ILE D1123 " --> pdb=" O   LEU D1137 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   LEU D1137 " --> pdb=" O   ILE D1123 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   CYS D1138 " --> pdb=" O   VAL D1149 " (cutoff:3.500A)

    882 hydrogen bonds defined for protein.
    2601 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.25

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 3570
        1.31 -     1.43: 5335
        1.43 -     1.56: 12365
        1.56 -     1.69: 26
        1.69 -     1.82: 260
  Bond restraints: 21556
  Sorted by residual:
  bond pdb=" C6  BTI A1900 "
       pdb=" S1  BTI A1900 "
    ideal  model  delta    sigma   weight residual
    1.811  1.440  0.371 2.00e-02 2.50e+03 3.44e+02
  bond pdb=" C6  BTI D1900 "
       pdb=" S1  BTI D1900 "
    ideal  model  delta    sigma   weight residual
    1.811  1.442  0.369 2.00e-02 2.50e+03 3.40e+02
  bond pdb=" C6  BTI C1900 "
       pdb=" S1  BTI C1900 "
    ideal  model  delta    sigma   weight residual
    1.811  1.443  0.368 2.00e-02 2.50e+03 3.39e+02
  bond pdb=" C6  BTI B1900 "
       pdb=" S1  BTI B1900 "
    ideal  model  delta    sigma   weight residual
    1.811  1.443  0.368 2.00e-02 2.50e+03 3.38e+02
  bond pdb=" C3  BTI B1900 "
       pdb=" N3  BTI B1900 "
    ideal  model  delta    sigma   weight residual
    1.356  1.577 -0.221 2.00e-02 2.50e+03 1.22e+02
  ... (remaining 21551 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.80: 29199
        6.80 -    13.60: 13
       13.60 -    20.40: 4
       20.40 -    27.20: 2
       27.20 -    34.00: 2
  Bond angle restraints: 29220
  Sorted by residual:
  angle pdb=" C10 BTI C1900 "
        pdb=" C11 BTI C1900 "
        pdb=" O11 BTI C1900 "
      ideal   model   delta    sigma   weight residual
     125.49   91.49   34.00 3.00e+00 1.11e-01 1.28e+02
  angle pdb=" C10 BTI B1900 "
        pdb=" C11 BTI B1900 "
        pdb=" O11 BTI B1900 "
      ideal   model   delta    sigma   weight residual
     125.49   92.99   32.50 3.00e+00 1.11e-01 1.17e+02
  angle pdb=" C10 BTI A1900 "
        pdb=" C11 BTI A1900 "
        pdb=" O11 BTI A1900 "
      ideal   model   delta    sigma   weight residual
     125.49   99.42   26.07 3.00e+00 1.11e-01 7.55e+01
  angle pdb=" C10 BTI D1900 "
        pdb=" C11 BTI D1900 "
        pdb=" O11 BTI D1900 "
      ideal   model   delta    sigma   weight residual
     125.49  101.36   24.13 3.00e+00 1.11e-01 6.47e+01
  angle pdb=" C2  BTI B1900 "
        pdb=" S1  BTI B1900 "
        pdb=" C6  BTI B1900 "
      ideal   model   delta    sigma   weight residual
      89.29  106.58  -17.29 3.00e+00 1.11e-01 3.32e+01
  ... (remaining 29215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 11916
       17.47 -    34.93: 1006
       34.93 -    52.40: 179
       52.40 -    69.86: 20
       69.86 -    87.33: 15
  Dihedral angle restraints: 13136
    sinusoidal: 5300
      harmonic: 7836
  Sorted by residual:
  dihedral pdb=" CB  CYS D 752 "
           pdb=" SG  CYS D 752 "
           pdb=" SG  CYS D 786 "
           pdb=" CB  CYS D 786 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.35  -83.35     1      1.00e+01 1.00e-02 8.49e+01
  dihedral pdb=" CB  CYS A 752 "
           pdb=" SG  CYS A 752 "
           pdb=" SG  CYS A 786 "
           pdb=" CB  CYS A 786 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.68  -49.68     1      1.00e+01 1.00e-02 3.39e+01
  dihedral pdb=" CA  CYS B 786 "
           pdb=" C   CYS B 786 "
           pdb=" N   ALA B 787 "
           pdb=" CA  ALA B 787 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.23   24.77     0      5.00e+00 4.00e-02 2.45e+01
  ... (remaining 13133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 2410
       0.041 -    0.083: 614
       0.083 -    0.124: 220
       0.124 -    0.166: 15
       0.166 -    0.207: 5
  Chirality restraints: 3264
  Sorted by residual:
  chirality pdb=" C5  BTI C1900 "
            pdb=" C4  BTI C1900 "
            pdb=" C6  BTI C1900 "
            pdb=" N3  BTI C1900 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.73    2.94   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C5  BTI A1900 "
            pdb=" C4  BTI A1900 "
            pdb=" C6  BTI A1900 "
            pdb=" N3  BTI A1900 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.73    2.92   -0.19 2.00e-01 2.50e+01 8.94e-01
  chirality pdb=" C4  BTI C1900 "
            pdb=" C2  BTI C1900 "
            pdb=" C5  BTI C1900 "
            pdb=" N2  BTI C1900 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.75    2.57    0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 3261 not shown)

  Planarity restraints: 3828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 535 "   -0.055 5.00e-02 4.00e+02   8.35e-02 1.12e+01
        pdb=" N   PRO D 536 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO D 536 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO D 536 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 807 "    0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO B 808 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 808 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 808 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 807 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.64e+00
        pdb=" N   PRO D 808 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO D 808 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 808 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 3825 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 1086
        2.72 -     3.26: 23479
        3.26 -     3.81: 37347
        3.81 -     4.35: 43228
        4.35 -     4.90: 70120
  Nonbonded interactions: 175260
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 593 "
            pdb=" ND2 ASN B 597 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" OD2 ASP A 613 "
            pdb=" OH  TYR A 651 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" NE2 GLN A1075 "
            pdb=" OG  SER A1086 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" OG  SER D1066 "
            pdb=" O   GLN D1075 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OE1 GLU B 961 "
            pdb=" NH2 ARG B 964 "
     model   vdw
     2.188 3.120
  ... (remaining 175255 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: 0.02
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:             1.730
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     21.660
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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      :  0.009   0.635  21565  Z= 0.594
  Angle     :  0.822  33.998  29228  Z= 0.394
  Chirality :  0.042   0.207   3264
  Planarity :  0.005   0.083   3828
  Dihedral  : 13.247  87.331   8092
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 19.58
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  8.21 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.16), residues: 2728
  helix:  0.82 (0.16), residues: 1116
  sheet: -0.33 (0.28), residues: 344
  loop : -1.39 (0.17), residues: 1268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C1070 
 TYR   0.018   0.002   TYR B 951 
 PHE   0.024   0.002   PHE C1078 
 TRP   0.016   0.002   TRP A 838 
 HIS   0.005   0.001   HIS C 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00816 (21556)
  covalent geometry    : angle       0.82048 (29220)
  SS BOND              : bond        0.00711 (    4)
  SS BOND              : angle       3.08513 (    8)
  hydrogen bonds       : bond        0.18873 (  882)
  hydrogen bonds       : angle       7.62153 ( 2601)
  Misc. bond           : bond        0.28416 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9522 (mmp) cc_final: 0.9147 (mmm)
REVERT: A  566 MET cc_start: 0.5803 (ppp) cc_final: 0.5589 (ppp)
REVERT: A 1166 MET cc_start: 0.8807 (ptp) cc_final: 0.8289 (pmm)
REVERT: B  641 MET cc_start: 0.8239 (tmm) cc_final: 0.7886 (ppp)
REVERT: B  686 MET cc_start: 0.9269 (mpp) cc_final: 0.9000 (mpp)
REVERT: B  724 MET cc_start: 0.8967 (mmt) cc_final: 0.8398 (mmm)
REVERT: B 1116 MET cc_start: 0.8360 (mmm) cc_final: 0.7914 (ppp)
REVERT: B 1145 MET cc_start: 0.6365 (ptt) cc_final: 0.5686 (ptt)
REVERT: C  754 MET cc_start: 0.9467 (ppp) cc_final: 0.9134 (ppp)
REVERT: C  755 LEU cc_start: 0.9704 (mt) cc_final: 0.9327 (mt)
REVERT: C  783 MET cc_start: 0.9073 (tpp) cc_final: 0.8863 (tpp)
REVERT: C  804 MET cc_start: 0.8607 (tpp) cc_final: 0.8143 (tpp)
REVERT: C 1145 MET cc_start: 0.5515 (pmm) cc_final: 0.4796 (pmm)
REVERT: D  574 HIS cc_start: 0.8922 (m-70) cc_final: 0.8687 (m170)
REVERT: D  604 MET cc_start: 0.8388 (tpt) cc_final: 0.8119 (tpp)
REVERT: D  810 MET cc_start: 0.9017 (mmp) cc_final: 0.8440 (mmm)
REVERT: D  881 MET cc_start: 0.9230 (mmp) cc_final: 0.9028 (mmm)
REVERT: D  947 PHE cc_start: 0.9254 (t80) cc_final: 0.9046 (t80)
REVERT: D 1098 MET cc_start: 0.6401 (mmt) cc_final: 0.6198 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1520
  time to fit residues: 40.6940
Evaluate side-chains
  144 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 197 optimal weight:    0.0670
   chunk 215 optimal weight:    6.9990
   chunk 20 optimal weight:   40.0000
   chunk 132 optimal weight:   20.0000
   chunk 261 optimal weight:    1.9990
   chunk 248 optimal weight:    1.9990
   chunk 207 optimal weight:    0.0970
   chunk 155 optimal weight:    3.9990
   chunk 244 optimal weight:    7.9990
   chunk 183 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    1.6322

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 956 HIS
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 653 ASN
C 899 GLN
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 506 HIS
** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.047173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.035287 restraints weight = 231104.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.035945 restraints weight = 181262.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.036435 restraints weight = 150944.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.036811 restraints weight = 131573.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.037087 restraints weight = 118333.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  21565  Z= 0.137
  Angle     :  0.649   9.134  29228  Z= 0.323
  Chirality :  0.043   0.267   3264
  Planarity :  0.005   0.057   3828
  Dihedral  :  5.358  58.848   3016
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.96 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  6.91 %
    Favored  : 92.77 %
  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 are not related in a simple way.
  whole: -0.51 (0.16), residues: 2728
  helix:  0.68 (0.16), residues: 1164
  sheet: -0.09 (0.29), residues: 338
  loop : -1.42 (0.17), residues: 1226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 842 
 TYR   0.014   0.002   TYR B 834 
 PHE   0.015   0.001   PHE B 947 
 TRP   0.020   0.002   TRP A 838 
 HIS   0.006   0.001   HIS B1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (21556)
  covalent geometry    : angle       0.64870 (29220)
  SS BOND              : bond        0.00232 (    4)
  SS BOND              : angle       1.77433 (    8)
  hydrogen bonds       : bond        0.04396 (  882)
  hydrogen bonds       : angle       6.05973 ( 2601)
  Misc. bond           : bond        0.00106 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9559 (mmp) cc_final: 0.9134 (mmm)
REVERT: A  566 MET cc_start: 0.5559 (ppp) cc_final: 0.5308 (ppp)
REVERT: A  854 MET cc_start: 0.6155 (tmm) cc_final: 0.5656 (tmm)
REVERT: A  900 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (mmt)
REVERT: A 1012 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6439 (ptp)
REVERT: A 1153 MET cc_start: 0.8360 (ppp) cc_final: 0.7918 (ppp)
REVERT: A 1166 MET cc_start: 0.8592 (ptp) cc_final: 0.8002 (pmm)
REVERT: B  671 MET cc_start: 0.6641 (tpt) cc_final: 0.6333 (tpt)
REVERT: B  686 MET cc_start: 0.9168 (mpp) cc_final: 0.8875 (mpp)
REVERT: B 1145 MET cc_start: 0.6527 (ptt) cc_final: 0.5621 (ptt)
REVERT: C  508 MET cc_start: 0.8699 (mmt) cc_final: 0.8259 (mmp)
REVERT: C  724 MET cc_start: 0.8679 (mmm) cc_final: 0.8460 (mmm)
REVERT: C  754 MET cc_start: 0.9297 (ppp) cc_final: 0.8906 (ppp)
REVERT: C  755 LEU cc_start: 0.9650 (mt) cc_final: 0.9132 (mt)
REVERT: C  783 MET cc_start: 0.9019 (tpp) cc_final: 0.8781 (tpp)
REVERT: C  804 MET cc_start: 0.8541 (tpp) cc_final: 0.8095 (tpp)
REVERT: C  881 MET cc_start: 0.9276 (tpp) cc_final: 0.9052 (tpp)
REVERT: D  508 MET cc_start: 0.9197 (mmp) cc_final: 0.8991 (mmp)
REVERT: D  574 HIS cc_start: 0.8884 (m-70) cc_final: 0.8634 (m-70)
REVERT: D  604 MET cc_start: 0.8122 (tpt) cc_final: 0.7786 (tpp)
REVERT: D  810 MET cc_start: 0.9013 (mmp) cc_final: 0.8569 (mmm)
REVERT: D  854 MET cc_start: 0.8084 (ttt) cc_final: 0.7726 (ttt)
REVERT: D  881 MET cc_start: 0.9334 (mmp) cc_final: 0.8963 (mmm)
REVERT: D  947 PHE cc_start: 0.9152 (t80) cc_final: 0.8946 (t80)
REVERT: D 1098 MET cc_start: 0.6549 (mmt) cc_final: 0.6311 (mmt)
  outliers start: 7
  outliers final: 3
  residues processed: 160
  average time/residue: 0.1427
  time to fit residues: 37.5574
Evaluate side-chains
  150 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1012 MET
Chi-restraints excluded: chain B residue  944 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  729 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 241 optimal weight:    9.9990
   chunk 172 optimal weight:    8.9990
   chunk 3 optimal weight:   50.0000
   chunk 190 optimal weight:    0.0000
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 213 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 267 optimal weight:    7.9990
   chunk 94 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    2.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 873 ASN
A1040 GLN
A1059 HIS
** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 GLN
C 510 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.046976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.035077 restraints weight = 233751.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.035741 restraints weight = 182927.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.036238 restraints weight = 152105.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.036612 restraints weight = 132293.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.036848 restraints weight = 119083.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  21565  Z= 0.128
  Angle     :  0.615   9.987  29228  Z= 0.304
  Chirality :  0.041   0.153   3264
  Planarity :  0.004   0.049   3828
  Dihedral  :  5.083  55.869   3016
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  9.80 %
    Favored  : 89.54 %
  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 are not related in a simple way.
  whole: -0.48 (0.16), residues: 2728
  helix:  0.72 (0.16), residues: 1178
  sheet: -0.08 (0.29), residues: 338
  loop : -1.42 (0.17), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1070 
 TYR   0.016   0.001   TYR A 834 
 PHE   0.020   0.001   PHE B 674 
 TRP   0.018   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (21556)
  covalent geometry    : angle       0.61498 (29220)
  SS BOND              : bond        0.00475 (    4)
  SS BOND              : angle       1.37093 (    8)
  hydrogen bonds       : bond        0.03786 (  882)
  hydrogen bonds       : angle       5.77210 ( 2601)
  Misc. bond           : bond        0.00084 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9553 (mmp) cc_final: 0.9159 (mmm)
REVERT: A  566 MET cc_start: 0.5469 (ppp) cc_final: 0.5241 (ppp)
REVERT: A  900 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7848 (mmt)
REVERT: A  921 MET cc_start: 0.7855 (ptt) cc_final: 0.7574 (ppp)
REVERT: A 1012 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6395 (ptp)
REVERT: A 1153 MET cc_start: 0.8272 (ppp) cc_final: 0.7785 (ppp)
REVERT: A 1166 MET cc_start: 0.8514 (ptp) cc_final: 0.7898 (pmm)
REVERT: B  508 MET cc_start: 0.9126 (mmp) cc_final: 0.8881 (mmm)
REVERT: B  616 MET cc_start: 0.7649 (mmp) cc_final: 0.7342 (mmp)
REVERT: B  671 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6295 (tpt)
REVERT: B  686 MET cc_start: 0.9220 (mpp) cc_final: 0.8939 (mpp)
REVERT: B 1145 MET cc_start: 0.6758 (ptt) cc_final: 0.5756 (ptt)
REVERT: C  508 MET cc_start: 0.8740 (mmt) cc_final: 0.8263 (mmp)
REVERT: C  616 MET cc_start: 0.8534 (mpp) cc_final: 0.8242 (mmp)
REVERT: C  754 MET cc_start: 0.9291 (ppp) cc_final: 0.8864 (ppp)
REVERT: C  755 LEU cc_start: 0.9680 (mt) cc_final: 0.9187 (mt)
REVERT: C  783 MET cc_start: 0.9050 (tpp) cc_final: 0.8749 (tpp)
REVERT: C  804 MET cc_start: 0.8537 (tpp) cc_final: 0.8284 (tpp)
REVERT: D  574 HIS cc_start: 0.8917 (m-70) cc_final: 0.8682 (m90)
REVERT: D  604 MET cc_start: 0.8091 (tpt) cc_final: 0.7701 (tpp)
REVERT: D  616 MET cc_start: 0.8157 (mmp) cc_final: 0.7825 (mmp)
REVERT: D  810 MET cc_start: 0.9019 (mmp) cc_final: 0.8572 (mmm)
REVERT: D  854 MET cc_start: 0.8231 (ttt) cc_final: 0.7968 (ttt)
REVERT: D  881 MET cc_start: 0.9367 (mmp) cc_final: 0.9076 (mmm)
REVERT: D 1098 MET cc_start: 0.6742 (mmt) cc_final: 0.6524 (mmt)
REVERT: D 1153 MET cc_start: 0.8949 (pmm) cc_final: 0.8549 (pmm)
  outliers start: 15
  outliers final: 6
  residues processed: 162
  average time/residue: 0.1470
  time to fit residues: 38.5662
Evaluate side-chains
  155 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1012 MET
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  752 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 263 optimal weight:   10.0000
   chunk 163 optimal weight:   20.0000
   chunk 147 optimal weight:    6.9990
   chunk 238 optimal weight:    8.9990
   chunk 159 optimal weight:    3.9990
   chunk 254 optimal weight:    0.8980
   chunk 228 optimal weight:    4.9990
   chunk 253 optimal weight:    8.9990
   chunk 104 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 139 optimal weight:   10.0000
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 640 GLN
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1040 GLN
B 506 HIS
B 510 ASN
B 669 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 873 ASN
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 574 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.045890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.034105 restraints weight = 236966.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.034693 restraints weight = 186714.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.035163 restraints weight = 157674.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.035536 restraints weight = 138081.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.035786 restraints weight = 124089.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  21565  Z= 0.177
  Angle     :  0.638   9.547  29228  Z= 0.317
  Chirality :  0.041   0.171   3264
  Planarity :  0.004   0.045   3828
  Dihedral  :  5.099  54.278   3016
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.70 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.75 %
    Favored  : 86.97 %
  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 are not related in a simple way.
  whole: -0.45 (0.16), residues: 2728
  helix:  0.78 (0.16), residues: 1158
  sheet: -0.12 (0.29), residues: 338
  loop : -1.40 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B1054 
 TYR   0.013   0.002   TYR B 951 
 PHE   0.017   0.002   PHE B 763 
 TRP   0.015   0.002   TRP A 624 
 HIS   0.006   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (21556)
  covalent geometry    : angle       0.63804 (29220)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       1.15333 (    8)
  hydrogen bonds       : bond        0.03609 (  882)
  hydrogen bonds       : angle       5.75965 ( 2601)
  Misc. bond           : bond        0.00039 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 154
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9538 (mmp) cc_final: 0.9133 (mmp)
REVERT: A  616 MET cc_start: 0.7349 (mpp) cc_final: 0.7136 (mpp)
REVERT: A  690 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7827 (mmm)
REVERT: A  804 MET cc_start: 0.8609 (tpp) cc_final: 0.8132 (mmm)
REVERT: A  854 MET cc_start: 0.6263 (tmm) cc_final: 0.5440 (tmm)
REVERT: A 1012 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6399 (ptp)
REVERT: A 1106 LYS cc_start: 0.9565 (tptp) cc_final: 0.9246 (mmmt)
REVERT: A 1153 MET cc_start: 0.8307 (ppp) cc_final: 0.7669 (ppp)
REVERT: A 1166 MET cc_start: 0.8480 (ptp) cc_final: 0.7940 (pmm)
REVERT: B  508 MET cc_start: 0.9187 (mmp) cc_final: 0.8816 (mmm)
REVERT: B  616 MET cc_start: 0.7801 (mmp) cc_final: 0.7580 (mmp)
REVERT: B  671 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6622 (tpt)
REVERT: B  686 MET cc_start: 0.9230 (mpp) cc_final: 0.9009 (mpp)
REVERT: B 1012 MET cc_start: 0.8540 (pmm) cc_final: 0.8313 (pmm)
REVERT: B 1116 MET cc_start: 0.8076 (mmt) cc_final: 0.7074 (ppp)
REVERT: B 1143 MET cc_start: 0.8393 (tpt) cc_final: 0.8134 (tpt)
REVERT: C  616 MET cc_start: 0.8712 (mpp) cc_final: 0.8499 (mmm)
REVERT: C  754 MET cc_start: 0.9386 (ppp) cc_final: 0.9148 (ppp)
REVERT: C  783 MET cc_start: 0.9102 (tpp) cc_final: 0.8800 (tpp)
REVERT: C  804 MET cc_start: 0.8712 (tpp) cc_final: 0.8400 (tpp)
REVERT: D  574 HIS cc_start: 0.9066 (m90) cc_final: 0.8855 (m-70)
REVERT: D  604 MET cc_start: 0.8247 (tpt) cc_final: 0.7815 (tpp)
REVERT: D  616 MET cc_start: 0.8162 (mmp) cc_final: 0.7886 (mmp)
REVERT: D  810 MET cc_start: 0.9101 (mmp) cc_final: 0.8601 (mmm)
REVERT: D  881 MET cc_start: 0.9420 (mmp) cc_final: 0.9067 (mmm)
  outliers start: 29
  outliers final: 12
  residues processed: 176
  average time/residue: 0.1449
  time to fit residues: 41.5948
Evaluate side-chains
  165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1012 MET
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue  850 CYS
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 61 optimal weight:    0.0000
   chunk 79 optimal weight:   10.0000
   chunk 180 optimal weight:    0.9980
   chunk 202 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 145 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 71 optimal weight:   20.0000
   chunk 115 optimal weight:    0.0670
   chunk 170 optimal weight:   10.0000
   overall best weight:    3.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 HIS
B 510 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.046035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.034222 restraints weight = 235417.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.034881 restraints weight = 184324.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.035364 restraints weight = 153650.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.035689 restraints weight = 133773.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.035971 restraints weight = 121218.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  21565  Z= 0.138
  Angle     :  0.630  10.174  29228  Z= 0.309
  Chirality :  0.041   0.186   3264
  Planarity :  0.004   0.041   3828
  Dihedral  :  5.090  56.219   3016
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.15 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.68 %
    Favored  : 85.90 %
  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 are not related in a simple way.
  whole: -0.41 (0.16), residues: 2728
  helix:  0.83 (0.16), residues: 1164
  sheet: -0.13 (0.29), residues: 338
  loop : -1.39 (0.17), residues: 1226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1054 
 TYR   0.013   0.001   TYR A 834 
 PHE   0.012   0.001   PHE C1077 
 TRP   0.016   0.001   TRP A 838 
 HIS   0.005   0.001   HIS D 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (21556)
  covalent geometry    : angle       0.62964 (29220)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       1.10039 (    8)
  hydrogen bonds       : bond        0.03365 (  882)
  hydrogen bonds       : angle       5.63229 ( 2601)
  Misc. bond           : bond        0.00034 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9561 (mmp) cc_final: 0.9104 (mmp)
REVERT: A  690 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7772 (mmm)
REVERT: A  804 MET cc_start: 0.8593 (tpp) cc_final: 0.8226 (mmm)
REVERT: A  854 MET cc_start: 0.6425 (tmm) cc_final: 0.5450 (tmm)
REVERT: A  921 MET cc_start: 0.7829 (ptt) cc_final: 0.7433 (ppp)
REVERT: A 1106 LYS cc_start: 0.9531 (tptp) cc_final: 0.9218 (mmmt)
REVERT: A 1153 MET cc_start: 0.8403 (ppp) cc_final: 0.7807 (ppp)
REVERT: A 1166 MET cc_start: 0.8537 (ptp) cc_final: 0.8032 (pmm)
REVERT: B  508 MET cc_start: 0.9121 (mmp) cc_final: 0.8750 (mmm)
REVERT: B  671 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6402 (tpt)
REVERT: B  686 MET cc_start: 0.9260 (mpp) cc_final: 0.9006 (mpp)
REVERT: B  934 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8376 (pm20)
REVERT: B  959 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5338 (p90)
REVERT: B 1116 MET cc_start: 0.8083 (mmt) cc_final: 0.7175 (ppp)
REVERT: B 1143 MET cc_start: 0.8600 (tpt) cc_final: 0.8346 (tpt)
REVERT: C  754 MET cc_start: 0.9376 (ppp) cc_final: 0.9133 (ppp)
REVERT: C  783 MET cc_start: 0.9074 (tpp) cc_final: 0.8753 (tpp)
REVERT: C  804 MET cc_start: 0.8666 (tpp) cc_final: 0.8372 (tpp)
REVERT: D  566 MET cc_start: 0.4728 (ttt) cc_final: 0.4470 (tpp)
REVERT: D  574 HIS cc_start: 0.9048 (m90) cc_final: 0.8827 (m90)
REVERT: D  604 MET cc_start: 0.8275 (tpt) cc_final: 0.7779 (tpp)
REVERT: D  616 MET cc_start: 0.8129 (mmp) cc_final: 0.7865 (mmp)
REVERT: D  729 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5197 (pm20)
REVERT: D  810 MET cc_start: 0.9005 (mmp) cc_final: 0.8500 (mmm)
REVERT: D  854 MET cc_start: 0.8186 (ttt) cc_final: 0.7902 (ttt)
REVERT: D  881 MET cc_start: 0.9441 (mmp) cc_final: 0.9066 (mmm)
  outliers start: 32
  outliers final: 17
  residues processed: 171
  average time/residue: 0.1432
  time to fit residues: 40.1423
Evaluate side-chains
  165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  603 SER
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue  850 CYS
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  729 GLU
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue 1052 LEU
Chi-restraints excluded: chain D residue 1109 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 188 optimal weight:    0.9990
   chunk 126 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 270 optimal weight:    5.9990
   chunk 200 optimal weight:    4.9990
   chunk 230 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 256 optimal weight:    1.9990
   chunk 138 optimal weight:    0.4980
   chunk 197 optimal weight:    4.9990
   chunk 175 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1040 GLN
B 506 HIS
B 510 ASN
B 653 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.046335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.034420 restraints weight = 232798.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.035102 restraints weight = 181930.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.035578 restraints weight = 151198.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.035918 restraints weight = 131753.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.036203 restraints weight = 118919.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  21565  Z= 0.117
  Angle     :  0.636  11.879  29228  Z= 0.307
  Chirality :  0.041   0.223   3264
  Planarity :  0.004   0.040   3828
  Dihedral  :  5.030  59.702   3016
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.85 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.79 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.16), residues: 2728
  helix:  0.88 (0.16), residues: 1168
  sheet: -0.02 (0.29), residues: 328
  loop : -1.40 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1070 
 TYR   0.013   0.001   TYR D 845 
 PHE   0.011   0.001   PHE C1078 
 TRP   0.012   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (21556)
  covalent geometry    : angle       0.63598 (29220)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       1.11481 (    8)
  hydrogen bonds       : bond        0.03201 (  882)
  hydrogen bonds       : angle       5.44822 ( 2601)
  Misc. bond           : bond        0.00027 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9553 (mmp) cc_final: 0.9083 (mmp)
REVERT: A  641 MET cc_start: 0.8039 (tmm) cc_final: 0.7809 (tmm)
REVERT: A  690 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7689 (mmm)
REVERT: A  804 MET cc_start: 0.8655 (tpp) cc_final: 0.8250 (mmm)
REVERT: A  854 MET cc_start: 0.6148 (tmm) cc_final: 0.5142 (tmm)
REVERT: A  921 MET cc_start: 0.7744 (ptt) cc_final: 0.7374 (ppp)
REVERT: A 1106 LYS cc_start: 0.9522 (tptp) cc_final: 0.9203 (mmmt)
REVERT: A 1143 MET cc_start: 0.6885 (mtm) cc_final: 0.6580 (mtt)
REVERT: A 1153 MET cc_start: 0.8325 (ppp) cc_final: 0.7761 (ppp)
REVERT: A 1166 MET cc_start: 0.8558 (ptp) cc_final: 0.8042 (pmm)
REVERT: B  508 MET cc_start: 0.9031 (mmp) cc_final: 0.8732 (mmm)
REVERT: B  616 MET cc_start: 0.7572 (mmp) cc_final: 0.7312 (mmp)
REVERT: B  671 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6410 (tpt)
REVERT: B  686 MET cc_start: 0.9247 (mpp) cc_final: 0.9002 (mpp)
REVERT: B  934 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8346 (pm20)
REVERT: B  959 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5650 (p90)
REVERT: B 1078 PHE cc_start: 0.8816 (m-80) cc_final: 0.8535 (m-80)
REVERT: B 1116 MET cc_start: 0.7854 (mmt) cc_final: 0.7143 (ptm)
REVERT: B 1143 MET cc_start: 0.8595 (tpt) cc_final: 0.8364 (tpt)
REVERT: B 1145 MET cc_start: 0.6594 (ptt) cc_final: 0.6245 (ptt)
REVERT: C  754 MET cc_start: 0.9357 (ppp) cc_final: 0.9115 (ppp)
REVERT: C  783 MET cc_start: 0.9047 (tpp) cc_final: 0.8730 (tpp)
REVERT: C  804 MET cc_start: 0.8739 (tpp) cc_final: 0.8457 (tpp)
REVERT: D  566 MET cc_start: 0.4609 (ttt) cc_final: 0.4397 (tpp)
REVERT: D  574 HIS cc_start: 0.8953 (m90) cc_final: 0.8742 (m90)
REVERT: D  604 MET cc_start: 0.8206 (tpt) cc_final: 0.7697 (tpp)
REVERT: D  616 MET cc_start: 0.8099 (mmp) cc_final: 0.7840 (mmp)
REVERT: D  706 TYR cc_start: 0.6213 (t80) cc_final: 0.5748 (t80)
REVERT: D  810 MET cc_start: 0.8999 (mmp) cc_final: 0.8448 (mmm)
REVERT: D  854 MET cc_start: 0.8319 (ttt) cc_final: 0.8023 (ttt)
REVERT: D  881 MET cc_start: 0.9435 (mmp) cc_final: 0.9195 (mmm)
  outliers start: 30
  outliers final: 18
  residues processed: 175
  average time/residue: 0.1387
  time to fit residues: 39.9515
Evaluate side-chains
  165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  603 SER
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue  796 VAL
Chi-restraints excluded: chain D residue 1033 LEU
Chi-restraints excluded: chain D residue 1052 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 113 optimal weight:    0.0270
   chunk 268 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 114 optimal weight:    0.0570
   chunk 181 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 246 optimal weight:    1.9990
   chunk 129 optimal weight:   30.0000
   chunk 197 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    2.6162

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 934 GLN
B 506 HIS
B 510 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.045987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.034201 restraints weight = 233804.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.034818 restraints weight = 181078.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.035300 restraints weight = 151358.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.035631 restraints weight = 131894.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.035923 restraints weight = 118830.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  21565  Z= 0.131
  Angle     :  0.654  11.253  29228  Z= 0.316
  Chirality :  0.042   0.291   3264
  Planarity :  0.004   0.041   3828
  Dihedral  :  4.977  58.322   3016
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.04 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.67 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.16), residues: 2728
  helix:  0.91 (0.16), residues: 1168
  sheet:  0.07 (0.29), residues: 328
  loop : -1.39 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1074 
 TYR   0.011   0.001   TYR B 837 
 PHE   0.023   0.001   PHE C1078 
 TRP   0.011   0.001   TRP A 838 
 HIS   0.004   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (21556)
  covalent geometry    : angle       0.65424 (29220)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       0.97391 (    8)
  hydrogen bonds       : bond        0.03190 (  882)
  hydrogen bonds       : angle       5.43987 ( 2601)
  Misc. bond           : bond        0.00021 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9547 (mmp) cc_final: 0.9046 (mmp)
REVERT: A  641 MET cc_start: 0.7991 (tmm) cc_final: 0.7733 (tmm)
REVERT: A  690 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7708 (mmm)
REVERT: A  828 MET cc_start: 0.8837 (tpt) cc_final: 0.8430 (tpt)
REVERT: A  900 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8020 (mmm)
REVERT: A  921 MET cc_start: 0.7688 (ptt) cc_final: 0.7380 (ppp)
REVERT: A 1106 LYS cc_start: 0.9531 (tptp) cc_final: 0.9214 (mmmt)
REVERT: A 1153 MET cc_start: 0.8316 (ppp) cc_final: 0.7753 (ppp)
REVERT: A 1166 MET cc_start: 0.8564 (ptp) cc_final: 0.8032 (pmm)
REVERT: B  508 MET cc_start: 0.9020 (mmp) cc_final: 0.8704 (mmm)
REVERT: B  616 MET cc_start: 0.7681 (mmp) cc_final: 0.7323 (mmp)
REVERT: B  671 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6384 (tpt)
REVERT: B  686 MET cc_start: 0.9230 (mpp) cc_final: 0.8978 (mpp)
REVERT: B  921 MET cc_start: 0.9401 (mpp) cc_final: 0.9159 (mpp)
REVERT: B  934 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8354 (pm20)
REVERT: B  959 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5636 (p90)
REVERT: B 1012 MET cc_start: 0.7979 (pmm) cc_final: 0.7471 (pmm)
REVERT: B 1078 PHE cc_start: 0.8828 (m-80) cc_final: 0.8605 (m-80)
REVERT: B 1116 MET cc_start: 0.7709 (mmt) cc_final: 0.6899 (ptm)
REVERT: B 1143 MET cc_start: 0.8644 (tpt) cc_final: 0.8425 (tpt)
REVERT: B 1145 MET cc_start: 0.6593 (ptt) cc_final: 0.6247 (ptt)
REVERT: C  754 MET cc_start: 0.9366 (ppp) cc_final: 0.9134 (ppp)
REVERT: C  783 MET cc_start: 0.9068 (tpp) cc_final: 0.8740 (tpp)
REVERT: C  804 MET cc_start: 0.8762 (tpp) cc_final: 0.8449 (tpp)
REVERT: D  574 HIS cc_start: 0.8980 (m90) cc_final: 0.8763 (m90)
REVERT: D  604 MET cc_start: 0.8236 (tpt) cc_final: 0.7694 (tpp)
REVERT: D  616 MET cc_start: 0.8154 (mmp) cc_final: 0.7886 (mmp)
REVERT: D  706 TYR cc_start: 0.6178 (t80) cc_final: 0.5890 (t80)
REVERT: D  810 MET cc_start: 0.9039 (mmp) cc_final: 0.8554 (mmm)
REVERT: D  854 MET cc_start: 0.8404 (ttt) cc_final: 0.8135 (ttt)
REVERT: D  881 MET cc_start: 0.9469 (mmp) cc_final: 0.9225 (mmm)
  outliers start: 32
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1390
  time to fit residues: 38.7210
Evaluate side-chains
  168 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  839 GLU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue  850 CYS
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue  796 VAL
Chi-restraints excluded: chain D residue 1033 LEU
Chi-restraints excluded: chain D residue 1052 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 163 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 142 optimal weight:    0.2980
   chunk 271 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 92 optimal weight:    9.9990
   chunk 189 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0570
   chunk 96 optimal weight:    2.9990
   overall best weight:    2.4704

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 HIS
B 510 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.045954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.034142 restraints weight = 231361.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.034741 restraints weight = 179948.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.035228 restraints weight = 151575.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.035561 restraints weight = 131120.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.035838 restraints weight = 118419.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  21565  Z= 0.125
  Angle     :  0.659  11.522  29228  Z= 0.316
  Chirality :  0.042   0.268   3264
  Planarity :  0.004   0.040   3828
  Dihedral  :  4.947  55.767   3016
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.93 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.94 %
    Favored  : 83.69 %
  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 are not related in a simple way.
  whole: -0.29 (0.16), residues: 2728
  helix:  0.92 (0.16), residues: 1168
  sheet:  0.11 (0.29), residues: 328
  loop : -1.38 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1070 
 TYR   0.011   0.001   TYR C 837 
 PHE   0.010   0.001   PHE C1077 
 TRP   0.011   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (21556)
  covalent geometry    : angle       0.65932 (29220)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       1.03778 (    8)
  hydrogen bonds       : bond        0.03148 (  882)
  hydrogen bonds       : angle       5.37074 ( 2601)
  Misc. bond           : bond        0.00024 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9539 (mmp) cc_final: 0.9042 (mmp)
REVERT: A  566 MET cc_start: 0.5450 (ppp) cc_final: 0.5002 (ppp)
REVERT: A  641 MET cc_start: 0.7958 (tmm) cc_final: 0.7647 (tmm)
REVERT: A  690 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7701 (mmm)
REVERT: A  828 MET cc_start: 0.8883 (tpt) cc_final: 0.8489 (tpp)
REVERT: A  900 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7987 (mmm)
REVERT: A  921 MET cc_start: 0.7684 (ptt) cc_final: 0.7382 (ppp)
REVERT: A 1106 LYS cc_start: 0.9537 (tptp) cc_final: 0.9237 (mmmt)
REVERT: A 1153 MET cc_start: 0.8320 (ppp) cc_final: 0.7721 (ppp)
REVERT: A 1166 MET cc_start: 0.8561 (ptp) cc_final: 0.8034 (pmm)
REVERT: B  508 MET cc_start: 0.8987 (mmp) cc_final: 0.8750 (mmp)
REVERT: B  616 MET cc_start: 0.7726 (mmp) cc_final: 0.7430 (mmp)
REVERT: B  671 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6398 (tpt)
REVERT: B  686 MET cc_start: 0.9271 (mpp) cc_final: 0.9011 (mpp)
REVERT: B  921 MET cc_start: 0.9373 (mpp) cc_final: 0.9097 (mpp)
REVERT: B  934 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8326 (pm20)
REVERT: B  959 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.5751 (p90)
REVERT: B 1078 PHE cc_start: 0.8844 (m-80) cc_final: 0.8596 (m-80)
REVERT: B 1116 MET cc_start: 0.7702 (mmt) cc_final: 0.6884 (ptm)
REVERT: B 1143 MET cc_start: 0.8664 (tpt) cc_final: 0.8445 (tpt)
REVERT: B 1145 MET cc_start: 0.6596 (ptt) cc_final: 0.6259 (ptt)
REVERT: C  754 MET cc_start: 0.9379 (ppp) cc_final: 0.9137 (ppp)
REVERT: C  783 MET cc_start: 0.9064 (tpp) cc_final: 0.8771 (tpp)
REVERT: C  804 MET cc_start: 0.8806 (tpp) cc_final: 0.8503 (tpp)
REVERT: D  574 HIS cc_start: 0.9000 (m90) cc_final: 0.8758 (m90)
REVERT: D  604 MET cc_start: 0.8107 (tpt) cc_final: 0.7744 (tpp)
REVERT: D  616 MET cc_start: 0.8142 (mmp) cc_final: 0.7884 (mmp)
REVERT: D  706 TYR cc_start: 0.6292 (t80) cc_final: 0.5848 (t80)
REVERT: D  810 MET cc_start: 0.9006 (mmp) cc_final: 0.8540 (mmm)
REVERT: D  854 MET cc_start: 0.8429 (ttt) cc_final: 0.8197 (ttt)
REVERT: D  881 MET cc_start: 0.9487 (mmp) cc_final: 0.9273 (mmm)
  outliers start: 31
  outliers final: 22
  residues processed: 168
  average time/residue: 0.1390
  time to fit residues: 38.7399
Evaluate side-chains
  169 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  839 GLU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  671 MET
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue 1050 VAL
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue  796 VAL
Chi-restraints excluded: chain D residue 1033 LEU
Chi-restraints excluded: chain D residue 1052 LEU
Chi-restraints excluded: chain D residue 1166 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 100 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0870
   chunk 261 optimal weight:    8.9990
   chunk 191 optimal weight:    9.9990
   chunk 164 optimal weight:    5.9990
   chunk 241 optimal weight:    0.7980
   chunk 143 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   chunk 65 optimal weight:   50.0000
   chunk 179 optimal weight:    6.9990
   overall best weight:    2.6162

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 HIS
B 510 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.045731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.033920 restraints weight = 231769.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.034571 restraints weight = 181265.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.035064 restraints weight = 150909.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.035410 restraints weight = 130839.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.035660 restraints weight = 117836.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  21565  Z= 0.131
  Angle     :  0.684  14.802  29228  Z= 0.325
  Chirality :  0.042   0.270   3264
  Planarity :  0.004   0.040   3828
  Dihedral  :  4.936  55.021   3016
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.00 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.47 %
    Favored  : 83.24 %
  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 are not related in a simple way.
  whole: -0.30 (0.16), residues: 2728
  helix:  0.91 (0.16), residues: 1168
  sheet:  0.11 (0.29), residues: 328
  loop : -1.38 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.011   0.001   TYR C 837 
 PHE   0.023   0.001   PHE C1078 
 TRP   0.011   0.001   TRP A 838 
 HIS   0.004   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (21556)
  covalent geometry    : angle       0.68397 (29220)
  SS BOND              : bond        0.00300 (    4)
  SS BOND              : angle       1.03192 (    8)
  hydrogen bonds       : bond        0.03218 (  882)
  hydrogen bonds       : angle       5.37878 ( 2601)
  Misc. bond           : bond        0.00020 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9531 (mmp) cc_final: 0.9030 (mmp)
REVERT: A  566 MET cc_start: 0.5374 (ppp) cc_final: 0.4871 (ppp)
REVERT: A  641 MET cc_start: 0.8052 (tmm) cc_final: 0.7741 (tmm)
REVERT: A  690 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7708 (mmm)
REVERT: A  828 MET cc_start: 0.8860 (tpt) cc_final: 0.8490 (tpp)
REVERT: A  921 MET cc_start: 0.7710 (ptt) cc_final: 0.7355 (ppp)
REVERT: A 1106 LYS cc_start: 0.9557 (tptp) cc_final: 0.9286 (mmmt)
REVERT: A 1153 MET cc_start: 0.8328 (ppp) cc_final: 0.7714 (ppp)
REVERT: A 1166 MET cc_start: 0.8574 (ptp) cc_final: 0.8066 (pmm)
REVERT: B  508 MET cc_start: 0.9038 (mmp) cc_final: 0.8773 (mmp)
REVERT: B  616 MET cc_start: 0.7801 (mmp) cc_final: 0.7491 (mmp)
REVERT: B  686 MET cc_start: 0.9280 (mpp) cc_final: 0.8996 (mpp)
REVERT: B  934 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8295 (pm20)
REVERT: B  959 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5928 (p90)
REVERT: B 1012 MET cc_start: 0.8101 (pmm) cc_final: 0.7717 (pmm)
REVERT: B 1116 MET cc_start: 0.7651 (mmt) cc_final: 0.6828 (ptm)
REVERT: B 1143 MET cc_start: 0.8726 (tpt) cc_final: 0.8466 (tpt)
REVERT: B 1145 MET cc_start: 0.6600 (ptt) cc_final: 0.6161 (ptt)
REVERT: C  754 MET cc_start: 0.9391 (ppp) cc_final: 0.9156 (ppp)
REVERT: C  783 MET cc_start: 0.9104 (tpp) cc_final: 0.8808 (tmm)
REVERT: C  801 MET cc_start: 0.9268 (mmp) cc_final: 0.8960 (mmp)
REVERT: C  804 MET cc_start: 0.8793 (tpp) cc_final: 0.8505 (tpp)
REVERT: D  574 HIS cc_start: 0.9014 (m90) cc_final: 0.8763 (m90)
REVERT: D  604 MET cc_start: 0.8118 (tpt) cc_final: 0.7708 (tpp)
REVERT: D  616 MET cc_start: 0.8144 (mmp) cc_final: 0.7913 (mmp)
REVERT: D  706 TYR cc_start: 0.6487 (t80) cc_final: 0.5950 (t80)
REVERT: D  810 MET cc_start: 0.9003 (mmp) cc_final: 0.8528 (mmm)
REVERT: D  854 MET cc_start: 0.8381 (ttt) cc_final: 0.8165 (ttt)
REVERT: D  881 MET cc_start: 0.9488 (mmp) cc_final: 0.9198 (mmm)
  outliers start: 29
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1380
  time to fit residues: 38.0113
Evaluate side-chains
  169 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  839 GLU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue 1050 VAL
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue  796 VAL
Chi-restraints excluded: chain D residue 1033 LEU
Chi-restraints excluded: chain D residue 1052 LEU
Chi-restraints excluded: chain D residue 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 222 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 251 optimal weight:    5.9990
   chunk 243 optimal weight:    3.9990
   chunk 192 optimal weight:    8.9990
   chunk 267 optimal weight:    0.0570
   chunk 90 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 202 optimal weight:    7.9990
   overall best weight:    2.5504

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 HIS
B 510 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.045624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.033812 restraints weight = 233141.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.034429 restraints weight = 181703.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.034930 restraints weight = 150347.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.035285 restraints weight = 131682.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.035547 restraints weight = 118427.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  21565  Z= 0.131
  Angle     :  0.698  13.243  29228  Z= 0.330
  Chirality :  0.042   0.263   3264
  Planarity :  0.004   0.040   3828
  Dihedral  :  4.942  56.501   3016
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.18 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.51 %
    Favored  : 83.24 %
  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 are not related in a simple way.
  whole: -0.29 (0.16), residues: 2728
  helix:  0.93 (0.16), residues: 1166
  sheet:  0.08 (0.29), residues: 328
  loop : -1.39 (0.17), residues: 1234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 762 
 TYR   0.011   0.001   TYR C 837 
 PHE   0.012   0.001   PHE B1078 
 TRP   0.011   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (21556)
  covalent geometry    : angle       0.69758 (29220)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       1.00390 (    8)
  hydrogen bonds       : bond        0.03269 (  882)
  hydrogen bonds       : angle       5.36419 ( 2601)
  Misc. bond           : bond        0.00020 (    5)

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

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

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5456 Ramachandran restraints generated.
    2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9526 (mmp) cc_final: 0.9084 (mmp)
REVERT: A  566 MET cc_start: 0.5399 (ppp) cc_final: 0.5131 (ppp)
REVERT: A  641 MET cc_start: 0.8053 (tmm) cc_final: 0.7739 (tmm)
REVERT: A  690 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7675 (mmm)
REVERT: A  828 MET cc_start: 0.8871 (tpt) cc_final: 0.8502 (tpp)
REVERT: A  921 MET cc_start: 0.7635 (ptt) cc_final: 0.7235 (ppp)
REVERT: A 1106 LYS cc_start: 0.9576 (tptp) cc_final: 0.9311 (mmmt)
REVERT: A 1153 MET cc_start: 0.8329 (ppp) cc_final: 0.7760 (ppp)
REVERT: A 1166 MET cc_start: 0.8583 (ptp) cc_final: 0.8082 (pmm)
REVERT: B  508 MET cc_start: 0.9079 (mmp) cc_final: 0.8820 (mmp)
REVERT: B  616 MET cc_start: 0.7871 (mmp) cc_final: 0.7418 (mmp)
REVERT: B  671 MET cc_start: 0.6712 (tpt) cc_final: 0.6399 (tpt)
REVERT: B  686 MET cc_start: 0.9260 (mpp) cc_final: 0.8970 (mpp)
REVERT: B  921 MET cc_start: 0.9364 (mpp) cc_final: 0.9116 (mpp)
REVERT: B  934 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8178 (pm20)
REVERT: B  959 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5837 (p90)
REVERT: B 1012 MET cc_start: 0.8089 (pmm) cc_final: 0.7600 (pmm)
REVERT: B 1078 PHE cc_start: 0.8985 (m-80) cc_final: 0.8315 (t80)
REVERT: B 1116 MET cc_start: 0.7595 (mmt) cc_final: 0.6771 (ptm)
REVERT: B 1143 MET cc_start: 0.8720 (tpt) cc_final: 0.8459 (tpt)
REVERT: B 1145 MET cc_start: 0.6606 (ptt) cc_final: 0.6167 (ptt)
REVERT: C  754 MET cc_start: 0.9365 (ppp) cc_final: 0.9155 (ppp)
REVERT: C  783 MET cc_start: 0.9099 (tpp) cc_final: 0.8812 (tmm)
REVERT: C  801 MET cc_start: 0.9256 (mmp) cc_final: 0.8962 (mmp)
REVERT: C  804 MET cc_start: 0.8780 (tpp) cc_final: 0.8483 (tpp)
REVERT: D  574 HIS cc_start: 0.9002 (m90) cc_final: 0.8744 (m90)
REVERT: D  604 MET cc_start: 0.8175 (tpt) cc_final: 0.7816 (tpp)
REVERT: D  706 TYR cc_start: 0.6588 (t80) cc_final: 0.5986 (t80)
REVERT: D  730 LEU cc_start: 0.8227 (tp) cc_final: 0.8006 (mm)
REVERT: D  810 MET cc_start: 0.9029 (mmp) cc_final: 0.8579 (mmm)
REVERT: D  881 MET cc_start: 0.9506 (mmp) cc_final: 0.9210 (mmm)
REVERT: D 1153 MET cc_start: 0.9241 (pmm) cc_final: 0.8845 (pmm)
  outliers start: 28
  outliers final: 24
  residues processed: 165
  average time/residue: 0.1331
  time to fit residues: 36.8177
Evaluate side-chains
  171 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  752 CYS
Chi-restraints excluded: chain A residue  839 GLU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1086 SER
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  850 CYS
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
Chi-restraints excluded: chain B residue  952 ILE
Chi-restraints excluded: chain B residue  959 PHE
Chi-restraints excluded: chain B residue 1148 VAL
Chi-restraints excluded: chain C residue  722 TYR
Chi-restraints excluded: chain C residue  850 CYS
Chi-restraints excluded: chain C residue 1050 VAL
Chi-restraints excluded: chain C residue 1116 MET
Chi-restraints excluded: chain D residue  521 SER
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  690 MET
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue  796 VAL
Chi-restraints excluded: chain D residue 1033 LEU
Chi-restraints excluded: chain D residue 1052 LEU
Chi-restraints excluded: chain D residue 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 117 optimal weight:    5.9990
   chunk 226 optimal weight:    0.0070
   chunk 135 optimal weight:    0.0050
   chunk 267 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   chunk 114 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 168 optimal weight:    0.9980
   chunk 195 optimal weight:    5.9990
   overall best weight:    0.4814

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 669 ASN
B 506 HIS
B 510 ASN
** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.046609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.034458 restraints weight = 230063.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.035158 restraints weight = 177717.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.035671 restraints weight = 146794.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.036064 restraints weight = 127132.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.036355 restraints weight = 113749.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  21565  Z= 0.109
  Angle     :  0.694  12.787  29228  Z= 0.326
  Chirality :  0.043   0.297   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  4.836  58.615   3016
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.67 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 15.74 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.16), residues: 2728
  helix:  0.94 (0.16), residues: 1166
  sheet:  0.17 (0.29), residues: 328
  loop : -1.38 (0.17), residues: 1234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 762 
 TYR   0.013   0.001   TYR B 834 
 PHE   0.022   0.001   PHE C1078 
 TRP   0.010   0.001   TRP D 607 
 HIS   0.004   0.001   HIS A 998 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (21556)
  covalent geometry    : angle       0.69373 (29220)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       1.13595 (    8)
  hydrogen bonds       : bond        0.03142 (  882)
  hydrogen bonds       : angle       5.19667 ( 2601)
  Misc. bond           : bond        0.00021 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4200.41 seconds
wall clock time: 73 minutes 21.48 seconds (4401.48 seconds total)