Starting phenix.real_space_refine
on Wed Jun 18 17:31:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wta_32773/06_2025/7wta_32773.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wta_32773/06_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_32773/06_2025/7wta_32773.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wta_32773/06_2025/7wta_32773.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wta_32773/06_2025/7wta_32773.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wta_32773/06_2025/7wta_32773.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.89, per 1000 atoms: 0.66
  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: 5.33
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  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: 2.54
  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: 7.95

  Time building geometry restraints manager: 6.43 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: 0.06
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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.910
  Check model and map are aligned:         0.160
  Set scattering table:                    0.200
  Process input model:                     51.200
  Find NCS groups from input model:        0.920
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   58.240
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (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
 TRP   0.016   0.002   TRP A 838 
 HIS   0.005   0.001   HIS C 574 
 PHE   0.024   0.002   PHE C1078 
 TYR   0.018   0.002   TYR B 951 
 ARG   0.009   0.001   ARG C1070 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18873 (  882)
  hydrogen bonds       : angle       7.62153 ( 2601)
  SS BOND              : bond        0.00711 (    4)
  SS BOND              : angle       3.08513 (    8)
  covalent geometry    : bond        0.00816 (21556)
  covalent geometry    : angle       0.82048 (29220)
  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  : 2.539 
Fit side-chains
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9522 (mmp) cc_final: 0.9148 (mmm)
REVERT: A  566 MET cc_start: 0.5803 (ppp) cc_final: 0.5588 (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: 0.8397 (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: 0.9160 (ppp)
REVERT: C  755 LEU cc_start: 0.9704 (mt) cc_final: 0.9261 (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: 0.8441 (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: 0.6199 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.3467
  time to fit residues: 92.0602
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  : 2.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 229 optimal weight:    2.9990
   chunk 206 optimal weight:   10.0000
   chunk 114 optimal weight:   30.0000
   chunk 70 optimal weight:    0.0770
   chunk 139 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 213 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 129 optimal weight:    0.8980
   chunk 158 optimal weight:    1.9990
   chunk 247 optimal weight:   20.0000
   overall best weight:    1.3942

-------------------------------------------------------------------------------
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
** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 956 HIS
C 559 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.047331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.035422 restraints weight = 230127.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.036085 restraints weight = 181517.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.036580 restraints weight = 151045.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  21565  Z= 0.127
  Angle     :  0.648   9.283  29228  Z= 0.322
  Chirality :  0.043   0.247   3264
  Planarity :  0.005   0.057   3828
  Dihedral  :  5.343  58.555   3016
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.89 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.69 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.16), residues: 2728
  helix:  0.68 (0.16), residues: 1164
  sheet: -0.09 (0.29), residues: 338
  loop : -1.43 (0.17), residues: 1226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 838 
 HIS   0.006   0.001   HIS B1101 
 PHE   0.014   0.001   PHE B 947 
 TYR   0.014   0.001   TYR B 834 
 ARG   0.006   0.001   ARG A 842 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04351 (  882)
  hydrogen bonds       : angle       6.01868 ( 2601)
  SS BOND              : bond        0.00230 (    4)
  SS BOND              : angle       1.76926 (    8)
  covalent geometry    : bond        0.00274 (21556)
  covalent geometry    : angle       0.64784 (29220)
  Misc. bond           : bond        0.00488 (    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
  164 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 2.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9558 (mmp) cc_final: 0.9137 (mmm)
REVERT: A  566 MET cc_start: 0.5539 (ppp) cc_final: 0.5289 (ppp)
REVERT: A  854 MET cc_start: 0.6136 (tmm) cc_final: 0.5651 (tmm)
REVERT: A  900 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8022 (mmt)
REVERT: A 1012 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6472 (ptp)
REVERT: A 1153 MET cc_start: 0.8337 (ppp) cc_final: 0.7918 (ppp)
REVERT: A 1166 MET cc_start: 0.8562 (ptp) cc_final: 0.7958 (pmm)
REVERT: B  616 MET cc_start: 0.7697 (mmp) cc_final: 0.7418 (mmp)
REVERT: B  671 MET cc_start: 0.6647 (tpt) cc_final: 0.6301 (tpt)
REVERT: B  686 MET cc_start: 0.9176 (mpp) cc_final: 0.8892 (mpp)
REVERT: B 1145 MET cc_start: 0.6502 (ptt) cc_final: 0.5581 (ptt)
REVERT: C  508 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8192 (mmp)
REVERT: C  754 MET cc_start: 0.9283 (ppp) cc_final: 0.8945 (ppp)
REVERT: C  755 LEU cc_start: 0.9641 (mt) cc_final: 0.9054 (mt)
REVERT: C  783 MET cc_start: 0.8999 (tpp) cc_final: 0.8764 (tpp)
REVERT: C  804 MET cc_start: 0.8522 (tpp) cc_final: 0.8069 (tpp)
REVERT: C  881 MET cc_start: 0.9252 (tpp) cc_final: 0.9029 (tpp)
REVERT: D  508 MET cc_start: 0.9199 (mmp) cc_final: 0.8994 (mmp)
REVERT: D  574 HIS cc_start: 0.8818 (m-70) cc_final: 0.8581 (m-70)
REVERT: D  604 MET cc_start: 0.8120 (tpt) cc_final: 0.7770 (tpp)
REVERT: D  730 LEU cc_start: 0.8108 (tp) cc_final: 0.7897 (mm)
REVERT: D  810 MET cc_start: 0.8977 (mmp) cc_final: 0.8546 (mmm)
REVERT: D  854 MET cc_start: 0.8071 (ttt) cc_final: 0.7681 (ttt)
REVERT: D  881 MET cc_start: 0.9350 (mmp) cc_final: 0.9004 (mmm)
REVERT: D 1098 MET cc_start: 0.6608 (mmt) cc_final: 0.6362 (mmt)
  outliers start: 8
  outliers final: 3
  residues processed: 161
  average time/residue: 0.3128
  time to fit residues: 81.8438
Evaluate side-chains
  150 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 2.251 
-------------------------------------------------------------------------------
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 C residue  508 MET
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 219 optimal weight:   20.0000
   chunk 156 optimal weight:   20.0000
   chunk 186 optimal weight:    0.5980
   chunk 194 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 173 optimal weight:   10.0000
   chunk 168 optimal weight:    0.0010
   chunk 246 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    1.0790

-------------------------------------------------------------------------------
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
** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 919 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.047448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.035552 restraints weight = 229156.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.036235 restraints weight = 179946.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.036733 restraints weight = 149784.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  21565  Z= 0.113
  Angle     :  0.613  10.251  29228  Z= 0.300
  Chirality :  0.041   0.151   3264
  Planarity :  0.004   0.049   3828
  Dihedral  :  5.036  56.628   3016
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  9.97 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.16), residues: 2728
  helix:  0.75 (0.16), residues: 1166
  sheet: -0.04 (0.29), residues: 338
  loop : -1.44 (0.17), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 838 
 HIS   0.004   0.001   HIS A 998 
 PHE   0.019   0.001   PHE B 674 
 TYR   0.018   0.001   TYR A 834 
 ARG   0.006   0.000   ARG B1054 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  882)
  hydrogen bonds       : angle       5.71212 ( 2601)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       1.44424 (    8)
  covalent geometry    : bond        0.00248 (21556)
  covalent geometry    : angle       0.61287 (29220)
  Misc. bond           : bond        0.00141 (    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
  164 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 2.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9547 (mmp) cc_final: 0.9147 (mmm)
REVERT: A  566 MET cc_start: 0.5489 (ppp) cc_final: 0.5232 (ppp)
REVERT: A  690 MET cc_start: 0.8149 (tpt) cc_final: 0.7797 (mmm)
REVERT: A  900 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7850 (mmt)
REVERT: A  921 MET cc_start: 0.7757 (ptt) cc_final: 0.7462 (ppp)
REVERT: A 1012 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6431 (ptp)
REVERT: A 1153 MET cc_start: 0.8272 (ppp) cc_final: 0.7800 (ppp)
REVERT: A 1166 MET cc_start: 0.8465 (ptp) cc_final: 0.7826 (pmm)
REVERT: B  508 MET cc_start: 0.8932 (mmp) cc_final: 0.8470 (mmt)
REVERT: B  616 MET cc_start: 0.7436 (mmp) cc_final: 0.7126 (mmp)
REVERT: B  671 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6075 (tpt)
REVERT: B  686 MET cc_start: 0.9242 (mpp) cc_final: 0.8951 (mpp)
REVERT: B 1116 MET cc_start: 0.8307 (mmt) cc_final: 0.7383 (ptm)
REVERT: B 1145 MET cc_start: 0.6604 (ptt) cc_final: 0.5727 (ptt)
REVERT: C  508 MET cc_start: 0.8662 (mmt) cc_final: 0.8162 (mmp)
REVERT: C  616 MET cc_start: 0.8488 (mpp) cc_final: 0.8184 (mmp)
REVERT: C  754 MET cc_start: 0.9260 (ppp) cc_final: 0.8876 (ppp)
REVERT: C  755 LEU cc_start: 0.9668 (mt) cc_final: 0.9097 (mt)
REVERT: C  783 MET cc_start: 0.9017 (tpp) cc_final: 0.8713 (tpp)
REVERT: D  574 HIS cc_start: 0.8752 (m-70) cc_final: 0.8537 (m90)
REVERT: D  604 MET cc_start: 0.8118 (tpt) cc_final: 0.7697 (tpp)
REVERT: D  616 MET cc_start: 0.8136 (mmp) cc_final: 0.7817 (mmp)
REVERT: D  810 MET cc_start: 0.8939 (mmp) cc_final: 0.8500 (mmm)
REVERT: D  854 MET cc_start: 0.8203 (ttt) cc_final: 0.7958 (ttt)
REVERT: D  881 MET cc_start: 0.9360 (mmp) cc_final: 0.9071 (mmm)
REVERT: D 1098 MET cc_start: 0.6699 (mmt) cc_final: 0.6476 (mmt)
REVERT: D 1153 MET cc_start: 0.8942 (pmm) cc_final: 0.8528 (pmm)
  outliers start: 14
  outliers final: 5
  residues processed: 158
  average time/residue: 0.3149
  time to fit residues: 79.9975
Evaluate side-chains
  155 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 2.225 
-------------------------------------------------------------------------------
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 D residue  578 LEU
Chi-restraints excluded: chain D residue  629 GLU
Chi-restraints excluded: chain D residue  752 CYS
Chi-restraints excluded: chain D residue 1166 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 265 optimal weight:   20.0000
   chunk 144 optimal weight:    0.3980
   chunk 241 optimal weight:    8.9990
   chunk 248 optimal weight:   20.0000
   chunk 159 optimal weight:    0.9990
   chunk 261 optimal weight:   10.0000
   chunk 124 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 268 optimal weight:    8.9990
   chunk 133 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    3.8586

-------------------------------------------------------------------------------
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
A1135 GLN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 873 ASN
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 574 HIS ** 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 = 0.3527 r_free = 0.3527 target = 0.046135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.034305 restraints weight = 237985.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.034947 restraints weight = 187997.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.035395 restraints weight = 157326.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  21565  Z= 0.167
  Angle     :  0.632   9.766  29228  Z= 0.315
  Chirality :  0.041   0.146   3264
  Planarity :  0.004   0.045   3828
  Dihedral  :  5.019  53.845   3016
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.66 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.61 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.16), residues: 2728
  helix:  0.84 (0.16), residues: 1158
  sheet: -0.10 (0.29), residues: 338
  loop : -1.41 (0.17), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 624 
 HIS   0.005   0.001   HIS C 875 
 PHE   0.017   0.001   PHE B 763 
 TYR   0.013   0.002   TYR B 951 
 ARG   0.008   0.001   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  882)
  hydrogen bonds       : angle       5.68006 ( 2601)
  SS BOND              : bond        0.00315 (    4)
  SS BOND              : angle       1.18065 (    8)
  covalent geometry    : bond        0.00353 (21556)
  covalent geometry    : angle       0.63177 (29220)
  Misc. bond           : bond        0.00038 (    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
  184 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 2.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9538 (mmp) cc_final: 0.9161 (mmp)
REVERT: A  804 MET cc_start: 0.8565 (tpp) cc_final: 0.8078 (mmm)
REVERT: A  854 MET cc_start: 0.6216 (tmm) cc_final: 0.5405 (tmm)
REVERT: A  921 MET cc_start: 0.7951 (ptt) cc_final: 0.7513 (ppp)
REVERT: A 1012 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6419 (ptp)
REVERT: A 1106 LYS cc_start: 0.9570 (tptp) cc_final: 0.9241 (mmmt)
REVERT: A 1153 MET cc_start: 0.8293 (ppp) cc_final: 0.7748 (ppp)
REVERT: A 1166 MET cc_start: 0.8518 (ptp) cc_final: 0.7999 (pmm)
REVERT: B  508 MET cc_start: 0.8978 (mmp) cc_final: 0.8478 (mmt)
REVERT: B  566 MET cc_start: 0.8325 (tpp) cc_final: 0.8097 (tpp)
REVERT: B  616 MET cc_start: 0.7742 (mmp) cc_final: 0.7487 (mmp)
REVERT: B  671 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6544 (tpt)
REVERT: B  686 MET cc_start: 0.9246 (mpp) cc_final: 0.9026 (mpp)
REVERT: B 1012 MET cc_start: 0.8375 (pmm) cc_final: 0.8030 (pmm)
REVERT: B 1143 MET cc_start: 0.8459 (tpt) cc_final: 0.8231 (tpt)
REVERT: B 1145 MET cc_start: 0.6743 (ptt) cc_final: 0.5683 (ptt)
REVERT: C  754 MET cc_start: 0.9359 (ppp) cc_final: 0.9132 (ppp)
REVERT: C  783 MET cc_start: 0.9098 (tpp) cc_final: 0.8794 (tpp)
REVERT: D  566 MET cc_start: 0.4773 (ttt) cc_final: 0.4528 (tpp)
REVERT: D  604 MET cc_start: 0.8293 (tpt) cc_final: 0.7778 (tpp)
REVERT: D  616 MET cc_start: 0.8187 (mmp) cc_final: 0.7911 (mmp)
REVERT: D  810 MET cc_start: 0.9051 (mmp) cc_final: 0.8557 (mmm)
REVERT: D  881 MET cc_start: 0.9421 (mmp) cc_final: 0.9059 (mmm)
  outliers start: 31
  outliers final: 12
  residues processed: 177
  average time/residue: 0.3007
  time to fit residues: 86.3832
Evaluate side-chains
  162 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 2.282 
-------------------------------------------------------------------------------
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 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 223 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 96 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0020
   chunk 240 optimal weight:    9.9990
   chunk 161 optimal weight:   10.0000
   chunk 124 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 265 optimal weight:    4.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    3.5996

-------------------------------------------------------------------------------
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 653 ASN
B 669 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 574 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.045984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.034127 restraints weight = 236922.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.034788 restraints weight = 186383.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.035229 restraints weight = 154844.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  21565  Z= 0.155
  Angle     :  0.642  12.984  29228  Z= 0.316
  Chirality :  0.041   0.162   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  5.059  55.326   3016
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.26 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.03 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.16), residues: 2728
  helix:  0.80 (0.16), residues: 1170
  sheet: -0.11 (0.29), residues: 338
  loop : -1.41 (0.17), residues: 1220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.013   0.001   PHE C1077 
 TYR   0.013   0.001   TYR A 834 
 ARG   0.004   0.001   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  882)
  hydrogen bonds       : angle       5.61179 ( 2601)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       1.10147 (    8)
  covalent geometry    : bond        0.00331 (21556)
  covalent geometry    : angle       0.64184 (29220)
  Misc. bond           : bond        0.00037 (    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
  173 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 2.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9558 (mmp) cc_final: 0.9086 (mmp)
REVERT: A  804 MET cc_start: 0.8602 (tpp) cc_final: 0.7985 (tpp)
REVERT: A  854 MET cc_start: 0.6331 (tmm) cc_final: 0.5634 (tmm)
REVERT: A 1106 LYS cc_start: 0.9534 (tptp) cc_final: 0.9224 (mmmt)
REVERT: A 1153 MET cc_start: 0.8377 (ppp) cc_final: 0.7781 (ppp)
REVERT: A 1166 MET cc_start: 0.8528 (ptp) cc_final: 0.8017 (pmm)
REVERT: B  508 MET cc_start: 0.8985 (mmp) cc_final: 0.8432 (mmt)
REVERT: B  671 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6379 (tpt)
REVERT: B  686 MET cc_start: 0.9224 (mpp) cc_final: 0.8996 (mpp)
REVERT: B 1116 MET cc_start: 0.8120 (mmt) cc_final: 0.7296 (ptm)
REVERT: B 1145 MET cc_start: 0.6718 (ptt) cc_final: 0.6333 (ptt)
REVERT: C  616 MET cc_start: 0.8557 (mpp) cc_final: 0.8090 (mmp)
REVERT: C  754 MET cc_start: 0.9338 (ppp) cc_final: 0.9106 (ppp)
REVERT: C  783 MET cc_start: 0.9039 (tpp) cc_final: 0.8726 (tpp)
REVERT: C  804 MET cc_start: 0.8730 (tpp) cc_final: 0.8270 (tpp)
REVERT: D  566 MET cc_start: 0.5088 (ttt) cc_final: 0.4849 (tpp)
REVERT: D  574 HIS cc_start: 0.8983 (m90) cc_final: 0.8770 (m90)
REVERT: D  604 MET cc_start: 0.8258 (tpt) cc_final: 0.7735 (tpp)
REVERT: D  616 MET cc_start: 0.8098 (mmp) cc_final: 0.7848 (mmp)
REVERT: D  729 GLU cc_start: 0.5481 (OUTLIER) cc_final: 0.5133 (pm20)
REVERT: D  810 MET cc_start: 0.9005 (mmp) cc_final: 0.8479 (mmm)
REVERT: D  854 MET cc_start: 0.8150 (ttt) cc_final: 0.7919 (ttt)
REVERT: D  881 MET cc_start: 0.9461 (mmp) cc_final: 0.9208 (mmm)
  outliers start: 26
  outliers final: 14
  residues processed: 168
  average time/residue: 0.3384
  time to fit residues: 93.4882
Evaluate side-chains
  159 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 2.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  752 CYS
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  952 ILE
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 223 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 157 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   chunk 166 optimal weight:    6.9990
   chunk 135 optimal weight:   20.0000
   chunk 261 optimal weight:    7.9990
   chunk 3 optimal weight:   40.0000
   chunk 229 optimal weight:    4.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 899 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.045480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.033730 restraints weight = 237055.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.034357 restraints weight = 185508.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.034840 restraints weight = 155029.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  21565  Z= 0.163
  Angle     :  0.666  12.120  29228  Z= 0.325
  Chirality :  0.042   0.230   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  5.135  58.963   3016
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.59 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.05 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.16), residues: 2728
  helix:  0.80 (0.16), residues: 1170
  sheet: -0.13 (0.29), residues: 338
  loop : -1.39 (0.17), residues: 1220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 838 
 HIS   0.006   0.001   HIS B 574 
 PHE   0.014   0.001   PHE B 763 
 TYR   0.011   0.002   TYR B 951 
 ARG   0.005   0.001   ARG B1070 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  882)
  hydrogen bonds       : angle       5.59820 ( 2601)
  SS BOND              : bond        0.00345 (    4)
  SS BOND              : angle       1.05776 (    8)
  covalent geometry    : bond        0.00346 (21556)
  covalent geometry    : angle       0.66602 (29220)
  Misc. bond           : bond        0.00030 (    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
  178 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 2.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9545 (mmp) cc_final: 0.9031 (mmp)
REVERT: A  690 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7802 (mmm)
REVERT: A  804 MET cc_start: 0.8617 (tpp) cc_final: 0.7990 (tpp)
REVERT: A  854 MET cc_start: 0.6189 (tmm) cc_final: 0.5462 (tmm)
REVERT: A  921 MET cc_start: 0.7757 (ptt) cc_final: 0.7330 (ppp)
REVERT: A 1106 LYS cc_start: 0.9551 (tptp) cc_final: 0.9248 (mmmt)
REVERT: A 1153 MET cc_start: 0.8375 (ppp) cc_final: 0.7808 (ppp)
REVERT: A 1166 MET cc_start: 0.8516 (ptp) cc_final: 0.8011 (pmm)
REVERT: B  508 MET cc_start: 0.9084 (mmp) cc_final: 0.8486 (mmt)
REVERT: B  671 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6512 (tpt)
REVERT: B  686 MET cc_start: 0.9271 (mpp) cc_final: 0.9052 (mpp)
REVERT: B  934 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8388 (pm20)
REVERT: B  959 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5625 (p90)
REVERT: B 1012 MET cc_start: 0.8404 (pmm) cc_final: 0.8083 (pmm)
REVERT: B 1116 MET cc_start: 0.8080 (mmt) cc_final: 0.7268 (ptm)
REVERT: B 1145 MET cc_start: 0.6734 (ptt) cc_final: 0.6310 (ptt)
REVERT: C  616 MET cc_start: 0.8659 (mpp) cc_final: 0.8273 (mmp)
REVERT: C  754 MET cc_start: 0.9403 (ppp) cc_final: 0.9168 (ppp)
REVERT: C  783 MET cc_start: 0.9108 (tpp) cc_final: 0.8850 (tpp)
REVERT: C  804 MET cc_start: 0.8803 (tpp) cc_final: 0.8354 (tpp)
REVERT: D  574 HIS cc_start: 0.9033 (m90) cc_final: 0.8819 (m90)
REVERT: D  604 MET cc_start: 0.8345 (tpt) cc_final: 0.7828 (tpp)
REVERT: D  616 MET cc_start: 0.8146 (mmp) cc_final: 0.7909 (mmp)
REVERT: D  706 TYR cc_start: 0.6144 (t80) cc_final: 0.5584 (t80)
REVERT: D  810 MET cc_start: 0.9054 (mmp) cc_final: 0.8523 (mmm)
REVERT: D  854 MET cc_start: 0.8302 (ttt) cc_final: 0.8055 (ttt)
REVERT: D  881 MET cc_start: 0.9460 (mmp) cc_final: 0.9213 (mmm)
  outliers start: 31
  outliers final: 20
  residues processed: 172
  average time/residue: 0.2898
  time to fit residues: 82.0865
Evaluate side-chains
  169 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 2.264 
-------------------------------------------------------------------------------
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 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  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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 75 optimal weight:    0.0870
   chunk 32 optimal weight:    9.9990
   chunk 268 optimal weight:    0.6980
   chunk 62 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 143 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 146 optimal weight:    7.9990
   chunk 122 optimal weight:    7.9990
   chunk 149 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    2.7162

-------------------------------------------------------------------------------
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 919 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 = 0.3512 r_free = 0.3512 target = 0.045702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.033918 restraints weight = 234940.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.034558 restraints weight = 184082.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.035050 restraints weight = 153765.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2416

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= 0.132
  Angle     :  0.662  11.359  29228  Z= 0.320
  Chirality :  0.042   0.264   3264
  Planarity :  0.004   0.041   3828
  Dihedral  :  5.103  59.207   3016
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.15 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.63 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.16), residues: 2728
  helix:  0.84 (0.16), residues: 1170
  sheet: -0.04 (0.29), residues: 328
  loop : -1.41 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.023   0.001   PHE C1078 
 TYR   0.012   0.001   TYR C 837 
 ARG   0.003   0.000   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  882)
  hydrogen bonds       : angle       5.49461 ( 2601)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       1.09055 (    8)
  covalent geometry    : bond        0.00288 (21556)
  covalent geometry    : angle       0.66220 (29220)
  Misc. bond           : bond        0.00025 (    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
  174 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 2.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9531 (mmp) cc_final: 0.9022 (mmp)
REVERT: A  566 MET cc_start: 0.5449 (ppp) cc_final: 0.4973 (ppp)
REVERT: A  641 MET cc_start: 0.7956 (tmm) cc_final: 0.7691 (tmm)
REVERT: A  690 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7670 (mmm)
REVERT: A  900 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8083 (mmm)
REVERT: A  921 MET cc_start: 0.7759 (ptt) cc_final: 0.7411 (ppp)
REVERT: A 1106 LYS cc_start: 0.9571 (tptp) cc_final: 0.9270 (mmmt)
REVERT: A 1153 MET cc_start: 0.8283 (ppp) cc_final: 0.7727 (ppp)
REVERT: A 1166 MET cc_start: 0.8567 (ptp) cc_final: 0.8051 (pmm)
REVERT: B  508 MET cc_start: 0.9089 (mmp) cc_final: 0.8452 (mmt)
REVERT: B  616 MET cc_start: 0.7784 (mmp) cc_final: 0.7295 (mmp)
REVERT: B  671 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6575 (tpt)
REVERT: B  686 MET cc_start: 0.9275 (mpp) cc_final: 0.9045 (mpp)
REVERT: B  921 MET cc_start: 0.9435 (mpp) cc_final: 0.9196 (mpp)
REVERT: B  934 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8358 (pm20)
REVERT: B  959 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5771 (p90)
REVERT: B 1116 MET cc_start: 0.7976 (mmt) cc_final: 0.7115 (ptm)
REVERT: B 1145 MET cc_start: 0.6691 (ptt) cc_final: 0.6229 (ptt)
REVERT: C  616 MET cc_start: 0.8595 (mpp) cc_final: 0.8235 (mmp)
REVERT: C  754 MET cc_start: 0.9396 (ppp) cc_final: 0.9158 (ppp)
REVERT: C  783 MET cc_start: 0.9132 (tpp) cc_final: 0.8806 (tpp)
REVERT: C  804 MET cc_start: 0.8810 (tpp) cc_final: 0.8433 (tpp)
REVERT: D  574 HIS cc_start: 0.9014 (m90) cc_final: 0.8800 (m90)
REVERT: D  604 MET cc_start: 0.8277 (tpt) cc_final: 0.7863 (tpp)
REVERT: D  616 MET cc_start: 0.8187 (mmp) cc_final: 0.7932 (mmp)
REVERT: D  706 TYR cc_start: 0.6218 (t80) cc_final: 0.5922 (t80)
REVERT: D  810 MET cc_start: 0.9044 (mmp) cc_final: 0.8580 (mmm)
REVERT: D  854 MET cc_start: 0.8359 (ttt) cc_final: 0.8116 (ttt)
REVERT: D  881 MET cc_start: 0.9458 (mmp) cc_final: 0.9229 (mmm)
  outliers start: 29
  outliers final: 18
  residues processed: 168
  average time/residue: 0.2970
  time to fit residues: 83.8696
Evaluate side-chains
  165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 2.351 
-------------------------------------------------------------------------------
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  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 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 241 optimal weight:    1.9990
   chunk 157 optimal weight:    1.9990
   chunk 179 optimal weight:    0.1980
   chunk 159 optimal weight:    0.9980
   chunk 173 optimal weight:   10.0000
   chunk 83 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 258 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   chunk 144 optimal weight:    0.3980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 919 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 = 0.3537 r_free = 0.3537 target = 0.046584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.034623 restraints weight = 232867.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.035313 restraints weight = 181297.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.035819 restraints weight = 149436.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  21565  Z= 0.109
  Angle     :  0.678  14.934  29228  Z= 0.320
  Chirality :  0.042   0.188   3264
  Planarity :  0.004   0.041   3828
  Dihedral  :  4.970  59.002   3016
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.74 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.38 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.16), residues: 2728
  helix:  0.89 (0.16), residues: 1170
  sheet:  0.10 (0.29), residues: 328
  loop : -1.40 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.010   0.001   PHE B 947 
 TYR   0.012   0.001   TYR B 834 
 ARG   0.004   0.000   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  882)
  hydrogen bonds       : angle       5.32131 ( 2601)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       1.17912 (    8)
  covalent geometry    : bond        0.00243 (21556)
  covalent geometry    : angle       0.67825 (29220)
  Misc. bond           : bond        0.00043 (    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
  174 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 2.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9533 (mmp) cc_final: 0.9047 (mmp)
REVERT: A  566 MET cc_start: 0.5250 (ppp) cc_final: 0.4786 (ppp)
REVERT: A  641 MET cc_start: 0.7950 (tmm) cc_final: 0.7669 (tmm)
REVERT: A  690 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7628 (mmm)
REVERT: A  854 MET cc_start: 0.5944 (tmm) cc_final: 0.5549 (tmm)
REVERT: A  921 MET cc_start: 0.7644 (ptt) cc_final: 0.7346 (ppp)
REVERT: A 1106 LYS cc_start: 0.9541 (tptp) cc_final: 0.9237 (mmmt)
REVERT: A 1143 MET cc_start: 0.6438 (mtt) cc_final: 0.4998 (pmm)
REVERT: A 1153 MET cc_start: 0.8309 (ppp) cc_final: 0.7758 (ppp)
REVERT: A 1166 MET cc_start: 0.8566 (ptp) cc_final: 0.8037 (pmm)
REVERT: B  508 MET cc_start: 0.8976 (mmp) cc_final: 0.8376 (mmt)
REVERT: B  616 MET cc_start: 0.7575 (mmp) cc_final: 0.7267 (mmp)
REVERT: B  671 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6425 (tpt)
REVERT: B  686 MET cc_start: 0.9287 (mpp) cc_final: 0.9026 (mpp)
REVERT: B  724 MET cc_start: 0.8771 (mmt) cc_final: 0.8514 (mmm)
REVERT: B  921 MET cc_start: 0.9385 (mpp) cc_final: 0.9080 (mpp)
REVERT: B  934 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8292 (pm20)
REVERT: B  959 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5804 (p90)
REVERT: B 1078 PHE cc_start: 0.8902 (m-80) cc_final: 0.8243 (t80)
REVERT: B 1145 MET cc_start: 0.6659 (ptt) cc_final: 0.5718 (ptt)
REVERT: C  616 MET cc_start: 0.8590 (mpp) cc_final: 0.8223 (mmp)
REVERT: C  754 MET cc_start: 0.9398 (ppp) cc_final: 0.9158 (ppp)
REVERT: C  783 MET cc_start: 0.9090 (tpp) cc_final: 0.8748 (tpp)
REVERT: C  804 MET cc_start: 0.8790 (tpp) cc_final: 0.8441 (tpp)
REVERT: D  574 HIS cc_start: 0.8880 (m90) cc_final: 0.8647 (m90)
REVERT: D  604 MET cc_start: 0.8143 (tpt) cc_final: 0.7802 (tpp)
REVERT: D  616 MET cc_start: 0.8125 (mmp) cc_final: 0.7872 (mmp)
REVERT: D  706 TYR cc_start: 0.6238 (t80) cc_final: 0.5807 (t80)
REVERT: D  810 MET cc_start: 0.8971 (mmp) cc_final: 0.8527 (mmm)
REVERT: D  854 MET cc_start: 0.8376 (ttt) cc_final: 0.8122 (ttt)
REVERT: D  881 MET cc_start: 0.9475 (mmp) cc_final: 0.9117 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 167
  average time/residue: 0.3078
  time to fit residues: 85.2046
Evaluate side-chains
  161 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 2.220 
-------------------------------------------------------------------------------
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 B residue  671 MET
Chi-restraints excluded: chain B residue  910 SER
Chi-restraints excluded: chain B residue  934 GLN
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 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 1166 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 259 optimal weight:   20.0000
   chunk 231 optimal weight:   20.0000
   chunk 118 optimal weight:    0.1980
   chunk 74 optimal weight:    0.0470
   chunk 102 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 221 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 255 optimal weight:    5.9990
   chunk 184 optimal weight:   20.0000
   chunk 28 optimal weight:    0.0370
   overall best weight:    0.8560

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.046749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.034729 restraints weight = 231788.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.035426 restraints weight = 179079.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.035940 restraints weight = 147708.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2714

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= 0.108
  Angle     :  0.701  18.136  29228  Z= 0.326
  Chirality :  0.042   0.233   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  4.859  58.945   3016
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.74 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.74 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.16), residues: 2728
  helix:  0.92 (0.16), residues: 1166
  sheet:  0.21 (0.29), residues: 328
  loop : -1.43 (0.17), residues: 1234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 838 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.022   0.001   PHE C1078 
 TYR   0.011   0.001   TYR B 834 
 ARG   0.003   0.000   ARG B 581 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03145 (  882)
  hydrogen bonds       : angle       5.24555 ( 2601)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       1.09973 (    8)
  covalent geometry    : bond        0.00242 (21556)
  covalent geometry    : angle       0.70084 (29220)
  Misc. bond           : bond        0.00026 (    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
  171 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 2.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9551 (mmp) cc_final: 0.9122 (mmp)
REVERT: A  641 MET cc_start: 0.7953 (tmm) cc_final: 0.7666 (tmm)
REVERT: A  690 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7764 (mmm)
REVERT: A  921 MET cc_start: 0.7626 (ptt) cc_final: 0.7295 (ppp)
REVERT: A 1106 LYS cc_start: 0.9538 (tptp) cc_final: 0.9262 (mmmt)
REVERT: A 1143 MET cc_start: 0.6563 (mtt) cc_final: 0.6014 (pmm)
REVERT: A 1153 MET cc_start: 0.8300 (ppp) cc_final: 0.7741 (ppp)
REVERT: A 1166 MET cc_start: 0.8522 (ptp) cc_final: 0.7989 (pmm)
REVERT: B  508 MET cc_start: 0.8968 (mmp) cc_final: 0.8352 (mmt)
REVERT: B  616 MET cc_start: 0.7605 (mmp) cc_final: 0.7301 (mmp)
REVERT: B  671 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6345 (tpt)
REVERT: B  686 MET cc_start: 0.9318 (mpp) cc_final: 0.9040 (mpp)
REVERT: B  934 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8251 (pm20)
REVERT: B  959 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5651 (p90)
REVERT: B 1012 MET cc_start: 0.8192 (pmm) cc_final: 0.7655 (pmm)
REVERT: B 1145 MET cc_start: 0.6661 (ptt) cc_final: 0.5673 (ptt)
REVERT: C  616 MET cc_start: 0.8569 (mpp) cc_final: 0.8242 (mmp)
REVERT: C  754 MET cc_start: 0.9395 (ppp) cc_final: 0.9169 (ppp)
REVERT: C  783 MET cc_start: 0.9108 (tpp) cc_final: 0.8787 (tpp)
REVERT: C  804 MET cc_start: 0.8807 (tpp) cc_final: 0.8462 (tpp)
REVERT: D  574 HIS cc_start: 0.8862 (m90) cc_final: 0.8651 (m90)
REVERT: D  604 MET cc_start: 0.8345 (tpt) cc_final: 0.7854 (tpp)
REVERT: D  616 MET cc_start: 0.8098 (mmp) cc_final: 0.7884 (mmp)
REVERT: D  706 TYR cc_start: 0.6438 (t80) cc_final: 0.5929 (t80)
REVERT: D  810 MET cc_start: 0.8961 (mmp) cc_final: 0.8520 (mmm)
REVERT: D  854 MET cc_start: 0.8386 (ttt) cc_final: 0.8179 (ttt)
REVERT: D  881 MET cc_start: 0.9480 (mmp) cc_final: 0.9126 (mmm)
REVERT: D 1153 MET cc_start: 0.9252 (pmm) cc_final: 0.8875 (pmm)
  outliers start: 26
  outliers final: 19
  residues processed: 163
  average time/residue: 0.2849
  time to fit residues: 77.1039
Evaluate side-chains
  165 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 2.270 
-------------------------------------------------------------------------------
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 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 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 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 259 optimal weight:    9.9990
   chunk 149 optimal weight:    4.9990
   chunk 227 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 235 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 146 optimal weight:    8.9990
   chunk 83 optimal weight:    9.9990
   chunk 157 optimal weight:    3.9990
   chunk 252 optimal weight:    8.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 875 HIS
** 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 = 0.3508 r_free = 0.3508 target = 0.045471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.033676 restraints weight = 235966.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.034330 restraints weight = 184653.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.034794 restraints weight = 153012.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  21565  Z= 0.159
  Angle     :  0.717  14.366  29228  Z= 0.341
  Chirality :  0.042   0.242   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  4.948  58.080   3016
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.55 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.13 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.16), residues: 2728
  helix:  0.93 (0.16), residues: 1166
  sheet: -0.04 (0.29), residues: 346
  loop : -1.33 (0.17), residues: 1216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 624 
 HIS   0.006   0.001   HIS D 574 
 PHE   0.014   0.001   PHE C1077 
 TYR   0.013   0.001   TYR B 951 
 ARG   0.005   0.001   ARG A 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  882)
  hydrogen bonds       : angle       5.38484 ( 2601)
  SS BOND              : bond        0.00303 (    4)
  SS BOND              : angle       0.98685 (    8)
  covalent geometry    : bond        0.00339 (21556)
  covalent geometry    : angle       0.71737 (29220)
  Misc. bond           : bond        0.00023 (    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
  167 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 2.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.9529 (mmp) cc_final: 0.9040 (mmp)
REVERT: A  566 MET cc_start: 0.5195 (ppp) cc_final: 0.4936 (ppp)
REVERT: A  641 MET cc_start: 0.7979 (tmm) cc_final: 0.7608 (tmm)
REVERT: A  690 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7653 (mmm)
REVERT: A  921 MET cc_start: 0.7625 (ptt) cc_final: 0.7246 (ppp)
REVERT: A 1106 LYS cc_start: 0.9581 (tptp) cc_final: 0.9318 (mmmt)
REVERT: A 1143 MET cc_start: 0.6668 (mtt) cc_final: 0.6105 (pmm)
REVERT: A 1153 MET cc_start: 0.8329 (ppp) cc_final: 0.7757 (ppp)
REVERT: A 1166 MET cc_start: 0.8540 (ptp) cc_final: 0.8056 (pmm)
REVERT: B  508 MET cc_start: 0.9045 (mmp) cc_final: 0.8425 (mmt)
REVERT: B  616 MET cc_start: 0.7922 (mmp) cc_final: 0.7503 (mmp)
REVERT: B  671 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6823 (tpp)
REVERT: B  686 MET cc_start: 0.9282 (mpp) cc_final: 0.9015 (mpp)
REVERT: B  921 MET cc_start: 0.9406 (mpp) cc_final: 0.9023 (mpp)
REVERT: B  934 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8270 (pm20)
REVERT: B  959 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5928 (p90)
REVERT: B 1012 MET cc_start: 0.8118 (pmm) cc_final: 0.7704 (pmm)
REVERT: B 1078 PHE cc_start: 0.9025 (m-80) cc_final: 0.8369 (t80)
REVERT: B 1145 MET cc_start: 0.6649 (ptt) cc_final: 0.5698 (ptt)
REVERT: C  616 MET cc_start: 0.8615 (mpp) cc_final: 0.8288 (mmp)
REVERT: C  783 MET cc_start: 0.9116 (tpp) cc_final: 0.8829 (tmm)
REVERT: C  804 MET cc_start: 0.8875 (tpp) cc_final: 0.8508 (tpp)
REVERT: D  574 HIS cc_start: 0.9015 (m90) cc_final: 0.8766 (m90)
REVERT: D  604 MET cc_start: 0.8296 (tpt) cc_final: 0.7867 (tpp)
REVERT: D  616 MET cc_start: 0.8295 (mmp) cc_final: 0.8055 (mmp)
REVERT: D  706 TYR cc_start: 0.6622 (t80) cc_final: 0.6025 (t80)
REVERT: D  730 LEU cc_start: 0.8245 (tp) cc_final: 0.7988 (mm)
REVERT: D  810 MET cc_start: 0.9033 (mmp) cc_final: 0.8582 (mmm)
REVERT: D  881 MET cc_start: 0.9504 (mmp) cc_final: 0.9167 (mmm)
REVERT: D 1153 MET cc_start: 0.9230 (pmm) cc_final: 0.8870 (pmm)
  outliers start: 23
  outliers final: 18
  residues processed: 159
  average time/residue: 0.2924
  time to fit residues: 77.3497
Evaluate side-chains
  166 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 2.286 
-------------------------------------------------------------------------------
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 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 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  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 1166 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 45 optimal weight:    0.0370
   chunk 185 optimal weight:    3.9990
   chunk 255 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 225 optimal weight:    0.0670
   chunk 200 optimal weight:    7.9990
   chunk 227 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0670
   chunk 174 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 144 optimal weight:    0.2980
   overall best weight:    0.8936

-------------------------------------------------------------------------------
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
A1040 GLN
B 506 HIS
B 510 ASN
** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1081 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.046436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.034850 restraints weight = 230249.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.035441 restraints weight = 184006.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.035859 restraints weight = 155884.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  21565  Z= 0.109
  Angle     :  0.703  14.406  29228  Z= 0.329
  Chirality :  0.042   0.193   3264
  Planarity :  0.004   0.042   3828
  Dihedral  :  4.841  54.166   3016
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.96 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.36 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.16), residues: 2728
  helix:  0.92 (0.16), residues: 1166
  sheet:  0.11 (0.29), residues: 336
  loop : -1.39 (0.17), residues: 1226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 838 
 HIS   0.004   0.001   HIS A 998 
 PHE   0.022   0.001   PHE C1078 
 TYR   0.013   0.001   TYR B 834 
 ARG   0.005   0.000   ARG A 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03116 (  882)
  hydrogen bonds       : angle       5.19989 ( 2601)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       1.00929 (    8)
  covalent geometry    : bond        0.00245 (21556)
  covalent geometry    : angle       0.70294 (29220)
  Misc. bond           : bond        0.00022 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7192.55 seconds
wall clock time: 125 minutes 37.17 seconds (7537.17 seconds total)