Starting phenix.real_space_refine
on Mon Mar 25 22:50:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895_trim.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895_trim.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/03_2024/8e4p_27895_trim.pdb"
  }
  resolution = 3.59
  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=   0.003 sd=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C   17736      2.51       5
     N    4396      2.21       5
     O    4692      1.98       5
     H   24392      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  616": "OE1" <-> "OE2"
    Residue "A TYR  999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU 1056": "OE1" <-> "OE2"
    Residue "B GLU  616": "OE1" <-> "OE2"
    Residue "B TYR  999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU 1056": "OE1" <-> "OE2"
    Residue "C GLU  616": "OE1" <-> "OE2"
    Residue "C TYR  999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU 1056": "OE1" <-> "OE2"
    Residue "D GLU  616": "OE1" <-> "OE2"
    Residue "D TYR  999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU 1056": "OE1" <-> "OE2"
  Time to flip residues: 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 51336
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 12733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 899, 12733
          Classifications: {'peptide': 899}
          Link IDs: {'PTRANS': 19, 'TRANS': 879}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 729
          Unresolved non-hydrogen angles: 906
          Unresolved non-hydrogen dihedrals: 595
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 452
    Chain: "B"
      Number of atoms: 12733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 899, 12733
          Classifications: {'peptide': 899}
          Link IDs: {'PTRANS': 19, 'TRANS': 879}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 729
          Unresolved non-hydrogen angles: 906
          Unresolved non-hydrogen dihedrals: 595
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 452
    Chain: "C"
      Number of atoms: 12733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 899, 12733
          Classifications: {'peptide': 899}
          Link IDs: {'PTRANS': 19, 'TRANS': 879}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 729
          Unresolved non-hydrogen angles: 906
          Unresolved non-hydrogen dihedrals: 595
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 452
    Chain: "D"
      Number of atoms: 12733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 899, 12733
          Classifications: {'peptide': 899}
          Link IDs: {'PTRANS': 19, 'TRANS': 879}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 729
          Unresolved non-hydrogen angles: 906
          Unresolved non-hydrogen dihedrals: 595
          Unresolved non-hydrogen chiralities: 45
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 452
    Chain: "A"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 101
          Unusual residues: {'Y01': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 101
          Unusual residues: {'Y01': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
    Chain: "C"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 101
          Unusual residues: {'Y01': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
    Chain: "D"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 101
          Unusual residues: {'Y01': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
  Time building chain proxies: 22.53, per 1000 atoms: 0.44
  Number of scatterers: 51336
  At special positions: 0
  Unit cell: (152.28, 152.28, 149.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     120     16.00
     O    4692      8.00
     N    4396      7.00
     C   17736      6.00
     H   24392      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 40.06
  Conformation dependent library (CDL) restraints added in 6.1 seconds
  

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6848

  Finding SS restraints...
    Secondary structure from input PDB file:
      172 helices and 4 sheets defined
      75.0% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 50
    Processing helix  chain 'A' and resid 125 through 137
    Processing helix  chain 'A' and resid 158 through 176
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.685A  pdb=" N   TYR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 287
      removed outlier: 4.265A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 322
      removed outlier: 3.795A  pdb=" N   SER A 322 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 343
    Processing helix  chain 'A' and resid 351 through 362
      removed outlier: 3.806A  pdb=" N   LEU A 362 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 369
    Processing helix  chain 'A' and resid 370 through 386
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.742A  pdb=" N   THR A 418 " --> pdb=" O   LYS A 414 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 437
      removed outlier: 3.911A  pdb=" N   GLN A 429 " --> pdb=" O   ASN A 425 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TRP A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 445
    Processing helix  chain 'A' and resid 458 through 468
    Processing helix  chain 'A' and resid 470 through 480
      removed outlier: 3.758A  pdb=" N   ASN A 480 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 489 through 499
    Processing helix  chain 'A' and resid 502 through 517
      removed outlier: 3.556A  pdb=" N   ASN A 517 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 533
      removed outlier: 3.588A  pdb=" N   PHE A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 571
    Processing helix  chain 'A' and resid 573 through 584
    Processing helix  chain 'A' and resid 587 through 604
      removed outlier: 3.671A  pdb=" N   VAL A 604 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 636
    Processing helix  chain 'A' and resid 637 through 645
      removed outlier: 3.650A  pdb=" N   VAL A 645 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 664
    Processing helix  chain 'A' and resid 665 through 670
    Processing helix  chain 'A' and resid 671 through 684
    Processing helix  chain 'A' and resid 691 through 701
      removed outlier: 3.556A  pdb=" N   ILE A 695 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 708
    Processing helix  chain 'A' and resid 723 through 733
    Processing helix  chain 'A' and resid 733 through 758
      removed outlier: 3.587A  pdb=" N   LEU A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 790
    Processing helix  chain 'A' and resid 791 through 795
    Processing helix  chain 'A' and resid 796 through 817
      removed outlier: 3.629A  pdb=" N   ILE A 810 " --> pdb=" O   LEU A 806 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA A 811 " --> pdb=" O   PHE A 807 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 812 " --> pdb=" O   TYR A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 852
      removed outlier: 3.897A  pdb=" N   ILE A 837 " --> pdb=" O   CYS A 833 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 838 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 890
      removed outlier: 4.152A  pdb=" N   ALA A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 913
      removed outlier: 3.606A  pdb=" N   GLU A 906 " --> pdb=" O   SER A 902 " (cutoff:3.500A)
      Proline residue:  A 907  - end of helix
    Processing helix  chain 'A' and resid 955 through 979
    Processing helix  chain 'A' and resid 979 through 985
      removed outlier: 4.012A  pdb=" N   VAL A 983 " --> pdb=" O   PHE A 979 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY A 984 " --> pdb=" O   GLY A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1008
      removed outlier: 3.526A  pdb=" N   TRP A 994 " --> pdb=" O   ASN A 990 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 995 " --> pdb=" O   ASP A 991 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1029
      removed outlier: 4.432A  pdb=" N   VAL A1017 " --> pdb=" O   PHE A1013 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   PHE A1018 " --> pdb=" O   PRO A1014 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA A1019 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1075
      removed outlier: 3.606A  pdb=" N   ALA A1071 " --> pdb=" O   ILE A1067 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASN A1072 " --> pdb=" O   ASN A1068 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER A1075 " --> pdb=" O   ALA A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1104
      removed outlier: 3.565A  pdb=" N   ILE A1103 " --> pdb=" O   ILE A1099 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS A1104 " --> pdb=" O   ALA A1100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
    Processing helix  chain 'B' and resid 125 through 137
    Processing helix  chain 'B' and resid 158 through 176
    Processing helix  chain 'B' and resid 187 through 202
      removed outlier: 3.685A  pdb=" N   TYR B 191 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 287
      removed outlier: 4.264A  pdb=" N   LEU B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 322
      removed outlier: 3.795A  pdb=" N   SER B 322 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 343
    Processing helix  chain 'B' and resid 351 through 362
      removed outlier: 3.806A  pdb=" N   LEU B 362 " --> pdb=" O   LEU B 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 369
    Processing helix  chain 'B' and resid 370 through 386
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 3.742A  pdb=" N   THR B 418 " --> pdb=" O   LYS B 414 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN B 419 " --> pdb=" O   ALA B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 437
      removed outlier: 3.911A  pdb=" N   GLN B 429 " --> pdb=" O   ASN B 425 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TRP B 436 " --> pdb=" O   LEU B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 445
    Processing helix  chain 'B' and resid 458 through 468
    Processing helix  chain 'B' and resid 470 through 480
      removed outlier: 3.758A  pdb=" N   ASN B 480 " --> pdb=" O   LEU B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 488
    Processing helix  chain 'B' and resid 489 through 499
    Processing helix  chain 'B' and resid 502 through 517
      removed outlier: 3.555A  pdb=" N   ASN B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 533
      removed outlier: 3.588A  pdb=" N   PHE B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 571
    Processing helix  chain 'B' and resid 573 through 584
    Processing helix  chain 'B' and resid 587 through 604
      removed outlier: 3.671A  pdb=" N   VAL B 604 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 636
    Processing helix  chain 'B' and resid 637 through 645
      removed outlier: 3.650A  pdb=" N   VAL B 645 " --> pdb=" O   GLU B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 664
    Processing helix  chain 'B' and resid 665 through 670
    Processing helix  chain 'B' and resid 671 through 684
    Processing helix  chain 'B' and resid 691 through 701
      removed outlier: 3.556A  pdb=" N   ILE B 695 " --> pdb=" O   LYS B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 708
    Processing helix  chain 'B' and resid 723 through 733
    Processing helix  chain 'B' and resid 733 through 758
      removed outlier: 3.587A  pdb=" N   LEU B 757 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 790
    Processing helix  chain 'B' and resid 791 through 795
    Processing helix  chain 'B' and resid 796 through 817
      removed outlier: 3.629A  pdb=" N   ILE B 810 " --> pdb=" O   LEU B 806 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B 811 " --> pdb=" O   PHE B 807 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY B 812 " --> pdb=" O   TYR B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 852
      removed outlier: 3.897A  pdb=" N   ILE B 837 " --> pdb=" O   CYS B 833 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B 838 " --> pdb=" O   LEU B 834 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 856 through 890
      removed outlier: 4.152A  pdb=" N   ALA B 880 " --> pdb=" O   VAL B 876 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 895 through 913
      removed outlier: 3.606A  pdb=" N   GLU B 906 " --> pdb=" O   SER B 902 " (cutoff:3.500A)
      Proline residue:  B 907  - end of helix
    Processing helix  chain 'B' and resid 955 through 979
    Processing helix  chain 'B' and resid 979 through 985
      removed outlier: 4.012A  pdb=" N   VAL B 983 " --> pdb=" O   PHE B 979 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY B 984 " --> pdb=" O   GLY B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 989 through 1008
      removed outlier: 3.526A  pdb=" N   TRP B 994 " --> pdb=" O   ASN B 990 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS B 995 " --> pdb=" O   ASP B 991 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B1008 " --> pdb=" O   GLU B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1012 through 1029
      removed outlier: 4.433A  pdb=" N   VAL B1017 " --> pdb=" O   PHE B1013 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   PHE B1018 " --> pdb=" O   PRO B1014 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ALA B1019 " --> pdb=" O   PHE B1015 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1075
      removed outlier: 3.605A  pdb=" N   ALA B1071 " --> pdb=" O   ILE B1067 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN B1072 " --> pdb=" O   ASN B1068 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER B1075 " --> pdb=" O   ALA B1071 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1078 through 1104
      removed outlier: 3.566A  pdb=" N   ILE B1103 " --> pdb=" O   ILE B1099 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS B1104 " --> pdb=" O   ALA B1100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
    Processing helix  chain 'C' and resid 125 through 137
    Processing helix  chain 'C' and resid 158 through 176
    Processing helix  chain 'C' and resid 187 through 202
      removed outlier: 3.685A  pdb=" N   TYR C 191 " --> pdb=" O   GLY C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 287
      removed outlier: 4.265A  pdb=" N   LEU C 277 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 309 through 322
      removed outlier: 3.795A  pdb=" N   SER C 322 " --> pdb=" O   THR C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 343
    Processing helix  chain 'C' and resid 351 through 362
      removed outlier: 3.806A  pdb=" N   LEU C 362 " --> pdb=" O   LEU C 358 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 362 through 369
    Processing helix  chain 'C' and resid 370 through 386
    Processing helix  chain 'C' and resid 403 through 419
      removed outlier: 3.741A  pdb=" N   THR C 418 " --> pdb=" O   LYS C 414 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN C 419 " --> pdb=" O   ALA C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 437
      removed outlier: 3.911A  pdb=" N   GLN C 429 " --> pdb=" O   ASN C 425 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TRP C 436 " --> pdb=" O   LEU C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 445
    Processing helix  chain 'C' and resid 458 through 468
    Processing helix  chain 'C' and resid 470 through 480
      removed outlier: 3.758A  pdb=" N   ASN C 480 " --> pdb=" O   LEU C 476 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 488
    Processing helix  chain 'C' and resid 489 through 499
    Processing helix  chain 'C' and resid 502 through 517
      removed outlier: 3.556A  pdb=" N   ASN C 517 " --> pdb=" O   LYS C 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 518 through 533
      removed outlier: 3.588A  pdb=" N   PHE C 523 " --> pdb=" O   ALA C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 571
    Processing helix  chain 'C' and resid 573 through 584
    Processing helix  chain 'C' and resid 587 through 604
      removed outlier: 3.671A  pdb=" N   VAL C 604 " --> pdb=" O   THR C 600 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 636
    Processing helix  chain 'C' and resid 637 through 645
      removed outlier: 3.650A  pdb=" N   VAL C 645 " --> pdb=" O   GLU C 641 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 655 through 664
    Processing helix  chain 'C' and resid 665 through 670
    Processing helix  chain 'C' and resid 671 through 684
    Processing helix  chain 'C' and resid 691 through 701
      removed outlier: 3.556A  pdb=" N   ILE C 695 " --> pdb=" O   LYS C 691 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 702 through 708
    Processing helix  chain 'C' and resid 723 through 733
    Processing helix  chain 'C' and resid 733 through 758
      removed outlier: 3.587A  pdb=" N   LEU C 757 " --> pdb=" O   ALA C 753 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 765 through 790
    Processing helix  chain 'C' and resid 791 through 795
    Processing helix  chain 'C' and resid 796 through 817
      removed outlier: 3.629A  pdb=" N   ILE C 810 " --> pdb=" O   LEU C 806 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA C 811 " --> pdb=" O   PHE C 807 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY C 812 " --> pdb=" O   TYR C 808 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 821 through 852
      removed outlier: 3.898A  pdb=" N   ILE C 837 " --> pdb=" O   CYS C 833 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE C 838 " --> pdb=" O   LEU C 834 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 856 through 890
      removed outlier: 4.152A  pdb=" N   ALA C 880 " --> pdb=" O   VAL C 876 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 895 through 913
      removed outlier: 3.606A  pdb=" N   GLU C 906 " --> pdb=" O   SER C 902 " (cutoff:3.500A)
      Proline residue:  C 907  - end of helix
    Processing helix  chain 'C' and resid 955 through 979
    Processing helix  chain 'C' and resid 979 through 985
      removed outlier: 4.012A  pdb=" N   VAL C 983 " --> pdb=" O   PHE C 979 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY C 984 " --> pdb=" O   GLY C 980 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 989 through 1008
      removed outlier: 3.526A  pdb=" N   TRP C 994 " --> pdb=" O   ASN C 990 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS C 995 " --> pdb=" O   ASP C 991 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG C1008 " --> pdb=" O   GLU C1004 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1012 through 1029
      removed outlier: 4.433A  pdb=" N   VAL C1017 " --> pdb=" O   PHE C1013 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   PHE C1018 " --> pdb=" O   PRO C1014 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA C1019 " --> pdb=" O   PHE C1015 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1048 through 1075
      removed outlier: 3.605A  pdb=" N   ALA C1071 " --> pdb=" O   ILE C1067 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN C1072 " --> pdb=" O   ASN C1068 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER C1075 " --> pdb=" O   ALA C1071 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1078 through 1104
      removed outlier: 3.566A  pdb=" N   ILE C1103 " --> pdb=" O   ILE C1099 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS C1104 " --> pdb=" O   ALA C1100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 50
    Processing helix  chain 'D' and resid 125 through 137
    Processing helix  chain 'D' and resid 158 through 176
    Processing helix  chain 'D' and resid 187 through 202
      removed outlier: 3.685A  pdb=" N   TYR D 191 " --> pdb=" O   GLY D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 287
      removed outlier: 4.264A  pdb=" N   LEU D 277 " --> pdb=" O   VAL D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 322
      removed outlier: 3.796A  pdb=" N   SER D 322 " --> pdb=" O   THR D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 334 through 343
    Processing helix  chain 'D' and resid 351 through 362
      removed outlier: 3.805A  pdb=" N   LEU D 362 " --> pdb=" O   LEU D 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 369
    Processing helix  chain 'D' and resid 370 through 386
    Processing helix  chain 'D' and resid 403 through 419
      removed outlier: 3.742A  pdb=" N   THR D 418 " --> pdb=" O   LYS D 414 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN D 419 " --> pdb=" O   ALA D 415 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 425 through 437
      removed outlier: 3.911A  pdb=" N   GLN D 429 " --> pdb=" O   ASN D 425 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TRP D 436 " --> pdb=" O   LEU D 432 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 438 through 445
    Processing helix  chain 'D' and resid 458 through 468
    Processing helix  chain 'D' and resid 470 through 480
      removed outlier: 3.758A  pdb=" N   ASN D 480 " --> pdb=" O   LEU D 476 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 483 through 488
    Processing helix  chain 'D' and resid 489 through 499
    Processing helix  chain 'D' and resid 502 through 517
      removed outlier: 3.556A  pdb=" N   ASN D 517 " --> pdb=" O   LYS D 513 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 518 through 533
      removed outlier: 3.588A  pdb=" N   PHE D 523 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 559 through 571
    Processing helix  chain 'D' and resid 573 through 584
    Processing helix  chain 'D' and resid 587 through 604
      removed outlier: 3.671A  pdb=" N   VAL D 604 " --> pdb=" O   THR D 600 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 607 through 636
    Processing helix  chain 'D' and resid 637 through 645
      removed outlier: 3.650A  pdb=" N   VAL D 645 " --> pdb=" O   GLU D 641 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 655 through 664
    Processing helix  chain 'D' and resid 665 through 670
    Processing helix  chain 'D' and resid 671 through 684
    Processing helix  chain 'D' and resid 691 through 701
      removed outlier: 3.556A  pdb=" N   ILE D 695 " --> pdb=" O   LYS D 691 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 702 through 708
    Processing helix  chain 'D' and resid 723 through 733
    Processing helix  chain 'D' and resid 733 through 758
      removed outlier: 3.586A  pdb=" N   LEU D 757 " --> pdb=" O   ALA D 753 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 765 through 790
    Processing helix  chain 'D' and resid 791 through 795
    Processing helix  chain 'D' and resid 796 through 817
      removed outlier: 3.630A  pdb=" N   ILE D 810 " --> pdb=" O   LEU D 806 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA D 811 " --> pdb=" O   PHE D 807 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY D 812 " --> pdb=" O   TYR D 808 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 821 through 852
      removed outlier: 3.897A  pdb=" N   ILE D 837 " --> pdb=" O   CYS D 833 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE D 838 " --> pdb=" O   LEU D 834 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 856 through 890
      removed outlier: 4.153A  pdb=" N   ALA D 880 " --> pdb=" O   VAL D 876 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 913
      removed outlier: 3.606A  pdb=" N   GLU D 906 " --> pdb=" O   SER D 902 " (cutoff:3.500A)
      Proline residue:  D 907  - end of helix
    Processing helix  chain 'D' and resid 955 through 979
    Processing helix  chain 'D' and resid 979 through 985
      removed outlier: 4.012A  pdb=" N   VAL D 983 " --> pdb=" O   PHE D 979 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY D 984 " --> pdb=" O   GLY D 980 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 989 through 1008
      removed outlier: 3.526A  pdb=" N   TRP D 994 " --> pdb=" O   ASN D 990 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS D 995 " --> pdb=" O   ASP D 991 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG D1008 " --> pdb=" O   GLU D1004 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1012 through 1029
      removed outlier: 4.433A  pdb=" N   VAL D1017 " --> pdb=" O   PHE D1013 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   PHE D1018 " --> pdb=" O   PRO D1014 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA D1019 " --> pdb=" O   PHE D1015 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1048 through 1075
      removed outlier: 3.606A  pdb=" N   ALA D1071 " --> pdb=" O   ILE D1067 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN D1072 " --> pdb=" O   ASN D1068 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER D1075 " --> pdb=" O   ALA D1071 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1078 through 1104
      removed outlier: 3.565A  pdb=" N   ILE D1103 " --> pdb=" O   ILE D1099 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS D1104 " --> pdb=" O   ALA D1100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119
      removed outlier: 3.805A  pdb=" N   LEU A 260 " --> pdb=" O   LYS A 116 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU A 262 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA A 211 " --> pdb=" O   HIS A 259 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   LEU A 261 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLY A 213 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL A 263 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ALA A 215 " --> pdb=" O   VAL A 263 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU A 144 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   PHE A 304 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE A 146 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ILE A 301 " --> pdb=" O   CYS A 326 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL A 328 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   CYS A 303 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 116 through 119
      removed outlier: 3.805A  pdb=" N   LEU B 260 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA B 211 " --> pdb=" O   HIS B 259 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   LEU B 261 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLY B 213 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL B 263 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ALA B 215 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU B 144 " --> pdb=" O   VAL B 302 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   PHE B 304 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE B 146 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ILE B 301 " --> pdb=" O   CYS B 326 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL B 328 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   CYS B 303 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 119
      removed outlier: 3.805A  pdb=" N   LEU C 260 " --> pdb=" O   LYS C 116 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU C 262 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA C 211 " --> pdb=" O   HIS C 259 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LEU C 261 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLY C 213 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL C 263 " --> pdb=" O   GLY C 213 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ALA C 215 " --> pdb=" O   VAL C 263 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU C 144 " --> pdb=" O   VAL C 302 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   PHE C 304 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE C 146 " --> pdb=" O   PHE C 304 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE C 301 " --> pdb=" O   CYS C 326 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL C 328 " --> pdb=" O   ILE C 301 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   CYS C 303 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 116 through 119
      removed outlier: 3.805A  pdb=" N   LEU D 260 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU D 262 " --> pdb=" O   LEU D 118 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA D 211 " --> pdb=" O   HIS D 259 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   LEU D 261 " --> pdb=" O   ALA D 211 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLY D 213 " --> pdb=" O   LEU D 261 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL D 263 " --> pdb=" O   GLY D 213 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ALA D 215 " --> pdb=" O   VAL D 263 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU D 144 " --> pdb=" O   VAL D 302 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   PHE D 304 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE D 146 " --> pdb=" O   PHE D 304 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE D 301 " --> pdb=" O   CYS D 326 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL D 328 " --> pdb=" O   ILE D 301 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   CYS D 303 " --> pdb=" O   VAL D 328 " (cutoff:3.500A)

    1905 hydrogen bonds defined for protein.
    5643 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: 19.40

  Time building geometry restraints manager: 41.65 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 24332
        1.03 -     1.23: 97
        1.23 -     1.42: 11631
        1.42 -     1.62: 15724
        1.62 -     1.81: 180
  Bond restraints: 51964
  Sorted by residual:
  bond pdb=" CAY Y01 D1202 "
       pdb=" OAW Y01 D1202 "
    ideal  model  delta    sigma   weight residual
    1.332  1.431 -0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" CAY Y01 C1202 "
       pdb=" OAW Y01 C1202 "
    ideal  model  delta    sigma   weight residual
    1.332  1.431 -0.099 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" CAY Y01 B1203 "
       pdb=" OAW Y01 B1203 "
    ideal  model  delta    sigma   weight residual
    1.332  1.430 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" CAY Y01 C1203 "
       pdb=" OAW Y01 C1203 "
    ideal  model  delta    sigma   weight residual
    1.332  1.430 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" CAY Y01 A1202 "
       pdb=" OAW Y01 A1202 "
    ideal  model  delta    sigma   weight residual
    1.332  1.430 -0.098 2.00e-02 2.50e+03 2.42e+01
  ... (remaining 51959 not shown)

  Histogram of bond angle deviations from ideal:
       93.45 -   101.57: 55
      101.57 -   109.70: 34977
      109.70 -   117.83: 32183
      117.83 -   125.95: 25307
      125.95 -   134.08: 582
  Bond angle restraints: 93104
  Sorted by residual:
  angle pdb=" CAT Y01 A1201 "
        pdb=" CBH Y01 A1201 "
        pdb=" CBF Y01 A1201 "
      ideal   model   delta    sigma   weight residual
     108.46   93.45   15.01 3.00e+00 1.11e-01 2.50e+01
  angle pdb=" CAT Y01 D1201 "
        pdb=" CBH Y01 D1201 "
        pdb=" CBF Y01 D1201 "
      ideal   model   delta    sigma   weight residual
     108.46   93.46   15.00 3.00e+00 1.11e-01 2.50e+01
  angle pdb=" CAT Y01 B1201 "
        pdb=" CBH Y01 B1201 "
        pdb=" CBF Y01 B1201 "
      ideal   model   delta    sigma   weight residual
     108.46   93.47   14.99 3.00e+00 1.11e-01 2.50e+01
  angle pdb=" CAT Y01 C1201 "
        pdb=" CBH Y01 C1201 "
        pdb=" CBF Y01 C1201 "
      ideal   model   delta    sigma   weight residual
     108.46   93.50   14.96 3.00e+00 1.11e-01 2.49e+01
  angle pdb=" CAT Y01 A1203 "
        pdb=" CBH Y01 A1203 "
        pdb=" CBF Y01 A1203 "
      ideal   model   delta    sigma   weight residual
     108.46   93.52   14.94 3.00e+00 1.11e-01 2.48e+01
  ... (remaining 93099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 23080
       16.39 -    32.78: 1800
       32.78 -    49.17: 442
       49.17 -    65.57: 178
       65.57 -    81.96: 12
  Dihedral angle restraints: 25512
    sinusoidal: 12760
      harmonic: 12752
  Sorted by residual:
  dihedral pdb=" CA  LYS D 856 "
           pdb=" C   LYS D 856 "
           pdb=" N   ILE D 857 "
           pdb=" CA  ILE D 857 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.01  -15.99     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LYS A 856 "
           pdb=" C   LYS A 856 "
           pdb=" N   ILE A 857 "
           pdb=" CA  ILE A 857 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.04  -15.96     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LYS B 856 "
           pdb=" C   LYS B 856 "
           pdb=" N   ILE B 857 "
           pdb=" CA  ILE B 857 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.06  -15.94     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 25509 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 4303
       0.089 -    0.178: 129
       0.178 -    0.267: 24
       0.267 -    0.356: 12
       0.356 -    0.445: 24
  Chirality restraints: 4492
  Sorted by residual:
  chirality pdb=" CBF Y01 B1202 "
            pdb=" CAS Y01 B1202 "
            pdb=" CBD Y01 B1202 "
            pdb=" CBH Y01 B1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.89    0.44 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" CBF Y01 A1202 "
            pdb=" CAS Y01 A1202 "
            pdb=" CBD Y01 A1202 "
            pdb=" CBH Y01 A1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.89    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CBF Y01 C1202 "
            pdb=" CAS Y01 C1202 "
            pdb=" CBD Y01 C1202 "
            pdb=" CBH Y01 C1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.89    0.44 2.00e-01 2.50e+01 4.92e+00
  ... (remaining 4489 not shown)

  Planarity restraints: 8108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 324 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO C 325 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C 325 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 325 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 862 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   ARG B 862 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ARG B 862 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET B 863 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 324 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO B 325 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 325 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 325 "    0.023 5.00e-02 4.00e+02
  ... (remaining 8105 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 3150
        2.21 -     2.81: 101361
        2.81 -     3.41: 133923
        3.41 -     4.00: 164334
        4.00 -     4.60: 258149
  Nonbonded interactions: 660917
  Sorted by model distance:
  nonbonded pdb=" O   ASN D 821 "
            pdb=" HG  SER D 824 "
     model   vdw
     1.615 1.850
  nonbonded pdb=" O   ASN A 821 "
            pdb=" HG  SER A 824 "
     model   vdw
     1.616 1.850
  nonbonded pdb=" O   ASN C 821 "
            pdb=" HG  SER C 824 "
     model   vdw
     1.617 1.850
  nonbonded pdb=" O   ASN B 821 "
            pdb=" HG  SER B 824 "
     model   vdw
     1.617 1.850
  nonbonded pdb=" O   GLY D 183 "
            pdb=" H   ASP D 254 "
     model   vdw
     1.633 1.850
  ... (remaining 660912 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.800
  Extract box with map and model:          9.750
  Check model and map are aligned:         0.760
  Set scattering table:                    0.430
  Process input model:                     154.010
  Find NCS groups from input model:        2.540
  Set up NCS constraints:                  0.250
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  172.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099  27572  Z= 0.235
  Angle     :  0.752  15.011  37712  Z= 0.310
  Chirality :  0.051   0.445   4492
  Planarity :  0.003   0.041   4632
  Dihedral  : 13.211  81.958   9608
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.15), residues: 3508
  helix:  2.89 (0.11), residues: 2472
  sheet:  0.08 (0.41), residues: 184
  loop : -0.76 (0.19), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 798 
 HIS   0.003   0.000   HIS D 845 
 PHE   0.022   0.001   PHE C 900 
 TYR   0.009   0.001   TYR B 999 
 ARG   0.002   0.000   ARG C 890 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  218 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 3.792 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.7461
  time to fit residues: 267.9591
Evaluate side-chains
  205 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 4.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 300 optimal weight:    5.9990
   chunk 269 optimal weight:   20.0000
   chunk 149 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 182 optimal weight:    0.9990
   chunk 144 optimal weight:    0.5980
   chunk 279 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 169 optimal weight:    3.9990
   chunk 207 optimal weight:    6.9990
   chunk 323 optimal weight:    1.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN
B 255 ASN
B 483 ASN
C 483 ASN
D 483 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  27572  Z= 0.245
  Angle     :  0.513   5.154  37712  Z= 0.275
  Chirality :  0.035   0.133   4492
  Planarity :  0.003   0.036   4632
  Dihedral  :  6.368  59.944   4624
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 17.55 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.14), residues: 3508
  helix:  2.85 (0.10), residues: 2516
  sheet: -0.06 (0.40), residues: 176
  loop : -0.57 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 567 
 HIS   0.003   0.001   HIS A 845 
 PHE   0.021   0.001   PHE C 900 
 TYR   0.013   0.001   TYR A1020 
 ARG   0.002   0.000   ARG A 829 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  205 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 4.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 4
  residues processed: 205
  average time/residue: 0.7386
  time to fit residues: 253.9893
Evaluate side-chains
  178 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 174
  time to evaluate  : 4.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain D residue  724 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 179 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 269 optimal weight:   20.0000
   chunk 220 optimal weight:    0.8980
   chunk 89 optimal weight:   30.0000
   chunk 323 optimal weight:    0.5980
   chunk 349 optimal weight:    3.9990
   chunk 288 optimal weight:    4.9990
   chunk 321 optimal weight:    3.9990
   chunk 110 optimal weight:    6.9990
   chunk 259 optimal weight:    0.6980
   overall best weight:    2.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  27572  Z= 0.199
  Angle     :  0.463   4.813  37712  Z= 0.249
  Chirality :  0.034   0.143   4492
  Planarity :  0.003   0.039   4632
  Dihedral  :  5.956  56.643   4624
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 17.46 %
    Favored  : 82.04 %
  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:  3.09 (0.14), residues: 3508
  helix:  2.96 (0.10), residues: 2524
  sheet: -0.12 (0.40), residues: 176
  loop : -0.55 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 567 
 HIS   0.003   0.001   HIS D 845 
 PHE   0.018   0.001   PHE C 900 
 TYR   0.013   0.001   TYR B 808 
 ARG   0.001   0.000   ARG B1079 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 4.177 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 9
  residues processed: 194
  average time/residue: 0.7589
  time to fit residues: 244.2540
Evaluate side-chains
  174 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 4.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  724 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 319 optimal weight:    2.9990
   chunk 243 optimal weight:    7.9990
   chunk 168 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 154 optimal weight:    5.9990
   chunk 217 optimal weight:    6.9990
   chunk 325 optimal weight:    2.9990
   chunk 344 optimal weight:    5.9990
   chunk 169 optimal weight:    0.9990
   chunk 308 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 429 GLN
B 429 GLN
C 429 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  27572  Z= 0.268
  Angle     :  0.491   4.893  37712  Z= 0.273
  Chirality :  0.035   0.145   4492
  Planarity :  0.003   0.037   4632
  Dihedral  :  6.141  59.663   4624
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 18.62 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.14), residues: 3508
  helix:  2.77 (0.10), residues: 2540
  sheet: -0.47 (0.39), residues: 176
  loop : -0.65 (0.20), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 567 
 HIS   0.004   0.001   HIS D 845 
 PHE   0.019   0.001   PHE C 900 
 TYR   0.012   0.001   TYR A1005 
 ARG   0.003   0.000   ARG B1079 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  177 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 4.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  678 LEU cc_start: 0.9280 (mt) cc_final: 0.8969 (tp)
REVERT: B  678 LEU cc_start: 0.9279 (mt) cc_final: 0.8969 (tp)
REVERT: C  678 LEU cc_start: 0.9280 (mt) cc_final: 0.8969 (tp)
REVERT: D  678 LEU cc_start: 0.9281 (mt) cc_final: 0.8970 (tp)
  outliers start: 19
  outliers final: 11
  residues processed: 176
  average time/residue: 0.6583
  time to fit residues: 201.6962
Evaluate side-chains
  164 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 4.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  841 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 286 optimal weight:    9.9990
   chunk 195 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 256 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 293 optimal weight:   10.0000
   chunk 237 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 175 optimal weight:    5.9990
   chunk 308 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  27572  Z= 0.207
  Angle     :  0.457   4.824  37712  Z= 0.250
  Chirality :  0.034   0.151   4492
  Planarity :  0.003   0.039   4632
  Dihedral  :  5.850  53.671   4624
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.49 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.14), residues: 3508
  helix:  2.85 (0.10), residues: 2540
  sheet: -0.43 (0.40), residues: 176
  loop : -0.72 (0.19), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 567 
 HIS   0.003   0.001   HIS A 845 
 PHE   0.016   0.001   PHE B 900 
 TYR   0.010   0.001   TYR C 999 
 ARG   0.004   0.000   ARG D1079 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  191 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 4.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7862 (m-80)
REVERT: A  678 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8914 (tt)
REVERT: B  304 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7750 (m-80)
REVERT: B  678 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8914 (tt)
REVERT: C  304 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7755 (m-80)
REVERT: C  678 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8914 (tt)
REVERT: D  304 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7754 (m-80)
REVERT: D  678 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8914 (tt)
  outliers start: 29
  outliers final: 11
  residues processed: 185
  average time/residue: 0.6674
  time to fit residues: 213.9123
Evaluate side-chains
  170 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 4.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  678 LEU
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 309 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 202 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 344 optimal weight:    4.9990
   chunk 285 optimal weight:    0.7980
   chunk 159 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 180 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  27572  Z= 0.179
  Angle     :  0.439   5.341  37712  Z= 0.240
  Chirality :  0.034   0.157   4492
  Planarity :  0.003   0.038   4632
  Dihedral  :  5.721  52.764   4624
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.25 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.14), residues: 3508
  helix:  2.93 (0.10), residues: 2536
  sheet: -0.42 (0.40), residues: 176
  loop : -0.75 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 567 
 HIS   0.003   0.001   HIS D 845 
 PHE   0.016   0.001   PHE C 900 
 TYR   0.010   0.001   TYR B 999 
 ARG   0.002   0.000   ARG A 784 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 4.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7878 (m-80)
REVERT: A  678 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8903 (tp)
REVERT: B  304 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7847 (m-80)
REVERT: B  678 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8903 (tp)
REVERT: C  304 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7849 (m-80)
REVERT: C  678 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8903 (tp)
REVERT: D  304 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7849 (m-80)
REVERT: D  678 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8904 (tp)
  outliers start: 45
  outliers final: 22
  residues processed: 206
  average time/residue: 0.6507
  time to fit residues: 233.3085
Evaluate side-chains
  186 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 4.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  841 LEU
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  458 LEU
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  678 LEU
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 332 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 196 optimal weight:    5.9990
   chunk 251 optimal weight:    4.9990
   chunk 194 optimal weight:    4.9990
   chunk 289 optimal weight:    9.9990
   chunk 192 optimal weight:    9.9990
   chunk 343 optimal weight:    0.4980
   chunk 214 optimal weight:    3.9990
   chunk 209 optimal weight:    2.9990
   chunk 158 optimal weight:    2.9990
   overall best weight:    2.8988

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

Flipped N/Q/H residues before XYZ refinement:
C 429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  27572  Z= 0.267
  Angle     :  0.481   5.078  37712  Z= 0.269
  Chirality :  0.035   0.147   4492
  Planarity :  0.003   0.038   4632
  Dihedral  :  5.867  52.428   4624
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.99 %
    Favored  : 79.57 %
  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:  2.70 (0.14), residues: 3508
  helix:  2.75 (0.10), residues: 2532
  sheet: -0.65 (0.39), residues: 176
  loop : -0.92 (0.19), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 567 
 HIS   0.004   0.001   HIS B 845 
 PHE   0.017   0.001   PHE B 900 
 TYR   0.012   0.001   TYR B 633 
 ARG   0.003   0.000   ARG A 842 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  191 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 4.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7962 (m-80)
REVERT: B  304 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7925 (m-80)
REVERT: C  304 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7928 (m-80)
REVERT: D  304 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7926 (m-80)
  outliers start: 35
  outliers final: 23
  residues processed: 186
  average time/residue: 0.7020
  time to fit residues: 229.3504
Evaluate side-chains
  171 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 4.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  900 PHE
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  900 PHE
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  900 PHE
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  458 LEU
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 212 optimal weight:    4.9990
   chunk 137 optimal weight:    0.9980
   chunk 204 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 218 optimal weight:    2.9990
   chunk 233 optimal weight:    0.6980
   chunk 169 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 269 optimal weight:   30.0000
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  27572  Z= 0.162
  Angle     :  0.437   5.004  37712  Z= 0.238
  Chirality :  0.034   0.133   4492
  Planarity :  0.003   0.039   4632
  Dihedral  :  5.704  52.105   4624
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.15 %
    Favored  : 79.41 %
  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:  2.88 (0.14), residues: 3508
  helix:  2.89 (0.10), residues: 2532
  sheet: -0.49 (0.41), residues: 172
  loop : -0.92 (0.20), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 567 
 HIS   0.003   0.001   HIS B 845 
 PHE   0.015   0.001   PHE D 900 
 TYR   0.012   0.001   TYR B 999 
 ARG   0.001   0.000   ARG D 890 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 4.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7883 (m-80)
REVERT: B  304 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7908 (m-80)
REVERT: C  304 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7910 (m-80)
REVERT: D  304 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7907 (m-80)
  outliers start: 35
  outliers final: 25
  residues processed: 187
  average time/residue: 0.6461
  time to fit residues: 210.6296
Evaluate side-chains
  175 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 4.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  900 PHE
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  883 VAL
Chi-restraints excluded: chain B residue  900 PHE
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  883 VAL
Chi-restraints excluded: chain C residue  900 PHE
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  458 LEU
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 312 optimal weight:    2.9990
   chunk 328 optimal weight:    0.8980
   chunk 299 optimal weight:    6.9990
   chunk 319 optimal weight:    2.9990
   chunk 192 optimal weight:   10.0000
   chunk 139 optimal weight:    5.9990
   chunk 251 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 288 optimal weight:    6.9990
   chunk 302 optimal weight:    2.9990
   chunk 318 optimal weight:    0.6980
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  27572  Z= 0.210
  Angle     :  0.455   5.333  37712  Z= 0.251
  Chirality :  0.034   0.132   4492
  Planarity :  0.003   0.039   4632
  Dihedral  :  5.726  51.711   4624
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.48 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.14), residues: 3508
  helix:  2.82 (0.10), residues: 2536
  sheet: -0.61 (0.41), residues: 172
  loop : -0.96 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 567 
 HIS   0.003   0.001   HIS D 845 
 PHE   0.016   0.001   PHE C 900 
 TYR   0.010   0.001   TYR A1005 
 ARG   0.002   0.000   ARG B 842 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  193 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 157
  time to evaluate  : 4.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8000 (m-80)
REVERT: B  304 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7949 (m-80)
REVERT: C  304 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7950 (m-80)
REVERT: D  304 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7949 (m-80)
  outliers start: 36
  outliers final: 29
  residues processed: 186
  average time/residue: 0.6855
  time to fit residues: 222.0771
Evaluate side-chains
  185 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 4.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  900 PHE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  900 PHE
Chi-restraints excluded: chain B residue  903 VAL
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  900 PHE
Chi-restraints excluded: chain C residue  903 VAL
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  458 LEU
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  900 PHE
Chi-restraints excluded: chain D residue  903 VAL
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 209 optimal weight:    0.8980
   chunk 338 optimal weight:    3.9990
   chunk 206 optimal weight:    6.9990
   chunk 160 optimal weight:    3.9990
   chunk 235 optimal weight:    3.9990
   chunk 354 optimal weight:   10.0000
   chunk 326 optimal weight:    2.9990
   chunk 282 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 218 optimal weight:    2.9990
   chunk 173 optimal weight:    4.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  27572  Z= 0.279
  Angle     :  0.484   5.412  37712  Z= 0.272
  Chirality :  0.035   0.142   4492
  Planarity :  0.003   0.037   4632
  Dihedral  :  5.905  51.993   4624
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.65 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.14), residues: 3508
  helix:  2.66 (0.10), residues: 2536
  sheet: -0.89 (0.39), residues: 172
  loop : -1.09 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 567 
 HIS   0.003   0.001   HIS A 845 
 PHE   0.017   0.001   PHE C 900 
 TYR   0.011   0.001   TYR A 633 
 ARG   0.003   0.000   ARG A 784 

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

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

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7016 Ramachandran restraints generated.
    3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue VAL   42 is missing expected H atoms. Skipping.
Residue ILE   45 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Residue TYR  117 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue LEU  120 is missing expected H atoms. Skipping.
Residue SER  121 is missing expected H atoms. Skipping.
Residue THR  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue THR  128 is missing expected H atoms. Skipping.
Residue LEU  132 is missing expected H atoms. Skipping.
Residue THR  134 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue THR  141 is missing expected H atoms. Skipping.
Residue ILE  146 is missing expected H atoms. Skipping.
Residue THR  149 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue TYR  186 is missing expected H atoms. Skipping.
Residue LYS  190 is missing expected H atoms. Skipping.
Residue MET  219 is missing expected H atoms. Skipping.
Residue SER  221 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue MET  242 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue VAL  263 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue LYS  276 is missing expected H atoms. Skipping.
Residue LYS  283 is missing expected H atoms. Skipping.
Residue LYS  314 is missing expected H atoms. Skipping.
Residue LYS  321 is missing expected H atoms. Skipping.
Residue LYS  323 is missing expected H atoms. Skipping.
Residue ILE  324 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LYS  357 is missing expected H atoms. Skipping.
Residue LEU  358 is missing expected H atoms. Skipping.
Residue VAL  359 is missing expected H atoms. Skipping.
Residue LEU  362 is missing expected H atoms. Skipping.
Residue THR  365 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue LEU  381 is missing expected H atoms. Skipping.
Residue LYS  382 is missing expected H atoms. Skipping.
Residue ILE  384 is missing expected H atoms. Skipping.
Residue LEU  385 is missing expected H atoms. Skipping.
Residue LEU  412 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  557 is missing expected H atoms. Skipping.
Residue LYS  694 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  733 is missing expected H atoms. Skipping.
Residue SER  762 is missing expected H atoms. Skipping.
Residue VAL  763 is missing expected H atoms. Skipping.
Residue LEU  797 is missing expected H atoms. Skipping.
Residue MET  801 is missing expected H atoms. Skipping.
Residue SER  819 is missing expected H atoms. Skipping.
Residue LYS  822 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue VAL  986 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1026 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1030 is missing expected H atoms. Skipping.
Residue LYS 1070 is missing expected H atoms. Skipping.
Residue SER 1075 is missing expected H atoms. Skipping.
Residue LEU 1085 is missing expected H atoms. Skipping.
Residue SER 1087 is missing expected H atoms. Skipping.
Residue LYS 1088 is missing expected H atoms. Skipping.
Residue LEU 1089 is missing expected H atoms. Skipping.
Residue LEU 1092 is missing expected H atoms. Skipping.
Residue LYS 1093 is missing expected H atoms. Skipping.
Residue SER 1094 is missing expected H atoms. Skipping.
Residue LEU 1095 is missing expected H atoms. Skipping.
Residue LEU 1096 is missing expected H atoms. Skipping.
Residue LYS 1097 is missing expected H atoms. Skipping.
Residue ILE 1099 is missing expected H atoms. Skipping.
Residue ILE 1103 is missing expected H atoms. Skipping.
Evaluate side-chains
  192 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 154
  time to evaluate  : 4.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8020 (m-80)
REVERT: B  304 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8039 (m-80)
REVERT: C  304 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8039 (m-80)
REVERT: D  304 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8038 (m-80)
  outliers start: 38
  outliers final: 29
  residues processed: 188
  average time/residue: 0.6939
  time to fit residues: 230.3225
Evaluate side-chains
  185 residues out of total 3208 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 3.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  900 PHE
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  900 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  966 SER
Chi-restraints excluded: chain C residue  304 PHE
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  900 PHE
Chi-restraints excluded: chain C residue  962 ILE
Chi-restraints excluded: chain C residue  966 SER
Chi-restraints excluded: chain D residue  304 PHE
Chi-restraints excluded: chain D residue  393 VAL
Chi-restraints excluded: chain D residue  458 LEU
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  724 LEU
Chi-restraints excluded: chain D residue  900 PHE
Chi-restraints excluded: chain D residue  903 VAL
Chi-restraints excluded: chain D residue  962 ILE
Chi-restraints excluded: chain D residue  966 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 356
   random chunks:
   chunk 224 optimal weight:    4.9990
   chunk 300 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 260 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0020
   chunk 78 optimal weight:    3.9990
   chunk 282 optimal weight:   30.0000
   chunk 118 optimal weight:    7.9990
   chunk 290 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    1.1194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.104865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.082485 restraints weight = 206599.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086070 restraints weight = 89226.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.088428 restraints weight = 52968.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  27572  Z= 0.145
  Angle     :  0.436   5.431  37712  Z= 0.237
  Chirality :  0.034   0.135   4492
  Planarity :  0.003   0.040   4632
  Dihedral  :  5.687  51.539   4624
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 19.56 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.14), residues: 3508
  helix:  2.86 (0.10), residues: 2536
  sheet: -0.67 (0.40), residues: 172
  loop : -0.99 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 567 
 HIS   0.003   0.001   HIS A 845 
 PHE   0.014   0.001   PHE D 900 
 TYR   0.010   0.001   TYR A 905 
 ARG   0.001   0.000   ARG A 890 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6978.54 seconds
wall clock time: 125 minutes 12.93 seconds (7512.93 seconds total)