Starting phenix.real_space_refine
on Fri Oct 11 13:03:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6d_44255/10_2024/9b6d_44255_trim.cif"
  }
  resolution = 3.3
  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=   0.001 sd=   0.048
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     116      5.16       5
     C   18908      2.51       5
     N    4604      2.21       5
     O    5036      1.98       5
     H   25920      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 54584
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 13475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 933, 13475
          Classifications: {'peptide': 933}
          Link IDs: {'PTRANS': 23, 'TRANS': 909}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 637
          Unresolved non-hydrogen angles: 784
          Unresolved non-hydrogen dihedrals: 528
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 372
    Chain: "A"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 171
          Unusual residues: {'Y01': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 37.93, per 1000 atoms: 0.69
  Number of scatterers: 54584
  At special positions: 0
  Unit cell: (155.1, 155.1, 158.4, 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     116     16.00
     O    5036      8.00
     N    4604      7.00
     C   18908      6.00
     H   25920      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 303 " - pdb=" SG  CYS A 326 " distance=2.09
    Simple disulfide: pdb=" SG  CYS A 929 " - pdb=" SG  CYS A 940 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 11.33
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7112

  Finding SS restraints...
    Secondary structure from input PDB file:
      184 helices and 4 sheets defined
      72.2% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 50
      removed outlier: 3.977A  pdb=" N   PHE A  44 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 136
    Processing helix  chain 'A' and resid 158 through 176
    Processing helix  chain 'A' and resid 187 through 202
    Processing helix  chain 'A' and resid 274 through 288
      removed outlier: 3.515A  pdb=" N   TYR A 284 " --> pdb=" O   GLN A 280 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 322
      removed outlier: 3.933A  pdb=" N   LEU A 313 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER A 322 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 343
    Processing helix  chain 'A' and resid 351 through 362
    Processing helix  chain 'A' and resid 362 through 369
    Processing helix  chain 'A' and resid 370 through 387
      removed outlier: 3.530A  pdb=" N   ILE A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   SER A 376 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 420
      removed outlier: 4.447A  pdb=" N   GLU A 420 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 436
      removed outlier: 3.798A  pdb=" N   TRP A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 457 through 469
      removed outlier: 4.488A  pdb=" N   VAL A 461 " --> pdb=" O   ASP A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 480
    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 516
    Processing helix  chain 'A' and resid 518 through 533
      removed outlier: 3.731A  pdb=" N   THR A 522 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 571
      removed outlier: 3.594A  pdb=" N   ALA A 563 " --> pdb=" O   HIS A 559 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN A 571 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 586 through 603
      removed outlier: 3.685A  pdb=" N   LEU A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS A 603 " --> pdb=" O   LYS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 636
      removed outlier: 3.655A  pdb=" N   ALA A 611 " --> pdb=" O   ASP A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
    Processing helix  chain 'A' and resid 655 through 663
    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: 3.521A  pdb=" N   ILE A 695 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.897A  pdb=" N   GLY A 706 " --> pdb=" O   PRO A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 731
      removed outlier: 3.549A  pdb=" N   PHE A 730 " --> pdb=" O   TYR A 726 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 731 " --> pdb=" O   TYR A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 759
    Processing helix  chain 'A' and resid 765 through 789
    Processing helix  chain 'A' and resid 790 through 795
    Processing helix  chain 'A' and resid 796 through 817
      removed outlier: 3.516A  pdb=" N   VAL A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 841
      removed outlier: 3.798A  pdb=" N   LEU A 825 " --> pdb=" O   ASN A 821 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 841 " --> pdb=" O   ILE A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 847
      removed outlier: 4.092A  pdb=" N   HIS A 845 " --> pdb=" O   LEU A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 859
      removed outlier: 3.581A  pdb=" N   MET A 859 " --> pdb=" O   PRO A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 862
      No H-bonds generated for 'chain 'A' and resid 860 through 862'
    Processing helix  chain 'A' and resid 863 through 890
      removed outlier: 3.722A  pdb=" N   VAL A 867 " --> pdb=" O   MET A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 904
    Processing helix  chain 'A' and resid 904 through 910
    Processing helix  chain 'A' and resid 952 through 969
      removed outlier: 3.841A  pdb=" N   THR A 956 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
      Proline residue:  A 958  - end of helix
      removed outlier: 3.770A  pdb=" N   ILE A 969 " --> pdb=" O   LEU A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 1008
      removed outlier: 5.052A  pdb=" N   GLU A 988 " --> pdb=" O   GLY A 984 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ASN A 989 " --> pdb=" O   ILE A 985 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ASP A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   GLN A 992 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL A 993 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE A1000 " --> pdb=" O   PHE A 996 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1027
      removed outlier: 4.477A  pdb=" N   VAL A1017 " --> pdb=" O   PHE A1013 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   PHE A1018 " --> pdb=" O   PRO A1014 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA A1019 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR A1020 " --> pdb=" O   VAL A1016 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR A1022 " --> pdb=" O   PHE A1018 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL A1024 " --> pdb=" O   TYR A1020 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL A1025 " --> pdb=" O   PHE A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1073
    Processing helix  chain 'A' and resid 1076 through 1104
      removed outlier: 3.905A  pdb=" N   HIS A1080 " --> pdb=" O   GLU A1076 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER A1094 " --> pdb=" O   ASN A1090 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A1096 " --> pdb=" O   LEU A1092 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A1097 " --> pdb=" O   LYS A1093 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
    Processing helix  chain 'B' and resid 125 through 136
    Processing helix  chain 'B' and resid 158 through 176
    Processing helix  chain 'B' and resid 187 through 202
    Processing helix  chain 'B' and resid 274 through 288
      removed outlier: 3.514A  pdb=" N   TYR B 284 " --> pdb=" O   GLN B 280 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE B 285 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 322
      removed outlier: 3.932A  pdb=" N   LEU B 313 " --> pdb=" O   GLY B 309 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS B 314 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER B 322 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 343
    Processing helix  chain 'B' and resid 351 through 362
    Processing helix  chain 'B' and resid 362 through 369
    Processing helix  chain 'B' and resid 370 through 387
      removed outlier: 3.530A  pdb=" N   ILE B 374 " --> pdb=" O   PRO B 370 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU B 375 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   SER B 376 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 420
      removed outlier: 4.447A  pdb=" N   GLU B 420 " --> pdb=" O   PHE B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 436
      removed outlier: 3.799A  pdb=" N   TRP B 436 " --> pdb=" O   LEU B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 447
    Processing helix  chain 'B' and resid 457 through 469
      removed outlier: 4.488A  pdb=" N   VAL B 461 " --> pdb=" O   ASP B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 480
    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 516
    Processing helix  chain 'B' and resid 518 through 533
      removed outlier: 3.732A  pdb=" N   THR B 522 " --> pdb=" O   ASP B 518 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 571
      removed outlier: 3.595A  pdb=" N   ALA B 563 " --> pdb=" O   HIS B 559 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN B 571 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 582
    Processing helix  chain 'B' and resid 586 through 603
      removed outlier: 3.685A  pdb=" N   LEU B 601 " --> pdb=" O   LEU B 597 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS B 603 " --> pdb=" O   LYS B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 636
      removed outlier: 3.655A  pdb=" N   ALA B 611 " --> pdb=" O   ASP B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 636 through 646
    Processing helix  chain 'B' and resid 655 through 663
    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: 3.521A  pdb=" N   ILE B 695 " --> pdb=" O   LYS B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 706
      removed outlier: 3.899A  pdb=" N   GLY B 706 " --> pdb=" O   PRO B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 731
      removed outlier: 3.549A  pdb=" N   PHE B 730 " --> pdb=" O   TYR B 726 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE B 731 " --> pdb=" O   TYR B 727 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 733 through 759
    Processing helix  chain 'B' and resid 765 through 789
    Processing helix  chain 'B' and resid 790 through 795
    Processing helix  chain 'B' and resid 796 through 817
      removed outlier: 3.516A  pdb=" N   VAL B 800 " --> pdb=" O   ASP B 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 841
      removed outlier: 3.798A  pdb=" N   LEU B 825 " --> pdb=" O   ASN B 821 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B 841 " --> pdb=" O   ILE B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 847
      removed outlier: 4.092A  pdb=" N   HIS B 845 " --> pdb=" O   LEU B 841 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 853 through 859
      removed outlier: 3.581A  pdb=" N   MET B 859 " --> pdb=" O   PRO B 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 862
      No H-bonds generated for 'chain 'B' and resid 860 through 862'
    Processing helix  chain 'B' and resid 863 through 890
      removed outlier: 3.723A  pdb=" N   VAL B 867 " --> pdb=" O   MET B 863 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 895 through 904
    Processing helix  chain 'B' and resid 904 through 910
    Processing helix  chain 'B' and resid 952 through 969
      removed outlier: 3.841A  pdb=" N   THR B 956 " --> pdb=" O   PRO B 952 " (cutoff:3.500A)
      Proline residue:  B 958  - end of helix
      removed outlier: 3.769A  pdb=" N   ILE B 969 " --> pdb=" O   LEU B 965 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 969 through 1008
      removed outlier: 5.052A  pdb=" N   GLU B 988 " --> pdb=" O   GLY B 984 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN B 989 " --> pdb=" O   ILE B 985 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ASP B 991 " --> pdb=" O   GLN B 987 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   GLN B 992 " --> pdb=" O   GLU B 988 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL B 993 " --> pdb=" O   ASN B 989 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE B1000 " --> pdb=" O   PHE B 996 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG B1008 " --> pdb=" O   GLU B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1012 through 1027
      removed outlier: 4.477A  pdb=" N   VAL B1017 " --> pdb=" O   PHE B1013 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   PHE B1018 " --> pdb=" O   PRO B1014 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ALA B1019 " --> pdb=" O   PHE B1015 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR B1020 " --> pdb=" O   VAL B1016 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR B1022 " --> pdb=" O   PHE B1018 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL B1024 " --> pdb=" O   TYR B1020 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL B1025 " --> pdb=" O   PHE B1021 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1051 through 1073
    Processing helix  chain 'B' and resid 1076 through 1104
      removed outlier: 3.904A  pdb=" N   HIS B1080 " --> pdb=" O   GLU B1076 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER B1094 " --> pdb=" O   ASN B1090 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU B1095 " --> pdb=" O   ASP B1091 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU B1096 " --> pdb=" O   LEU B1092 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS B1097 " --> pdb=" O   LYS B1093 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 50
    Processing helix  chain 'C' and resid 125 through 136
    Processing helix  chain 'C' and resid 158 through 176
    Processing helix  chain 'C' and resid 187 through 202
    Processing helix  chain 'C' and resid 274 through 288
      removed outlier: 3.516A  pdb=" N   TYR C 284 " --> pdb=" O   GLN C 280 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 309 through 322
      removed outlier: 3.932A  pdb=" N   LEU C 313 " --> pdb=" O   GLY C 309 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS C 314 " --> pdb=" O   ARG C 310 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER C 322 " --> pdb=" O   THR C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 343
    Processing helix  chain 'C' and resid 351 through 362
    Processing helix  chain 'C' and resid 362 through 369
    Processing helix  chain 'C' and resid 370 through 387
      removed outlier: 3.530A  pdb=" N   ILE C 374 " --> pdb=" O   PRO C 370 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU C 375 " --> pdb=" O   GLU C 371 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   SER C 376 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 420
      removed outlier: 4.447A  pdb=" N   GLU C 420 " --> pdb=" O   PHE C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 426 through 436
      removed outlier: 3.798A  pdb=" N   TRP C 436 " --> pdb=" O   LEU C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 447
    Processing helix  chain 'C' and resid 457 through 469
      removed outlier: 4.488A  pdb=" N   VAL C 461 " --> pdb=" O   ASP C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 480
    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 516
    Processing helix  chain 'C' and resid 518 through 533
      removed outlier: 3.731A  pdb=" N   THR C 522 " --> pdb=" O   ASP C 518 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   PHE C 523 " --> pdb=" O   ALA C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 571
      removed outlier: 3.594A  pdb=" N   ALA C 563 " --> pdb=" O   HIS C 559 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN C 571 " --> pdb=" O   TRP C 567 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 582
    Processing helix  chain 'C' and resid 586 through 603
      removed outlier: 3.685A  pdb=" N   LEU C 601 " --> pdb=" O   LEU C 597 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LYS C 603 " --> pdb=" O   LYS C 599 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 636
      removed outlier: 3.655A  pdb=" N   ALA C 611 " --> pdb=" O   ASP C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 646
    Processing helix  chain 'C' and resid 655 through 663
    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: 3.521A  pdb=" N   ILE C 695 " --> pdb=" O   LYS C 691 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 702 through 706
      removed outlier: 3.897A  pdb=" N   GLY C 706 " --> pdb=" O   PRO C 703 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 722 through 731
      removed outlier: 3.549A  pdb=" N   PHE C 730 " --> pdb=" O   TYR C 726 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE C 731 " --> pdb=" O   TYR C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 733 through 759
    Processing helix  chain 'C' and resid 765 through 789
    Processing helix  chain 'C' and resid 790 through 795
    Processing helix  chain 'C' and resid 796 through 817
      removed outlier: 3.516A  pdb=" N   VAL C 800 " --> pdb=" O   ASP C 796 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 821 through 841
      removed outlier: 3.798A  pdb=" N   LEU C 825 " --> pdb=" O   ASN C 821 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU C 841 " --> pdb=" O   ILE C 837 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 841 through 847
      removed outlier: 4.091A  pdb=" N   HIS C 845 " --> pdb=" O   LEU C 841 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 853 through 859
      removed outlier: 3.580A  pdb=" N   MET C 859 " --> pdb=" O   PRO C 855 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 860 through 862
      No H-bonds generated for 'chain 'C' and resid 860 through 862'
    Processing helix  chain 'C' and resid 863 through 890
      removed outlier: 3.722A  pdb=" N   VAL C 867 " --> pdb=" O   MET C 863 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 895 through 904
    Processing helix  chain 'C' and resid 904 through 910
    Processing helix  chain 'C' and resid 952 through 969
      removed outlier: 3.842A  pdb=" N   THR C 956 " --> pdb=" O   PRO C 952 " (cutoff:3.500A)
      Proline residue:  C 958  - end of helix
      removed outlier: 3.769A  pdb=" N   ILE C 969 " --> pdb=" O   LEU C 965 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 969 through 1008
      removed outlier: 5.052A  pdb=" N   GLU C 988 " --> pdb=" O   GLY C 984 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ASN C 989 " --> pdb=" O   ILE C 985 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ASP C 991 " --> pdb=" O   GLN C 987 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   GLN C 992 " --> pdb=" O   GLU C 988 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL C 993 " --> pdb=" O   ASN C 989 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   PHE C1000 " --> pdb=" O   PHE C 996 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG C1008 " --> pdb=" O   GLU C1004 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1012 through 1027
      removed outlier: 4.478A  pdb=" N   VAL C1017 " --> pdb=" O   PHE C1013 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   PHE C1018 " --> pdb=" O   PRO C1014 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA C1019 " --> pdb=" O   PHE C1015 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR C1020 " --> pdb=" O   VAL C1016 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR C1022 " --> pdb=" O   PHE C1018 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL C1024 " --> pdb=" O   TYR C1020 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL C1025 " --> pdb=" O   PHE C1021 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1051 through 1073
    Processing helix  chain 'C' and resid 1076 through 1104
      removed outlier: 3.905A  pdb=" N   HIS C1080 " --> pdb=" O   GLU C1076 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER C1094 " --> pdb=" O   ASN C1090 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C1095 " --> pdb=" O   ASP C1091 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU C1096 " --> pdb=" O   LEU C1092 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS C1097 " --> pdb=" O   LYS C1093 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 50
    Processing helix  chain 'D' and resid 125 through 136
    Processing helix  chain 'D' and resid 158 through 176
    Processing helix  chain 'D' and resid 187 through 202
    Processing helix  chain 'D' and resid 274 through 288
      removed outlier: 3.515A  pdb=" N   TYR D 284 " --> pdb=" O   GLN D 280 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE D 285 " --> pdb=" O   LEU D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 322
      removed outlier: 3.933A  pdb=" N   LEU D 313 " --> pdb=" O   GLY D 309 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS D 314 " --> pdb=" O   ARG D 310 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER D 322 " --> pdb=" O   THR D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 343
    Processing helix  chain 'D' and resid 351 through 362
    Processing helix  chain 'D' and resid 362 through 369
    Processing helix  chain 'D' and resid 370 through 387
      removed outlier: 3.529A  pdb=" N   ILE D 374 " --> pdb=" O   PRO D 370 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU D 375 " --> pdb=" O   GLU D 371 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   SER D 376 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 420
      removed outlier: 4.447A  pdb=" N   GLU D 420 " --> pdb=" O   PHE D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 436
      removed outlier: 3.798A  pdb=" N   TRP D 436 " --> pdb=" O   LEU D 432 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 438 through 447
    Processing helix  chain 'D' and resid 457 through 469
      removed outlier: 4.488A  pdb=" N   VAL D 461 " --> pdb=" O   ASP D 457 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 470 through 480
    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 516
    Processing helix  chain 'D' and resid 518 through 533
      removed outlier: 3.731A  pdb=" N   THR D 522 " --> pdb=" O   ASP D 518 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE D 523 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 559 through 571
      removed outlier: 3.594A  pdb=" N   ALA D 563 " --> pdb=" O   HIS D 559 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN D 571 " --> pdb=" O   TRP D 567 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 573 through 582
    Processing helix  chain 'D' and resid 586 through 603
      removed outlier: 3.685A  pdb=" N   LEU D 601 " --> pdb=" O   LEU D 597 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   LYS D 603 " --> pdb=" O   LYS D 599 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 607 through 636
      removed outlier: 3.655A  pdb=" N   ALA D 611 " --> pdb=" O   ASP D 607 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 636 through 646
    Processing helix  chain 'D' and resid 655 through 663
    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: 3.522A  pdb=" N   ILE D 695 " --> pdb=" O   LYS D 691 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 702 through 706
      removed outlier: 3.897A  pdb=" N   GLY D 706 " --> pdb=" O   PRO D 703 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 722 through 731
      removed outlier: 3.549A  pdb=" N   PHE D 730 " --> pdb=" O   TYR D 726 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE D 731 " --> pdb=" O   TYR D 727 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 733 through 759
    Processing helix  chain 'D' and resid 765 through 789
    Processing helix  chain 'D' and resid 790 through 795
    Processing helix  chain 'D' and resid 796 through 817
      removed outlier: 3.516A  pdb=" N   VAL D 800 " --> pdb=" O   ASP D 796 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 821 through 841
      removed outlier: 3.798A  pdb=" N   LEU D 825 " --> pdb=" O   ASN D 821 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU D 841 " --> pdb=" O   ILE D 837 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 841 through 847
      removed outlier: 4.092A  pdb=" N   HIS D 845 " --> pdb=" O   LEU D 841 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 853 through 859
      removed outlier: 3.580A  pdb=" N   MET D 859 " --> pdb=" O   PRO D 855 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 860 through 862
      No H-bonds generated for 'chain 'D' and resid 860 through 862'
    Processing helix  chain 'D' and resid 863 through 890
      removed outlier: 3.723A  pdb=" N   VAL D 867 " --> pdb=" O   MET D 863 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 904
    Processing helix  chain 'D' and resid 904 through 910
    Processing helix  chain 'D' and resid 952 through 969
      removed outlier: 3.842A  pdb=" N   THR D 956 " --> pdb=" O   PRO D 952 " (cutoff:3.500A)
      Proline residue:  D 958  - end of helix
      removed outlier: 3.770A  pdb=" N   ILE D 969 " --> pdb=" O   LEU D 965 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 969 through 1008
      removed outlier: 5.051A  pdb=" N   GLU D 988 " --> pdb=" O   GLY D 984 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ASN D 989 " --> pdb=" O   ILE D 985 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ASP D 991 " --> pdb=" O   GLN D 987 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   GLN D 992 " --> pdb=" O   GLU D 988 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL D 993 " --> pdb=" O   ASN D 989 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE D1000 " --> pdb=" O   PHE D 996 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG D1008 " --> pdb=" O   GLU D1004 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1012 through 1027
      removed outlier: 4.477A  pdb=" N   VAL D1017 " --> pdb=" O   PHE D1013 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   PHE D1018 " --> pdb=" O   PRO D1014 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ALA D1019 " --> pdb=" O   PHE D1015 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR D1020 " --> pdb=" O   VAL D1016 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR D1022 " --> pdb=" O   PHE D1018 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL D1024 " --> pdb=" O   TYR D1020 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL D1025 " --> pdb=" O   PHE D1021 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1051 through 1073
    Processing helix  chain 'D' and resid 1076 through 1104
      removed outlier: 3.905A  pdb=" N   HIS D1080 " --> pdb=" O   GLU D1076 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER D1094 " --> pdb=" O   ASN D1090 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU D1095 " --> pdb=" O   ASP D1091 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU D1096 " --> pdb=" O   LEU D1092 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS D1097 " --> pdb=" O   LYS D1093 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120
      removed outlier: 3.531A  pdb=" N   LEU A 118 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE A 179 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   ILE A 214 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR A 181 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   ALA A 216 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   PHE A 304 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE A 146 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS A 303 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL A 329 " --> pdb=" O   CYS A 303 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ALA A 305 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 120
      removed outlier: 3.531A  pdb=" N   LEU B 118 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ILE B 179 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   ILE B 214 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR B 181 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   ALA B 216 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   PHE B 304 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE B 146 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS B 303 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL B 329 " --> pdb=" O   CYS B 303 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ALA B 305 " --> pdb=" O   VAL B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 120
      removed outlier: 3.530A  pdb=" N   LEU C 118 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE C 179 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   ILE C 214 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR C 181 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   ALA C 216 " --> pdb=" O   THR C 181 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   PHE C 304 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE C 146 " --> pdb=" O   PHE C 304 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS C 303 " --> pdb=" O   VAL C 327 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL C 329 " --> pdb=" O   CYS C 303 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ALA C 305 " --> pdb=" O   VAL C 329 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 120
      removed outlier: 3.531A  pdb=" N   LEU D 118 " --> pdb=" O   LEU D 260 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE D 179 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   ILE D 214 " --> pdb=" O   ILE D 179 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR D 181 " --> pdb=" O   ILE D 214 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   ALA D 216 " --> pdb=" O   THR D 181 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   PHE D 304 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE D 146 " --> pdb=" O   PHE D 304 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   CYS D 303 " --> pdb=" O   VAL D 327 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   VAL D 329 " --> pdb=" O   CYS D 303 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ALA D 305 " --> pdb=" O   VAL D 329 " (cutoff:3.500A)

    1812 hydrogen bonds defined for protein.
    5364 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: 18.95

  Time building geometry restraints manager: 13.63 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: 25884
        1.03 -     1.23: 123
        1.23 -     1.42: 12305
        1.42 -     1.62: 16800
        1.62 -     1.81: 180
  Bond restraints: 55292
  Sorted by residual:
  bond pdb=" CAY Y01 D1204 "
       pdb=" OAW Y01 D1204 "
    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 C1204 "
       pdb=" OAW Y01 C1204 "
    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 A1204 "
       pdb=" OAW Y01 A1204 "
    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 B1204 "
       pdb=" OAW Y01 B1204 "
    ideal  model  delta    sigma   weight residual
    1.332  1.430 -0.098 2.00e-02 2.50e+03 2.43e+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 2.39e+01
  ... (remaining 55287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 98251
        2.62 -     5.24: 673
        5.24 -     7.86: 100
        7.86 -    10.48: 34
       10.48 -    13.10: 26
  Bond angle restraints: 99084
  Sorted by residual:
  angle pdb=" CAT Y01 C1201 "
        pdb=" CBH Y01 C1201 "
        pdb=" CBF Y01 C1201 "
      ideal   model   delta    sigma   weight residual
     108.46   95.36   13.10 3.00e+00 1.11e-01 1.91e+01
  angle pdb=" CAT Y01 D1201 "
        pdb=" CBH Y01 D1201 "
        pdb=" CBF Y01 D1201 "
      ideal   model   delta    sigma   weight residual
     108.46   95.37   13.09 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" CAT Y01 B1201 "
        pdb=" CBH Y01 B1201 "
        pdb=" CBF Y01 B1201 "
      ideal   model   delta    sigma   weight residual
     108.46   95.37   13.09 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" CAT Y01 A1201 "
        pdb=" CBH Y01 A1201 "
        pdb=" CBF Y01 A1201 "
      ideal   model   delta    sigma   weight residual
     108.46   95.37   13.09 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" CAT Y01 D1204 "
        pdb=" CBH Y01 D1204 "
        pdb=" CBF Y01 D1204 "
      ideal   model   delta    sigma   weight residual
     108.46   95.55   12.91 3.00e+00 1.11e-01 1.85e+01
  ... (remaining 99079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 25523
       17.19 -    34.37: 1364
       34.37 -    51.56: 438
       51.56 -    68.74: 141
       68.74 -    85.93: 12
  Dihedral angle restraints: 27478
    sinusoidal: 14174
      harmonic: 13304
  Sorted by residual:
  dihedral pdb=" CA  GLY C 913 "
           pdb=" C   GLY C 913 "
           pdb=" N   GLN C 914 "
           pdb=" CA  GLN C 914 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  GLY A 913 "
           pdb=" C   GLY A 913 "
           pdb=" N   GLN A 914 "
           pdb=" CA  GLN A 914 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.73  -17.27     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  GLY B 913 "
           pdb=" C   GLY B 913 "
           pdb=" N   GLN B 914 "
           pdb=" CA  GLN B 914 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.73  -17.27     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 27475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 4358
       0.076 -    0.152: 304
       0.152 -    0.229: 18
       0.229 -    0.305: 36
       0.305 -    0.381: 48
  Chirality restraints: 4764
  Sorted by residual:
  chirality pdb=" CBH Y01 C1205 "
            pdb=" CAT Y01 C1205 "
            pdb=" CAZ Y01 C1205 "
            pdb=" CBF Y01 C1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -3.23    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CBH Y01 A1202 "
            pdb=" CAT Y01 A1202 "
            pdb=" CAZ Y01 A1202 "
            pdb=" CBF Y01 A1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -3.23    0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" CBH Y01 C1202 "
            pdb=" CAT Y01 C1202 "
            pdb=" CAZ Y01 C1202 "
            pdb=" CBF Y01 C1202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -3.23    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 4761 not shown)

  Planarity restraints: 8532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 304 "   -0.010 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" N   ALA D 305 "    0.032 2.00e-02 2.50e+03
        pdb=" CA  ALA D 305 "   -0.008 2.00e-02 2.50e+03
        pdb=" H   ALA D 305 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 304 "   -0.010 2.00e-02 2.50e+03   1.87e-02 3.51e+00
        pdb=" N   ALA C 305 "    0.032 2.00e-02 2.50e+03
        pdb=" CA  ALA C 305 "   -0.008 2.00e-02 2.50e+03
        pdb=" H   ALA C 305 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 304 "   -0.010 2.00e-02 2.50e+03   1.87e-02 3.51e+00
        pdb=" N   ALA B 305 "    0.032 2.00e-02 2.50e+03
        pdb=" CA  ALA B 305 "   -0.008 2.00e-02 2.50e+03
        pdb=" H   ALA B 305 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 8529 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 729
        2.10 -     2.72: 86448
        2.72 -     3.35: 147823
        3.35 -     3.97: 170495
        3.97 -     4.60: 279921
  Nonbonded interactions: 685416
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D1051 "
            pdb=" H   GLU D1051 "
     model   vdw
     1.472 2.450
  nonbonded pdb=" OE1 GLU C1051 "
            pdb=" H   GLU C1051 "
     model   vdw
     1.472 2.450
  nonbonded pdb=" OE1 GLU A1051 "
            pdb=" H   GLU A1051 "
     model   vdw
     1.472 2.450
  nonbonded pdb=" OE1 GLU B1051 "
            pdb=" H   GLU B1051 "
     model   vdw
     1.473 2.450
  nonbonded pdb=" O   PRO C 855 "
            pdb="HD21 ASN C 990 "
     model   vdw
     1.494 2.450
  ... (remaining 685411 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.790
  Extract box with map and model:          1.580
  Check model and map are aligned:         0.310
  Set scattering table:                    0.390
  Process input model:                     106.280
  Find NCS groups from input model:        1.400
  Set up NCS constraints:                  0.120
  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:2.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  114.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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      :  0.005   0.099  29372  Z= 0.341
  Angle     :  0.824  13.097  40208  Z= 0.362
  Chirality :  0.058   0.381   4764
  Planarity :  0.003   0.045   4936
  Dihedral  : 12.333  85.928  10796
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 12.14 %
    Favored  : 87.37 %
  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:  1.86 (0.14), residues: 3652
  helix:  2.40 (0.11), residues: 2412
  sheet:  0.13 (0.42), residues: 168
  loop : -1.42 (0.18), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 693 
 HIS   0.002   0.001   HIS C 389 
 PHE   0.021   0.002   PHE A  49 
 TYR   0.017   0.001   TYR A1022 
 ARG   0.006   0.000   ARG D 360 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  315 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 302
  time to evaluate  : 4.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 1
  residues processed: 310
  average time/residue: 0.6928
  time to fit residues: 339.7952
Evaluate side-chains
  248 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 3.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  930 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 314 optimal weight:    1.9990
   chunk 281 optimal weight:   10.0000
   chunk 156 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 190 optimal weight:    6.9990
   chunk 150 optimal weight:    8.9990
   chunk 291 optimal weight:   20.0000
   chunk 112 optimal weight:    6.9990
   chunk 177 optimal weight:    1.9990
   chunk 217 optimal weight:    0.0370
   chunk 337 optimal weight:    0.7980
   overall best weight:    1.9664

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

Flipped N/Q/H residues before XYZ refinement:
A 280 GLN
B 280 GLN
C 280 GLN
D 642 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  29372  Z= 0.276
  Angle     :  0.541   9.782  40208  Z= 0.295
  Chirality :  0.036   0.241   4764
  Planarity :  0.004   0.065   4936
  Dihedral  :  7.095  59.941   5329
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.03 %
    Favored  : 86.73 %
  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:  1.98 (0.14), residues: 3652
  helix:  2.48 (0.10), residues: 2456
  sheet:  0.02 (0.40), residues: 168
  loop : -1.47 (0.18), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 693 
 HIS   0.007   0.001   HIS D 389 
 PHE   0.018   0.002   PHE C 872 
 TYR   0.017   0.001   TYR A1022 
 ARG   0.004   0.000   ARG B 197 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  311 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 278
  time to evaluate  : 3.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  912 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8811 (p90)
REVERT: A 1020 TYR cc_start: 0.8252 (m-10) cc_final: 0.6324 (t80)
REVERT: A 1023 MET cc_start: 0.6763 (mmt) cc_final: 0.6562 (mmp)
REVERT: B  912 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8827 (p90)
REVERT: C  189 MET cc_start: 0.7496 (mtm) cc_final: 0.7136 (mtm)
REVERT: C  728 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7341 (p)
REVERT: D  728 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7455 (p)
REVERT: D  912 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8776 (p90)
  outliers start: 33
  outliers final: 19
  residues processed: 305
  average time/residue: 0.7031
  time to fit residues: 337.1798
Evaluate side-chains
  280 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 256
  time to evaluate  : 3.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain C residue  280 GLN
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  728 VAL
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain D residue  338 VAL
Chi-restraints excluded: chain D residue  728 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 187 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0980
   chunk 281 optimal weight:    4.9990
   chunk 230 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 338 optimal weight:    1.9990
   chunk 365 optimal weight:    3.9990
   chunk 301 optimal weight:    5.9990
   chunk 335 optimal weight:    7.9990
   chunk 115 optimal weight:    6.9990
   chunk 271 optimal weight:    3.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.139  29372  Z= 0.363
  Angle     :  0.559  15.128  40208  Z= 0.308
  Chirality :  0.038   0.275   4764
  Planarity :  0.004   0.061   4936
  Dihedral  :  6.803  59.958   5329
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.77 %
    Favored  : 86.73 %
  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:  1.71 (0.14), residues: 3652
  helix:  2.31 (0.10), residues: 2452
  sheet:  0.37 (0.41), residues: 148
  loop : -1.74 (0.17), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 682 
 HIS   0.005   0.001   HIS D 389 
 PHE   0.025   0.002   PHE C 487 
 TYR   0.016   0.001   TYR A1022 
 ARG   0.004   0.000   ARG C 197 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  318 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 278
  time to evaluate  : 3.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  750 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8936 (mt)
REVERT: A  912 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8834 (p90)
REVERT: A 1020 TYR cc_start: 0.8382 (m-10) cc_final: 0.6476 (t80)
REVERT: A 1069 THR cc_start: 0.8378 (m) cc_final: 0.8085 (p)
REVERT: B  912 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8831 (p90)
REVERT: B 1020 TYR cc_start: 0.8355 (m-10) cc_final: 0.6398 (t80)
REVERT: B 1069 THR cc_start: 0.8375 (m) cc_final: 0.8083 (p)
REVERT: C  493 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7663 (mm)
REVERT: C  912 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8786 (p90)
REVERT: D  728 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (p)
REVERT: D  912 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8772 (p90)
  outliers start: 40
  outliers final: 25
  residues processed: 305
  average time/residue: 0.7107
  time to fit residues: 339.2193
Evaluate side-chains
  288 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 256
  time to evaluate  : 3.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  850 SER
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain D residue  338 VAL
Chi-restraints excluded: chain D residue  728 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 334 optimal weight:    0.9990
   chunk 254 optimal weight:    1.9990
   chunk 175 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 161 optimal weight:    0.6980
   chunk 227 optimal weight:    0.0970
   chunk 339 optimal weight:    0.9980
   chunk 359 optimal weight:    0.9980
   chunk 177 optimal weight:    1.9990
   chunk 321 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  29372  Z= 0.162
  Angle     :  0.457   8.540  40208  Z= 0.251
  Chirality :  0.035   0.173   4764
  Planarity :  0.003   0.056   4936
  Dihedral  :  6.480  59.886   5329
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.74 %
    Favored  : 86.02 %
  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:  2.08 (0.14), residues: 3652
  helix:  2.61 (0.10), residues: 2452
  sheet:  0.51 (0.42), residues: 148
  loop : -1.65 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 693 
 HIS   0.004   0.000   HIS D 389 
 PHE   0.012   0.001   PHE C 870 
 TYR   0.012   0.001   TYR A1005 
 ARG   0.002   0.000   ARG C 532 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  297 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 264
  time to evaluate  : 3.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.5013 (t-100) cc_final: 0.4582 (t-100)
REVERT: A  912 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8791 (p90)
REVERT: A 1020 TYR cc_start: 0.8466 (m-10) cc_final: 0.6467 (t80)
REVERT: B  912 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8804 (p90)
REVERT: B 1069 THR cc_start: 0.8243 (m) cc_final: 0.7969 (p)
REVERT: C  912 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8767 (p90)
REVERT: D  912 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8732 (p90)
  outliers start: 33
  outliers final: 22
  residues processed: 285
  average time/residue: 0.7141
  time to fit residues: 319.9932
Evaluate side-chains
  278 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 252
  time to evaluate  : 3.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 299 optimal weight:    1.9990
   chunk 204 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 267 optimal weight:    1.9990
   chunk 148 optimal weight:    0.6980
   chunk 306 optimal weight:    6.9990
   chunk 248 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 183 optimal weight:   20.0000
   chunk 322 optimal weight:    0.4980
   chunk 90 optimal weight:   20.0000
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 968 ASN
D 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  29372  Z= 0.203
  Angle     :  0.461   8.723  40208  Z= 0.252
  Chirality :  0.035   0.153   4764
  Planarity :  0.003   0.053   4936
  Dihedral  :  6.351  59.926   5329
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.93 %
    Favored  : 85.41 %
  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:  2.22 (0.14), residues: 3652
  helix:  2.74 (0.10), residues: 2428
  sheet:  0.60 (0.43), residues: 148
  loop : -1.55 (0.18), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 693 
 HIS   0.004   0.000   HIS D 389 
 PHE   0.025   0.001   PHE A 487 
 TYR   0.012   0.001   TYR C1022 
 ARG   0.002   0.000   ARG D 160 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  310 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 266
  time to evaluate  : 3.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4952 (t-100) cc_final: 0.4552 (t-100)
REVERT: A  750 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8893 (mt)
REVERT: A  912 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8808 (p90)
REVERT: B  859 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8631 (ttp)
REVERT: B  912 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8799 (p90)
REVERT: C  493 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: C  859 MET cc_start: 0.8985 (ptm) cc_final: 0.8484 (ttp)
REVERT: C  912 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8731 (p90)
REVERT: D  859 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8604 (ttp)
REVERT: D  912 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8766 (p90)
  outliers start: 44
  outliers final: 25
  residues processed: 293
  average time/residue: 0.7222
  time to fit residues: 331.2194
Evaluate side-chains
  286 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 253
  time to evaluate  : 3.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  850 SER
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 323 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 211 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 359 optimal weight:    0.0870
   chunk 298 optimal weight:    7.9990
   chunk 166 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 188 optimal weight:    4.9990
   overall best weight:    1.7964

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

Flipped N/Q/H residues before XYZ refinement:
C 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  29372  Z= 0.228
  Angle     :  0.473   7.690  40208  Z= 0.259
  Chirality :  0.035   0.156   4764
  Planarity :  0.003   0.055   4936
  Dihedral  :  6.354  59.846   5329
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.98 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.08 (0.14), residues: 3652
  helix:  2.62 (0.10), residues: 2456
  sheet:  0.65 (0.44), residues: 148
  loop : -1.72 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 525 
 HIS   0.004   0.001   HIS D 389 
 PHE   0.029   0.001   PHE C 463 
 TYR   0.012   0.001   TYR D1022 
 ARG   0.003   0.000   ARG D 160 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  296 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 262
  time to evaluate  : 3.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4901 (t-100) cc_final: 0.4491 (t-100)
REVERT: A  859 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8612 (ttp)
REVERT: A  912 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8831 (p90)
REVERT: A 1005 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6375 (t80)
REVERT: A 1069 THR cc_start: 0.8304 (m) cc_final: 0.8086 (p)
REVERT: B  859 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8639 (ttp)
REVERT: B  912 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8827 (p90)
REVERT: B 1069 THR cc_start: 0.8345 (m) cc_final: 0.8121 (p)
REVERT: C  493 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7794 (mm)
REVERT: C  859 MET cc_start: 0.8989 (ptm) cc_final: 0.8531 (ttp)
REVERT: C  912 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8715 (p90)
REVERT: D  859 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8613 (ttp)
REVERT: D  912 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8770 (p90)
  outliers start: 34
  outliers final: 21
  residues processed: 281
  average time/residue: 0.7263
  time to fit residues: 318.3587
Evaluate side-chains
  276 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 246
  time to evaluate  : 3.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  493 LEU
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  850 SER
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain D residue  281 LEU
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 347 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 205 optimal weight:    6.9990
   chunk 262 optimal weight:    1.9990
   chunk 203 optimal weight:   10.0000
   chunk 302 optimal weight:    9.9990
   chunk 200 optimal weight:    7.9990
   chunk 358 optimal weight:    0.5980
   chunk 224 optimal weight:    0.9990
   chunk 218 optimal weight:   10.0000
   chunk 165 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  29372  Z= 0.202
  Angle     :  0.460   7.025  40208  Z= 0.252
  Chirality :  0.035   0.171   4764
  Planarity :  0.003   0.056   4936
  Dihedral  :  6.258  59.545   5329
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.36 %
    Favored  : 84.44 %
  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:  2.10 (0.14), residues: 3652
  helix:  2.65 (0.10), residues: 2456
  sheet:  0.72 (0.44), residues: 148
  loop : -1.75 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP C 525 
 HIS   0.003   0.000   HIS D 389 
 PHE   0.016   0.001   PHE B 487 
 TYR   0.013   0.001   TYR C1022 
 ARG   0.003   0.000   ARG D 160 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  285 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 253
  time to evaluate  : 3.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4927 (t-100) cc_final: 0.4511 (t-100)
REVERT: A  859 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8639 (ttp)
REVERT: A  912 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8802 (p90)
REVERT: A 1005 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6443 (t80)
REVERT: A 1069 THR cc_start: 0.8295 (m) cc_final: 0.8075 (p)
REVERT: B  859 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8572 (ttp)
REVERT: B  912 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8840 (p90)
REVERT: B 1069 THR cc_start: 0.8370 (m) cc_final: 0.8138 (p)
REVERT: C  859 MET cc_start: 0.8964 (ptm) cc_final: 0.8591 (ttp)
REVERT: C  912 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8721 (p90)
REVERT: C 1001 LEU cc_start: 0.8991 (tp) cc_final: 0.8324 (mt)
REVERT: D  859 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8571 (ttp)
REVERT: D  912 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8696 (p90)
  outliers start: 32
  outliers final: 22
  residues processed: 269
  average time/residue: 0.7266
  time to fit residues: 305.0514
Evaluate side-chains
  282 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 252
  time to evaluate  : 3.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain C residue 1016 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 221 optimal weight:    3.9990
   chunk 143 optimal weight:    3.9990
   chunk 214 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0030
   chunk 70 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 227 optimal weight:    4.9990
   chunk 244 optimal weight:    0.9980
   chunk 177 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 281 optimal weight:   10.0000
   overall best weight:    1.3794

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  29372  Z= 0.190
  Angle     :  0.452   5.787  40208  Z= 0.247
  Chirality :  0.035   0.141   4764
  Planarity :  0.003   0.060   4936
  Dihedral  :  6.161  58.779   5329
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.29 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.14), residues: 3652
  helix:  2.69 (0.10), residues: 2452
  sheet:  0.77 (0.44), residues: 148
  loop : -1.74 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 525 
 HIS   0.003   0.000   HIS D 389 
 PHE   0.032   0.001   PHE A 463 
 TYR   0.012   0.001   TYR D1022 
 ARG   0.002   0.000   ARG D 160 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  290 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 257
  time to evaluate  : 3.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4994 (t-100) cc_final: 0.4564 (t-100)
REVERT: A  859 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8599 (ttp)
REVERT: A  912 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8799 (p90)
REVERT: A 1001 LEU cc_start: 0.8911 (tp) cc_final: 0.8231 (mt)
REVERT: A 1005 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6493 (t80)
REVERT: B  859 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8605 (ttp)
REVERT: B  912 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8794 (p90)
REVERT: B 1001 LEU cc_start: 0.8933 (tp) cc_final: 0.8253 (mt)
REVERT: B 1069 THR cc_start: 0.8367 (m) cc_final: 0.8164 (p)
REVERT: C  859 MET cc_start: 0.8949 (ptm) cc_final: 0.8604 (ttp)
REVERT: C  912 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8740 (p90)
REVERT: C 1001 LEU cc_start: 0.8972 (tp) cc_final: 0.8324 (mt)
REVERT: D  859 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8583 (ttp)
REVERT: D  912 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8686 (p90)
REVERT: D 1001 LEU cc_start: 0.8969 (tp) cc_final: 0.8298 (mt)
  outliers start: 33
  outliers final: 24
  residues processed: 274
  average time/residue: 0.7224
  time to fit residues: 310.8348
Evaluate side-chains
  280 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 248
  time to evaluate  : 3.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  728 VAL
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain C residue 1016 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 326 optimal weight:    4.9990
   chunk 343 optimal weight:    0.5980
   chunk 313 optimal weight:    5.9990
   chunk 334 optimal weight:    0.7980
   chunk 201 optimal weight:    0.7980
   chunk 145 optimal weight:    2.9990
   chunk 262 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 301 optimal weight:    6.9990
   chunk 316 optimal weight:    3.9990
   chunk 332 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  29372  Z= 0.196
  Angle     :  0.457   7.332  40208  Z= 0.250
  Chirality :  0.035   0.191   4764
  Planarity :  0.003   0.061   4936
  Dihedral  :  6.092  59.759   5329
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.36 %
    Favored  : 84.40 %
  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:  2.14 (0.14), residues: 3652
  helix:  2.69 (0.10), residues: 2452
  sheet:  0.83 (0.44), residues: 148
  loop : -1.78 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 525 
 HIS   0.003   0.000   HIS D 389 
 PHE   0.013   0.001   PHE D 870 
 TYR   0.013   0.001   TYR D1022 
 ARG   0.003   0.000   ARG C 784 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  283 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 250
  time to evaluate  : 3.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4921 (t-100) cc_final: 0.4486 (t-100)
REVERT: A  859 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8592 (ttp)
REVERT: A  912 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8804 (p90)
REVERT: A 1001 LEU cc_start: 0.8909 (tp) cc_final: 0.8246 (mt)
REVERT: A 1005 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6497 (t80)
REVERT: B  859 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8621 (ttp)
REVERT: B  912 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8806 (p90)
REVERT: B 1001 LEU cc_start: 0.8905 (tp) cc_final: 0.8244 (mt)
REVERT: B 1069 THR cc_start: 0.8391 (m) cc_final: 0.8183 (p)
REVERT: C  859 MET cc_start: 0.8938 (ptm) cc_final: 0.8623 (ttp)
REVERT: C  863 MET cc_start: 0.8771 (mtt) cc_final: 0.8364 (mtt)
REVERT: C  912 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8739 (p90)
REVERT: C 1001 LEU cc_start: 0.8953 (tp) cc_final: 0.8301 (mt)
REVERT: D  859 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8597 (ttp)
REVERT: D  912 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8681 (p90)
REVERT: D 1001 LEU cc_start: 0.8940 (tp) cc_final: 0.8281 (mt)
  outliers start: 33
  outliers final: 24
  residues processed: 268
  average time/residue: 0.7877
  time to fit residues: 334.0652
Evaluate side-chains
  281 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 249
  time to evaluate  : 3.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  851 ARG
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  728 VAL
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain C residue 1016 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Chi-restraints excluded: chain D residue 1016 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 219 optimal weight:    5.9990
   chunk 353 optimal weight:    3.9990
   chunk 215 optimal weight:    2.9990
   chunk 167 optimal weight:    2.9990
   chunk 245 optimal weight:    2.9990
   chunk 370 optimal weight:   20.0000
   chunk 341 optimal weight:    1.9990
   chunk 295 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 227 optimal weight:    0.4980
   chunk 180 optimal weight:   10.0000
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
B 973 ASN
D 973 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  29372  Z= 0.277
  Angle     :  0.492   6.861  40208  Z= 0.270
  Chirality :  0.036   0.159   4764
  Planarity :  0.004   0.065   4936
  Dihedral  :  6.243  58.952   5329
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.10 %
    Favored  : 84.62 %
  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:  1.97 (0.14), residues: 3652
  helix:  2.57 (0.10), residues: 2448
  sheet:  0.86 (0.44), residues: 148
  loop : -1.89 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 525 
 HIS   0.003   0.001   HIS B 818 
 PHE   0.039   0.001   PHE C 463 
 TYR   0.012   0.001   TYR C1022 
 ARG   0.003   0.000   ARG D 160 

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

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

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7304 Ramachandran restraints generated.
    3652 Oldfield, 0 Emsley, 3652 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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 LYS   50 is missing expected H atoms. Skipping.
Residue LYS  116 is missing expected H atoms. Skipping.
Residue TYR  117 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  134 is missing expected H atoms. Skipping.
Residue LEU  139 is missing expected H atoms. Skipping.
Residue LYS  140 is missing expected H atoms. Skipping.
Residue LYS  153 is missing expected H atoms. Skipping.
Residue LEU  157 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue THR  184 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 VAL  220 is missing expected H atoms. Skipping.
Residue LEU  226 is missing expected H atoms. Skipping.
Residue TYR  240 is missing expected H atoms. Skipping.
Residue ILE  241 is missing expected H atoms. Skipping.
Residue LEU  250 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue LEU  262 is missing expected H atoms. Skipping.
Residue THR  272 is missing expected H atoms. Skipping.
Residue THR  289 is missing expected H atoms. Skipping.
Residue SER  290 is missing expected H atoms. Skipping.
Residue SER  293 is missing expected H atoms. Skipping.
Residue LYS  298 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 SER  332 is missing expected H atoms. Skipping.
Residue MET  353 is missing expected H atoms. Skipping.
Residue VAL  354 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 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 LYS  382 is missing expected H atoms. Skipping.
Residue LYS  395 is missing expected H atoms. Skipping.
Residue LYS  423 is missing expected H atoms. Skipping.
Residue THR  448 is missing expected H atoms. Skipping.
Residue SER  455 is missing expected H atoms. Skipping.
Residue LYS  468 is missing expected H atoms. Skipping.
Residue LYS  486 is missing expected H atoms. Skipping.
Residue THR  503 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue LYS  513 is missing expected H atoms. Skipping.
Residue TYR  516 is missing expected H atoms. Skipping.
Residue LYS  526 is missing expected H atoms. Skipping.
Residue LYS  585 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue VAL  604 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue LEU  639 is missing expected H atoms. Skipping.
Residue THR  690 is missing expected H atoms. Skipping.
Residue LEU  709 is missing expected H atoms. Skipping.
Residue LYS  714 is missing expected H atoms. Skipping.
Residue LYS  715 is missing expected H atoms. Skipping.
Residue LYS  721 is missing expected H atoms. Skipping.
Residue LYS  722 is missing expected H atoms. Skipping.
Residue SER  917 is missing expected H atoms. Skipping.
Residue TYR  924 is missing expected H atoms. Skipping.
Residue VAL 1025 is missing expected H atoms. Skipping.
Residue LYS 1027 is missing expected H atoms. Skipping.
Residue LYS 1066 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 MET 1078 is missing expected H atoms. Skipping.
Residue LEU 1085 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 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
  286 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 252
  time to evaluate  : 3.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 TRP cc_start: 0.4972 (t-100) cc_final: 0.4515 (t-100)
REVERT: A  859 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8639 (ttp)
REVERT: A  912 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8886 (p90)
REVERT: A 1001 LEU cc_start: 0.8945 (tp) cc_final: 0.8277 (mt)
REVERT: A 1005 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6500 (t80)
REVERT: B  859 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8619 (ttp)
REVERT: B  912 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8872 (p90)
REVERT: B 1001 LEU cc_start: 0.8963 (tp) cc_final: 0.8297 (mt)
REVERT: B 1069 THR cc_start: 0.8427 (m) cc_final: 0.8220 (p)
REVERT: C  859 MET cc_start: 0.8967 (ptm) cc_final: 0.8647 (ttp)
REVERT: C  863 MET cc_start: 0.8878 (mtt) cc_final: 0.8501 (mtt)
REVERT: C  912 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8783 (p90)
REVERT: C 1001 LEU cc_start: 0.9076 (tp) cc_final: 0.8382 (mt)
REVERT: C 1069 THR cc_start: 0.8255 (m) cc_final: 0.8029 (p)
REVERT: D  859 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8629 (ttp)
REVERT: D  912 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8675 (p90)
REVERT: D 1001 LEU cc_start: 0.8990 (tp) cc_final: 0.8325 (mt)
REVERT: D 1069 THR cc_start: 0.8436 (m) cc_final: 0.8224 (p)
  outliers start: 34
  outliers final: 24
  residues processed: 270
  average time/residue: 0.7537
  time to fit residues: 316.9013
Evaluate side-chains
  275 residues out of total 3340 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 243
  time to evaluate  : 3.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  851 ARG
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain A residue  912 PHE
Chi-restraints excluded: chain A residue  930 THR
Chi-restraints excluded: chain A residue  968 ASN
Chi-restraints excluded: chain A residue 1005 TYR
Chi-restraints excluded: chain A residue 1007 ASN
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  608 ILE
Chi-restraints excluded: chain B residue  758 MET
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  912 PHE
Chi-restraints excluded: chain B residue  930 THR
Chi-restraints excluded: chain B residue 1007 ASN
Chi-restraints excluded: chain B residue 1016 VAL
Chi-restraints excluded: chain C residue  728 VAL
Chi-restraints excluded: chain C residue  758 MET
Chi-restraints excluded: chain C residue  851 ARG
Chi-restraints excluded: chain C residue  912 PHE
Chi-restraints excluded: chain C residue  930 THR
Chi-restraints excluded: chain C residue 1007 ASN
Chi-restraints excluded: chain C residue 1016 VAL
Chi-restraints excluded: chain D residue  758 MET
Chi-restraints excluded: chain D residue  851 ARG
Chi-restraints excluded: chain D residue  859 MET
Chi-restraints excluded: chain D residue  912 PHE
Chi-restraints excluded: chain D residue  930 THR
Chi-restraints excluded: chain D residue 1007 ASN
Chi-restraints excluded: chain D residue 1016 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 372
   random chunks:
   chunk 234 optimal weight:    2.9990
   chunk 314 optimal weight:    0.4980
   chunk 90 optimal weight:    6.9990
   chunk 272 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 295 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 303 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
C 973 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.154675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.102206 restraints weight = 134121.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.57
r_work: 0.3192 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  29372  Z= 0.228
  Angle     :  0.473   6.487  40208  Z= 0.260
  Chirality :  0.035   0.172   4764
  Planarity :  0.003   0.061   4936
  Dihedral  :  6.146  58.052   5329
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.29 %
    Favored  : 84.55 %
  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:  2.03 (0.14), residues: 3652
  helix:  2.62 (0.10), residues: 2448
  sheet:  0.93 (0.44), residues: 148
  loop : -1.85 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 525 
 HIS   0.003   0.000   HIS D 389 
 PHE   0.023   0.001   PHE C 463 
 TYR   0.013   0.001   TYR D1022 
 ARG   0.002   0.000   ARG D 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8757.88 seconds
wall clock time: 151 minutes 54.39 seconds (9114.39 seconds total)