Starting phenix.real_space_refine
on Sun Feb 18 13:54:08 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3d_25655/02_2024/7t3d_25655.pdb"
  }
  resolution = 3.38
  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=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      93      5.16       5
     C   13923      2.51       5
     N    3744      2.21       5
     O    4362      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  119": "OE1" <-> "OE2"
    Residue "A PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   24": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   88": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  162": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   55": "OE1" <-> "OE2"
    Residue "D TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  119": "OE1" <-> "OE2"
    Residue "E PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   24": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   88": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  162": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU   55": "OE1" <-> "OE2"
    Residue "M TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  119": "OE1" <-> "OE2"
    Residue "F PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   24": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   88": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  162": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   55": "OE1" <-> "OE2"
    Residue "N TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 22122
  Number of models: 1
  Model: ""
    Number of chains: 27
    Chain: "A"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2529
          Classifications: {'peptide': 324}
          Link IDs: {'PTRANS': 19, 'TRANS': 304}
    Chain: "B"
      Number of atoms: 1326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1326
          Classifications: {'peptide': 163}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 829
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 900
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
    Chain: "H"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 872
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 3, 'TRANS': 106}
    Chain: "L"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 820
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "E"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2529
          Classifications: {'peptide': 324}
          Link IDs: {'PTRANS': 19, 'TRANS': 304}
    Chain: "G"
      Number of atoms: 1326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1326
          Classifications: {'peptide': 163}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "M"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 829
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "J"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 900
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
    Chain: "O"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 872
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 3, 'TRANS': 106}
    Chain: "Q"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 820
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 2529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2529
          Classifications: {'peptide': 324}
          Link IDs: {'PTRANS': 19, 'TRANS': 304}
    Chain: "I"
      Number of atoms: 1326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1326
          Classifications: {'peptide': 163}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "N"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 829
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "K"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 900
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
    Chain: "P"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 872
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 3, 'TRANS': 106}
    Chain: "R"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 820
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "S"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "T"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "U"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "I"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 11.89, per 1000 atoms: 0.54
  Number of scatterers: 22122
  At special positions: 0
  Unit cell: (142.6, 152.95, 161, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      93     16.00
     O    4362      8.00
     N    3744      7.00
     C   13923      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=30, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  14 " - pdb=" SG  CYS B 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A  76 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  14 " - pdb=" SG  CYS G 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  52 " - pdb=" SG  CYS E 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E  76 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  97 " - pdb=" SG  CYS E 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 281 " - pdb=" SG  CYS E 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 144 " - pdb=" SG  CYS G 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  22 " - pdb=" SG  CYS O  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS Q  23 " - pdb=" SG  CYS Q  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  14 " - pdb=" SG  CYS I 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  52 " - pdb=" SG  CYS F 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F  76 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  97 " - pdb=" SG  CYS F 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 281 " - pdb=" SG  CYS F 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I 144 " - pdb=" SG  CYS I 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  22 " - pdb=" SG  CYS P  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  23 " - pdb=" SG  CYS R  88 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG S   1 " - " NAG S   2 "
      " NAG T   1 " - " NAG T   2 "
      " NAG U   1 " - " NAG U   2 "
    NAG-ASN
      " NAG A 401 " - " ASN A  21 "
      " NAG A 402 " - " ASN A  33 "
      " NAG A 403 " - " ASN A 278 "
      " NAG A 404 " - " ASN A 289 "
      " NAG B 201 " - " ASN B 154 "
      " NAG E 401 " - " ASN E  21 "
      " NAG E 402 " - " ASN E  33 "
      " NAG E 403 " - " ASN E 278 "
      " NAG E 404 " - " ASN E 289 "
      " NAG F 401 " - " ASN F  21 "
      " NAG F 402 " - " ASN F  33 "
      " NAG F 403 " - " ASN F 278 "
      " NAG F 404 " - " ASN F 289 "
      " NAG G 201 " - " ASN G 154 "
      " NAG I 201 " - " ASN I 154 "
      " NAG S   1 " - " ASN A  94 "
      " NAG T   1 " - " ASN E  94 "
      " NAG U   1 " - " ASN F  94 "
  Time building additional restraints: 8.81
  Conformation dependent library (CDL) restraints added in 4.0 seconds
  

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5118

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 66 sheets defined
      16.2% alpha, 36.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 187 through 195
    Processing helix  chain 'B' and resid 37 through 58
    Processing helix  chain 'B' and resid 74 through 127
    Processing helix  chain 'B' and resid 145 through 154
    Processing helix  chain 'B' and resid 158 through 169
      removed outlier: 4.071A  pdb=" N   TYR B 162 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLU B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   GLU B 165 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.564A  pdb=" N   ILE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 83 through 87
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'E' and resid 65 through 72
    Processing helix  chain 'E' and resid 104 through 112
    Processing helix  chain 'E' and resid 187 through 195
    Processing helix  chain 'G' and resid 37 through 58
    Processing helix  chain 'G' and resid 74 through 127
    Processing helix  chain 'G' and resid 145 through 154
    Processing helix  chain 'G' and resid 158 through 169
      removed outlier: 4.071A  pdb=" N   TYR G 162 " --> pdb=" O   ASP G 158 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLU G 164 " --> pdb=" O   PRO G 160 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   GLU G 165 " --> pdb=" O   LYS G 161 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 83
      removed outlier: 3.565A  pdb=" N   ILE M  83 " --> pdb=" O   PRO M  80 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 28 through 32
    Processing helix  chain 'J' and resid 83 through 87
    Processing helix  chain 'O' and resid 61 through 64
    Processing helix  chain 'O' and resid 73 through 75
      No H-bonds generated for 'chain 'O' and resid 73 through 75'
    Processing helix  chain 'O' and resid 83 through 87
    Processing helix  chain 'F' and resid 65 through 72
    Processing helix  chain 'F' and resid 104 through 112
    Processing helix  chain 'F' and resid 187 through 195
    Processing helix  chain 'I' and resid 37 through 58
    Processing helix  chain 'I' and resid 74 through 127
    Processing helix  chain 'I' and resid 145 through 154
    Processing helix  chain 'I' and resid 158 through 169
      removed outlier: 4.071A  pdb=" N   TYR I 162 " --> pdb=" O   ASP I 158 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLU I 164 " --> pdb=" O   PRO I 160 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   GLU I 165 " --> pdb=" O   LYS I 161 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 79 through 83
      removed outlier: 3.565A  pdb=" N   ILE N  83 " --> pdb=" O   PRO N  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 28 through 32
    Processing helix  chain 'K' and resid 83 through 87
    Processing helix  chain 'P' and resid 61 through 64
    Processing helix  chain 'P' and resid 73 through 75
      No H-bonds generated for 'chain 'P' and resid 73 through 75'
    Processing helix  chain 'P' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36
      removed outlier: 6.645A  pdb=" N   CYS B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41
    Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54
      removed outlier: 5.984A  pdb=" N   LEU A  51 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   CYS A 277 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.268A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122
      removed outlier: 6.947A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   LEU A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122
      removed outlier: 6.947A  pdb=" N   TYR A 256 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141
      removed outlier: 4.936A  pdb=" N   CYS A 139 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 146 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288
      removed outlier: 4.141A  pdb=" N   CYS A 281 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7
      removed outlier: 5.593A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 14
      removed outlier: 6.422A  pdb=" N   LEU D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   TYR D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 14
      removed outlier: 3.530A  pdb=" N   THR D  97 " --> pdb=" O   HIS D  90 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7
      removed outlier: 6.319A  pdb=" N   SER C  17 " --> pdb=" O   SER C  82A" (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER C  82A" --> pdb=" O   SER C  17 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   SER C  19 " --> pdb=" O   GLN C  81 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLN C  81 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   SER C  21 " --> pdb=" O   TYR C  79 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TYR C  79 " --> pdb=" O   SER C  21 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ALA C  23 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   THR C  77 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.017A  pdb=" N   MET C  34 " --> pdb=" O   MET C  50 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   MET C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12
    Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.597A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.687A  pdb=" N   TRP L  35 " --> pdb=" O   ILE L  47 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 4.166A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 36
      removed outlier: 6.645A  pdb=" N   CYS G 137 " --> pdb=" O   ILE G 133 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 25 through 26
    Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41
    Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44
    Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 54
      removed outlier: 5.984A  pdb=" N   LEU E  51 " --> pdb=" O   HIS E 275 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   CYS E 277 " --> pdb=" O   LEU E  51 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 59 through 60
      removed outlier: 6.268A  pdb=" N   LEU E  59 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE E  87 " --> pdb=" O   ILE E 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD1
    Processing sheet with id=AD2, first strand: chain 'E' and resid 115 through 122
      removed outlier: 6.948A  pdb=" N   TYR E 256 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU E 179 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   LEU E 179 " --> pdb=" O   PRO E 254 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 122
      removed outlier: 6.948A  pdb=" N   TYR E 256 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU E 179 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141
      removed outlier: 4.937A  pdb=" N   CYS E 139 " --> pdb=" O   SER E 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER E 146 " --> pdb=" O   CYS E 139 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169
    Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 288
      removed outlier: 4.141A  pdb=" N   CYS E 281 " --> pdb=" O   ILE E 288 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'M' and resid 5 through 7
      removed outlier: 5.593A  pdb=" N   VAL M  19 " --> pdb=" O   ILE M  75 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 14
      removed outlier: 6.421A  pdb=" N   LEU M  33 " --> pdb=" O   TYR M  49 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   TYR M  49 " --> pdb=" O   LEU M  33 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TRP M  35 " --> pdb=" O   LEU M  47 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 14
      removed outlier: 3.530A  pdb=" N   THR M  97 " --> pdb=" O   HIS M  90 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 7
      removed outlier: 6.319A  pdb=" N   SER J  17 " --> pdb=" O   SER J  82A" (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   SER J  82A" --> pdb=" O   SER J  17 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   SER J  19 " --> pdb=" O   GLN J  81 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLN J  81 " --> pdb=" O   SER J  19 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   SER J  21 " --> pdb=" O   TYR J  79 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TYR J  79 " --> pdb=" O   SER J  21 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ALA J  23 " --> pdb=" O   THR J  77 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   THR J  77 " --> pdb=" O   ALA J  23 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12
      removed outlier: 7.016A  pdb=" N   MET J  34 " --> pdb=" O   MET J  50 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   MET J  50 " --> pdb=" O   MET J  34 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP J  36 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 12
    Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 7
    Processing sheet with id=AE5, first strand: chain 'O' and resid 57 through 59
      removed outlier: 6.598A  pdb=" N   TRP O  36 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   TYR O  50 " --> pdb=" O   MET O  34 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   MET O  34 " --> pdb=" O   TYR O  50 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 5
    Processing sheet with id=AE7, first strand: chain 'Q' and resid 10 through 13
      removed outlier: 6.687A  pdb=" N   TRP Q  35 " --> pdb=" O   ILE Q  47 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 13
      removed outlier: 4.167A  pdb=" N   THR Q  97 " --> pdb=" O   GLN Q  90 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'I' and resid 31 through 36
      removed outlier: 6.645A  pdb=" N   CYS I 137 " --> pdb=" O   ILE I 133 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'F' and resid 25 through 26
    Processing sheet with id=AF2, first strand: chain 'F' and resid 39 through 41
    Processing sheet with id=AF3, first strand: chain 'F' and resid 43 through 44
    Processing sheet with id=AF4, first strand: chain 'F' and resid 51 through 54
      removed outlier: 5.984A  pdb=" N   LEU F  51 " --> pdb=" O   HIS F 275 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   CYS F 277 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'F' and resid 59 through 60
      removed outlier: 6.268A  pdb=" N   LEU F  59 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE F  87 " --> pdb=" O   ILE F 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF5
    Processing sheet with id=AF6, first strand: chain 'F' and resid 115 through 122
      removed outlier: 6.948A  pdb=" N   TYR F 256 " --> pdb=" O   LEU F 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU F 179 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   LEU F 179 " --> pdb=" O   PRO F 254 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'F' and resid 115 through 122
      removed outlier: 6.948A  pdb=" N   TYR F 256 " --> pdb=" O   LEU F 179 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LEU F 179 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'F' and resid 136 through 141
      removed outlier: 4.937A  pdb=" N   CYS F 139 " --> pdb=" O   SER F 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER F 146 " --> pdb=" O   CYS F 139 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'F' and resid 164 through 169
    Processing sheet with id=AG1, first strand: chain 'F' and resid 286 through 288
      removed outlier: 4.141A  pdb=" N   CYS F 281 " --> pdb=" O   ILE F 288 " (cutoff:3.500A)
    Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 7
      removed outlier: 5.593A  pdb=" N   VAL N  19 " --> pdb=" O   ILE N  75 " (cutoff:3.500A)
    Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 14
      removed outlier: 6.422A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 14
      removed outlier: 3.530A  pdb=" N   THR N  97 " --> pdb=" O   HIS N  90 " (cutoff:3.500A)
    Processing sheet with id=AG5, first strand: chain 'K' and resid 3 through 7
      removed outlier: 6.318A  pdb=" N   SER K  17 " --> pdb=" O   SER K  82A" (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   SER K  82A" --> pdb=" O   SER K  17 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   SER K  19 " --> pdb=" O   GLN K  81 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLN K  81 " --> pdb=" O   SER K  19 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   SER K  21 " --> pdb=" O   TYR K  79 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TYR K  79 " --> pdb=" O   SER K  21 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ALA K  23 " --> pdb=" O   THR K  77 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   THR K  77 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
    Processing sheet with id=AG6, first strand: chain 'K' and resid 10 through 12
      removed outlier: 7.017A  pdb=" N   MET K  34 " --> pdb=" O   MET K  50 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   MET K  50 " --> pdb=" O   MET K  34 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP K  36 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 12
    Processing sheet with id=AG8, first strand: chain 'P' and resid 4 through 7
    Processing sheet with id=AG9, first strand: chain 'P' and resid 57 through 59
      removed outlier: 6.598A  pdb=" N   TRP P  36 " --> pdb=" O   VAL P  48 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   TYR P  50 " --> pdb=" O   MET P  34 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   MET P  34 " --> pdb=" O   TYR P  50 " (cutoff:3.500A)
    Processing sheet with id=AH1, first strand: chain 'R' and resid 4 through 5
    Processing sheet with id=AH2, first strand: chain 'R' and resid 10 through 13
      removed outlier: 6.687A  pdb=" N   TRP R  35 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing sheet with id=AH3, first strand: chain 'R' and resid 10 through 13
      removed outlier: 4.166A  pdb=" N   THR R  97 " --> pdb=" O   GLN R  90 " (cutoff:3.500A)

    990 hydrogen bonds defined for protein.
    2529 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: 8.99

  Time building geometry restraints manager: 9.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 5426
        1.32 -     1.47: 7825
        1.47 -     1.61: 9252
        1.61 -     1.75: 21
        1.75 -     1.89: 111
  Bond restraints: 22635
  Sorted by residual:
  bond pdb=" NE1 TRP J 103 "
       pdb=" CE2 TRP J 103 "
    ideal  model  delta    sigma   weight residual
    1.370  1.299  0.071 1.10e-02 8.26e+03 4.16e+01
  bond pdb=" NE1 TRP K 103 "
       pdb=" CE2 TRP K 103 "
    ideal  model  delta    sigma   weight residual
    1.370  1.299  0.071 1.10e-02 8.26e+03 4.14e+01
  bond pdb=" NE1 TRP C 103 "
       pdb=" CE2 TRP C 103 "
    ideal  model  delta    sigma   weight residual
    1.370  1.299  0.071 1.10e-02 8.26e+03 4.14e+01
  bond pdb=" CD2 TRP O 103 "
       pdb=" CE3 TRP O 103 "
    ideal  model  delta    sigma   weight residual
    1.398  1.501 -0.103 1.60e-02 3.91e+03 4.13e+01
  bond pdb=" CD2 TRP H 103 "
       pdb=" CE3 TRP H 103 "
    ideal  model  delta    sigma   weight residual
    1.398  1.501 -0.103 1.60e-02 3.91e+03 4.12e+01
  ... (remaining 22630 not shown)

  Histogram of bond angle deviations from ideal:
       95.35 -   103.16: 258
      103.16 -   110.96: 7873
      110.96 -   118.76: 10111
      118.76 -   126.56: 12139
      126.56 -   134.36: 312
  Bond angle restraints: 30693
  Sorted by residual:
  angle pdb=" N   ARG F 255 "
        pdb=" CA  ARG F 255 "
        pdb=" C   ARG F 255 "
      ideal   model   delta    sigma   weight residual
     113.43  101.93   11.50 1.26e+00 6.30e-01 8.33e+01
  angle pdb=" N   ARG A 255 "
        pdb=" CA  ARG A 255 "
        pdb=" C   ARG A 255 "
      ideal   model   delta    sigma   weight residual
     113.43  101.93   11.50 1.26e+00 6.30e-01 8.32e+01
  angle pdb=" N   ARG E 255 "
        pdb=" CA  ARG E 255 "
        pdb=" C   ARG E 255 "
      ideal   model   delta    sigma   weight residual
     113.43  101.94   11.49 1.26e+00 6.30e-01 8.31e+01
  angle pdb=" N   SER J  95 "
        pdb=" CA  SER J  95 "
        pdb=" C   SER J  95 "
      ideal   model   delta    sigma   weight residual
     113.16  124.41  -11.25 1.24e+00 6.50e-01 8.23e+01
  angle pdb=" N   SER K  95 "
        pdb=" CA  SER K  95 "
        pdb=" C   SER K  95 "
      ideal   model   delta    sigma   weight residual
     113.16  124.39  -11.23 1.24e+00 6.50e-01 8.20e+01
  ... (remaining 30688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 13184
       15.99 -    31.99: 346
       31.99 -    47.98: 93
       47.98 -    63.97: 81
       63.97 -    79.97: 18
  Dihedral angle restraints: 13722
    sinusoidal: 5682
      harmonic: 8040
  Sorted by residual:
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  92 "
           pdb=" CB  CYS K  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.18   43.82     1      1.00e+01 1.00e-02 2.67e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  92 "
           pdb=" CB  CYS C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.19   43.81     1      1.00e+01 1.00e-02 2.67e+01
  dihedral pdb=" CB  CYS J  22 "
           pdb=" SG  CYS J  22 "
           pdb=" SG  CYS J  92 "
           pdb=" CB  CYS J  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.22   43.78     1      1.00e+01 1.00e-02 2.67e+01
  ... (remaining 13719 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 2342
       0.097 -    0.194: 816
       0.194 -    0.291: 136
       0.291 -    0.387: 59
       0.387 -    0.484: 28
  Chirality restraints: 3381
  Sorted by residual:
  chirality pdb=" C1  NAG U   2 "
            pdb=" O4  NAG U   1 "
            pdb=" C2  NAG U   2 "
            pdb=" O5  NAG U   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.63    0.23 2.00e-02 2.50e+03 1.33e+02
  chirality pdb=" C1  NAG S   2 "
            pdb=" O4  NAG S   1 "
            pdb=" C2  NAG S   2 "
            pdb=" O5  NAG S   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.63    0.23 2.00e-02 2.50e+03 1.31e+02
  chirality pdb=" C1  NAG T   2 "
            pdb=" O4  NAG T   1 "
            pdb=" C2  NAG T   2 "
            pdb=" O5  NAG T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.63    0.23 2.00e-02 2.50e+03 1.31e+02
  ... (remaining 3378 not shown)

  Planarity restraints: 3945
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 154 "   -0.124 2.00e-02 2.50e+03   1.31e-01 2.15e+02
        pdb=" CG  ASN B 154 "    0.058 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 154 "    0.020 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 154 "    0.204 2.00e-02 2.50e+03
        pdb=" C1  NAG B 201 "   -0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN G 154 "   -0.124 2.00e-02 2.50e+03   1.31e-01 2.15e+02
        pdb=" CG  ASN G 154 "    0.057 2.00e-02 2.50e+03
        pdb=" OD1 ASN G 154 "    0.020 2.00e-02 2.50e+03
        pdb=" ND2 ASN G 154 "    0.204 2.00e-02 2.50e+03
        pdb=" C1  NAG G 201 "   -0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN I 154 "    0.124 2.00e-02 2.50e+03   1.31e-01 2.14e+02
        pdb=" CG  ASN I 154 "   -0.057 2.00e-02 2.50e+03
        pdb=" OD1 ASN I 154 "   -0.020 2.00e-02 2.50e+03
        pdb=" ND2 ASN I 154 "   -0.204 2.00e-02 2.50e+03
        pdb=" C1  NAG I 201 "    0.158 2.00e-02 2.50e+03
  ... (remaining 3942 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 591
        2.65 -     3.22: 20295
        3.22 -     3.78: 35696
        3.78 -     4.34: 49314
        4.34 -     4.90: 80236
  Nonbonded interactions: 186132
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN G  27 "
            pdb=" CZ2 TRP O  99 "
     model   vdw
     2.093 3.340
  nonbonded pdb=" OE1 GLN I  27 "
            pdb=" CZ2 TRP P  99 "
     model   vdw
     2.093 3.340
  nonbonded pdb=" OE1 GLN B  27 "
            pdb=" CZ2 TRP H  99 "
     model   vdw
     2.093 3.340
  nonbonded pdb=" OD2 ASP G 112 "
            pdb=" NZ  LYS G 116 "
     model   vdw
     2.401 2.520
  nonbonded pdb=" OD2 ASP I 112 "
            pdb=" NZ  LYS I 116 "
     model   vdw
     2.401 2.520
  ... (remaining 186127 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'J'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'M'
  selection = chain 'N'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'O'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'Q'
  selection = chain 'R'
}
ncs_group {
  reference = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
}

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:             1.710
  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:             0.020
  Extract box with map and model:          8.190
  Check model and map are aligned:         0.340
  Set scattering table:                    0.220
  Process input model:                     60.790
  Find NCS groups from input model:        1.510
  Set up NCS constraints:                  0.250
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   76.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
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      :  0.022   0.133  22635  Z= 1.446
  Angle     :  1.765  12.814  30693  Z= 1.185
  Chirality :  0.109   0.484   3381
  Planarity :  0.009   0.058   3927
  Dihedral  :  9.955  79.967   8514
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.15), residues: 2760
  helix:  0.81 (0.23), residues: 375
  sheet:  0.57 (0.18), residues: 726
  loop :  0.82 (0.15), residues: 1659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.009   TRP F  84 
 HIS   0.011   0.003   HIS I 142 
 PHE   0.039   0.008   PHE F 118 
 TYR   0.047   0.009   TYR O 102 
 ARG   0.013   0.002   ARG H  71 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  581 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 581
  time to evaluate  : 2.560 
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
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 VAL cc_start: 0.8820 (t) cc_final: 0.8538 (m)
REVERT: D    4 MET cc_start: 0.8441 (mmm) cc_final: 0.8183 (mmm)
REVERT: D   82 ASP cc_start: 0.8011 (m-30) cc_final: 0.7746 (m-30)
REVERT: C   72 ASP cc_start: 0.8197 (t0) cc_final: 0.7979 (t0)
REVERT: C   75 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8465 (mttt)
REVERT: C   83 THR cc_start: 0.8680 (t) cc_final: 0.7978 (p)
REVERT: C   96 ASP cc_start: 0.8203 (t0) cc_final: 0.7931 (t0)
REVERT: H    3 GLN cc_start: 0.7226 (mt0) cc_final: 0.6922 (mm-40)
REVERT: H  100 TYR cc_start: 0.7801 (t80) cc_final: 0.7433 (t80)
REVERT: L   17 GLU cc_start: 0.7099 (tt0) cc_final: 0.6803 (tt0)
REVERT: L   82 ASP cc_start: 0.6864 (m-30) cc_final: 0.6344 (m-30)
REVERT: E  148 TYR cc_start: 0.9109 (m-80) cc_final: 0.8837 (m-80)
REVERT: J   83 THR cc_start: 0.8577 (t) cc_final: 0.8003 (p)
REVERT: O    3 GLN cc_start: 0.7099 (mt0) cc_final: 0.6747 (mm-40)
REVERT: O  100 TYR cc_start: 0.7969 (t80) cc_final: 0.7636 (t80)
REVERT: Q   42 GLN cc_start: 0.8825 (mm-40) cc_final: 0.7941 (mp10)
REVERT: Q   82 ASP cc_start: 0.6981 (m-30) cc_final: 0.6581 (m-30)
REVERT: F   56 VAL cc_start: 0.8700 (t) cc_final: 0.8426 (m)
REVERT: N   82 ASP cc_start: 0.8006 (m-30) cc_final: 0.7615 (m-30)
REVERT: K   28 THR cc_start: 0.8642 (m) cc_final: 0.8270 (p)
REVERT: K   83 THR cc_start: 0.8724 (t) cc_final: 0.8144 (p)
REVERT: K   96 ASP cc_start: 0.8261 (t0) cc_final: 0.8050 (t0)
REVERT: P   34 MET cc_start: 0.8680 (mmm) cc_final: 0.8458 (mmm)
REVERT: R   17 GLU cc_start: 0.7038 (tt0) cc_final: 0.6759 (tt0)
REVERT: R   42 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7841 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 581
  average time/residue: 0.3793
  time to fit residues: 325.2767
Evaluate side-chains
  320 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 2.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 230 optimal weight:    0.9980
   chunk 206 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 139 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 213 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9990
   chunk 247 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 183 HIS
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 HIS
E 159 ASN
E 183 HIS
G  26 HIS
J   3 GLN
F 183 HIS
** I  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
R  27 GLN
R  37 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  22635  Z= 0.248
  Angle     :  0.683   8.009  30693  Z= 0.376
  Chirality :  0.044   0.165   3381
  Planarity :  0.005   0.070   3927
  Dihedral  :  5.993  62.600   3483
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  :  7.67 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.15), residues: 2760
  helix:  2.23 (0.25), residues: 378
  sheet:  0.44 (0.17), residues: 768
  loop :  0.34 (0.15), residues: 1614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 103 
 HIS   0.008   0.001   HIS I  72 
 PHE   0.021   0.002   PHE F 213 
 TYR   0.016   0.002   TYR I  94 
 ARG   0.009   0.001   ARG P  94 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  438 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 378
  time to evaluate  : 2.734 
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
   revert: symmetry clash
REVERT: B  158 ASP cc_start: 0.7880 (t0) cc_final: 0.6331 (p0)
REVERT: D    4 MET cc_start: 0.8367 (mmm) cc_final: 0.8062 (mmm)
REVERT: C   75 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8417 (mttt)
REVERT: H   93 VAL cc_start: 0.8367 (t) cc_final: 0.8115 (t)
REVERT: H  100 TYR cc_start: 0.7225 (t80) cc_final: 0.6993 (t80)
REVERT: L   17 GLU cc_start: 0.7035 (tt0) cc_final: 0.6791 (tt0)
REVERT: L   58 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6785 (mp)
REVERT: L   78 LEU cc_start: 0.6114 (tp) cc_final: 0.4441 (tt)
REVERT: L   79 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6263 (mt0)
REVERT: J    5 LEU cc_start: 0.8795 (mp) cc_final: 0.8528 (mp)
REVERT: J   96 ASP cc_start: 0.8358 (t0) cc_final: 0.8117 (t0)
REVERT: O   64 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6857 (mmmt)
REVERT: Q   42 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8099 (mp10)
REVERT: Q   53 THR cc_start: 0.7634 (m) cc_final: 0.7316 (p)
REVERT: Q   58 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6769 (mp)
REVERT: Q   78 LEU cc_start: 0.6589 (tp) cc_final: 0.4466 (tt)
REVERT: Q   79 GLN cc_start: 0.6781 (mm110) cc_final: 0.6058 (mt0)
REVERT: F  148 TYR cc_start: 0.9055 (m-80) cc_final: 0.8617 (m-80)
REVERT: N    4 MET cc_start: 0.8327 (mmm) cc_final: 0.8070 (mmm)
REVERT: N    5 THR cc_start: 0.8389 (m) cc_final: 0.8169 (p)
REVERT: R   17 GLU cc_start: 0.7013 (tt0) cc_final: 0.6755 (tt0)
REVERT: R   24 ARG cc_start: 0.7173 (mmp80) cc_final: 0.6900 (mmp80)
REVERT: R   42 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8196 (mp10)
REVERT: R   54 ARG cc_start: 0.7930 (ptm-80) cc_final: 0.7552 (ttm110)
REVERT: R   58 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6778 (mp)
REVERT: R   78 LEU cc_start: 0.6615 (tp) cc_final: 0.5146 (tt)
REVERT: R   79 GLN cc_start: 0.7082 (mm110) cc_final: 0.6645 (mt0)
  outliers start: 60
  outliers final: 38
  residues processed: 408
  average time/residue: 0.3598
  time to fit residues: 222.5699
Evaluate side-chains
  358 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 317
  time to evaluate  : 2.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  103 TRP
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue  159 ASN
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain G residue  116 LYS
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue  103 TRP
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain Q residue   10 THR
Chi-restraints excluded: chain Q residue   13 VAL
Chi-restraints excluded: chain Q residue   58 ILE
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain Q residue  105 GLU
Chi-restraints excluded: chain F residue   23 THR
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain I residue   72 HIS
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  103 TRP
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   98 THR
Chi-restraints excluded: chain R residue   10 THR
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  105 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 206 optimal weight:    4.9990
   chunk 168 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 248 optimal weight:    0.9990
   chunk 268 optimal weight:    9.9990
   chunk 221 optimal weight:    3.9990
   chunk 246 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 199 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 HIS
L  79 GLN
O   3 GLN
** I  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  72 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  22635  Z= 0.295
  Angle     :  0.625   8.639  30693  Z= 0.339
  Chirality :  0.043   0.151   3381
  Planarity :  0.005   0.068   3927
  Dihedral  :  5.438  56.451   3483
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  8.58 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.15), residues: 2760
  helix:  2.47 (0.25), residues: 378
  sheet:  0.41 (0.18), residues: 738
  loop :  0.09 (0.15), residues: 1644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP J 103 
 HIS   0.007   0.001   HIS I  72 
 PHE   0.021   0.002   PHE F 213 
 TYR   0.016   0.001   TYR P  32 
 ARG   0.006   0.001   ARG Q  54 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 326
  time to evaluate  : 2.342 
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: B  158 ASP cc_start: 0.7969 (t0) cc_final: 0.6651 (p0)
REVERT: C  102 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.6542 (p90)
REVERT: H   64 LYS cc_start: 0.7173 (mtmm) cc_final: 0.6963 (mmmt)
REVERT: H   93 VAL cc_start: 0.8386 (t) cc_final: 0.8124 (t)
REVERT: H  100 TYR cc_start: 0.7323 (t80) cc_final: 0.7068 (t80)
REVERT: L   54 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.6800 (mtp-110)
REVERT: L   58 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6572 (mp)
REVERT: O   64 LYS cc_start: 0.7413 (mtmm) cc_final: 0.6962 (mmmt)
REVERT: Q   42 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8010 (mp10)
REVERT: Q   58 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6836 (mp)
REVERT: Q   71 PHE cc_start: 0.7988 (m-80) cc_final: 0.7718 (m-80)
REVERT: F   56 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8704 (m)
REVERT: N    4 MET cc_start: 0.8469 (mmm) cc_final: 0.8238 (mmm)
REVERT: N  105 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4229 (mm-30)
REVERT: K  102 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7139 (p90)
REVERT: P   93 VAL cc_start: 0.8582 (t) cc_final: 0.8316 (t)
REVERT: R   42 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8118 (mp10)
  outliers start: 78
  outliers final: 51
  residues processed: 362
  average time/residue: 0.3570
  time to fit residues: 196.4708
Evaluate side-chains
  337 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 280
  time to evaluate  : 2.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  103 TRP
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   61 ASP
Chi-restraints excluded: chain J residue  101 GLU
Chi-restraints excluded: chain J residue  103 TRP
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain Q residue   46 LEU
Chi-restraints excluded: chain Q residue   58 ILE
Chi-restraints excluded: chain Q residue   85 VAL
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain Q residue  105 GLU
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain I residue   15 THR
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain N residue    1 ASP
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  105 GLU
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain K residue  103 TRP
Chi-restraints excluded: chain P residue    5 VAL
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   73 ASN
Chi-restraints excluded: chain R residue   10 THR
Chi-restraints excluded: chain R residue  104 VAL
Chi-restraints excluded: chain R residue  105 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 245 optimal weight:    4.9990
   chunk 186 optimal weight:    5.9990
   chunk 128 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 166 optimal weight:    8.9990
   chunk 249 optimal weight:    3.9990
   chunk 263 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 236 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 231 ASN
D  79 GLN
E 159 ASN
M  32 HIS
M  79 GLN
O   3 GLN
** I  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  32 HIS
N  79 GLN
** P   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.123  22635  Z= 0.623
  Angle     :  0.787  11.020  30693  Z= 0.417
  Chirality :  0.049   0.193   3381
  Planarity :  0.006   0.064   3927
  Dihedral  :  6.007  56.289   3483
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  :  9.79 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.15), residues: 2760
  helix:  1.71 (0.26), residues: 372
  sheet:  0.09 (0.18), residues: 729
  loop : -0.34 (0.14), residues: 1659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP C 103 
 HIS   0.011   0.002   HIS A 184 
 PHE   0.023   0.003   PHE A 213 
 TYR   0.026   0.003   TYR B  22 
 ARG   0.006   0.001   ARG Q  24 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 89
    poor density    : 294
  time to evaluate  : 2.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6226 (p90)
REVERT: H   72 ASP cc_start: 0.7300 (t0) cc_final: 0.6185 (t70)
REVERT: L   17 GLU cc_start: 0.6507 (tt0) cc_final: 0.6301 (tt0)
REVERT: L   42 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8030 (mm-40)
REVERT: L   58 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7224 (mp)
REVERT: L  103 LYS cc_start: 0.8758 (tppt) cc_final: 0.8472 (tppt)
REVERT: O   64 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7040 (mmmt)
REVERT: O  102 TYR cc_start: 0.7652 (m-80) cc_final: 0.7322 (m-80)
REVERT: Q   54 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.7112 (mtp-110)
REVERT: Q   58 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.6914 (mp)
REVERT: Q   71 PHE cc_start: 0.7921 (m-80) cc_final: 0.7653 (m-80)
REVERT: Q   79 GLN cc_start: 0.7279 (mm-40) cc_final: 0.6983 (mt0)
REVERT: I   59 MET cc_start: 0.8665 (ttm) cc_final: 0.8403 (tpp)
REVERT: I  158 ASP cc_start: 0.7981 (t0) cc_final: 0.6459 (p0)
REVERT: N  105 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.4607 (mm-30)
REVERT: P   34 MET cc_start: 0.8781 (mmm) cc_final: 0.7730 (mmp)
REVERT: R   79 GLN cc_start: 0.8211 (mt0) cc_final: 0.8001 (mt0)
  outliers start: 89
  outliers final: 64
  residues processed: 345
  average time/residue: 0.3432
  time to fit residues: 180.1068
Evaluate side-chains
  325 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 257
  time to evaluate  : 2.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   98 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  116 LYS
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   98 THR
Chi-restraints excluded: chain Q residue    5 THR
Chi-restraints excluded: chain Q residue   10 THR
Chi-restraints excluded: chain Q residue   58 ILE
Chi-restraints excluded: chain Q residue   75 ILE
Chi-restraints excluded: chain Q residue   85 VAL
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain I residue   40 SER
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  105 GLU
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   73 ASN
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   10 THR
Chi-restraints excluded: chain R residue   75 ILE
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 219 optimal weight:    3.9990
   chunk 149 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 196 optimal weight:    0.9980
   chunk 108 optimal weight:    0.7980
   chunk 225 optimal weight:    0.7980
   chunk 182 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   chunk 236 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
E 159 ASN
** O   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  30 GLN
** P   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  22635  Z= 0.208
  Angle     :  0.591  10.850  30693  Z= 0.312
  Chirality :  0.042   0.150   3381
  Planarity :  0.005   0.078   3927
  Dihedral  :  5.346  53.052   3483
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.33 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.15), residues: 2760
  helix:  2.35 (0.26), residues: 375
  sheet:  0.25 (0.18), residues: 720
  loop : -0.35 (0.14), residues: 1665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  35 
 HIS   0.004   0.001   HIS E  18 
 PHE   0.013   0.001   PHE F 213 
 TYR   0.018   0.001   TYR P  32 
 ARG   0.003   0.000   ARG L  61 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 306
  time to evaluate  : 2.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    4 MET cc_start: 0.8651 (mmm) cc_final: 0.8371 (ttm)
REVERT: C  102 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.6658 (p90)
REVERT: H   72 ASP cc_start: 0.7251 (t0) cc_final: 0.7008 (t70)
REVERT: L   24 ARG cc_start: 0.7182 (mmp80) cc_final: 0.6847 (mmp80)
REVERT: L   42 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7846 (mm-40)
REVERT: L   54 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7310 (mtp-110)
REVERT: L   58 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7135 (mp)
REVERT: J  102 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7207 (p90)
REVERT: O   64 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7133 (mmmt)
REVERT: O  102 TYR cc_start: 0.7507 (m-80) cc_final: 0.7249 (m-80)
REVERT: Q   42 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7762 (mp10)
REVERT: Q   58 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6954 (mp)
REVERT: Q   71 PHE cc_start: 0.7907 (m-80) cc_final: 0.7559 (m-80)
REVERT: R   54 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.7673 (ttp-170)
REVERT: R   79 GLN cc_start: 0.8194 (mt0) cc_final: 0.7933 (mt0)
  outliers start: 61
  outliers final: 37
  residues processed: 339
  average time/residue: 0.3529
  time to fit residues: 183.5857
Evaluate side-chains
  328 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 286
  time to evaluate  : 2.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  103 TRP
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue   58 ILE
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain N residue    1 ASP
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   73 ASN
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 237 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 154 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 264 optimal weight:    5.9990
   chunk 219 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
E 159 ASN
E 226 GLN
** O   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
** P   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.096  22635  Z= 0.511
  Angle     :  0.699  10.818  30693  Z= 0.367
  Chirality :  0.045   0.139   3381
  Planarity :  0.005   0.074   3927
  Dihedral  :  5.580  51.922   3483
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 10.88 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.15), residues: 2760
  helix:  1.95 (0.26), residues: 372
  sheet:  0.06 (0.18), residues: 720
  loop : -0.52 (0.14), residues: 1668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP K 103 
 HIS   0.009   0.002   HIS A 184 
 PHE   0.020   0.002   PHE F 213 
 TYR   0.018   0.002   TYR Q  49 
 ARG   0.007   0.001   ARG Q  54 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 82
    poor density    : 282
  time to evaluate  : 2.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 ASP cc_start: 0.8136 (t0) cc_final: 0.6678 (p0)
REVERT: C  102 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6274 (p90)
REVERT: H   34 MET cc_start: 0.8728 (mmm) cc_final: 0.8456 (mmm)
REVERT: H   72 ASP cc_start: 0.7327 (t0) cc_final: 0.7072 (t0)
REVERT: L   42 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7720 (mp-120)
REVERT: L   54 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7272 (mtp-110)
REVERT: L   61 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7216 (ttp-110)
REVERT: G  158 ASP cc_start: 0.8180 (t0) cc_final: 0.6549 (p0)
REVERT: M    4 MET cc_start: 0.8908 (mmm) cc_final: 0.8420 (ttm)
REVERT: O   64 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7029 (mmmt)
REVERT: O   72 ASP cc_start: 0.7703 (t0) cc_final: 0.7309 (t0)
REVERT: O  102 TYR cc_start: 0.7616 (m-80) cc_final: 0.7367 (m-80)
REVERT: Q   42 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7696 (mp10)
REVERT: Q   54 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7202 (mtp-110)
REVERT: K   82 MET cc_start: 0.8290 (tpp) cc_final: 0.7715 (mtp)
REVERT: P   34 MET cc_start: 0.9084 (mmm) cc_final: 0.8732 (mmp)
REVERT: P   58 TYR cc_start: 0.7291 (m-80) cc_final: 0.7041 (m-80)
REVERT: P   73 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7362 (p0)
REVERT: R    4 MET cc_start: 0.7359 (tpt) cc_final: 0.7133 (tpt)
REVERT: R   54 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7667 (ttp-170)
REVERT: R   61 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7589 (mtp180)
REVERT: R   79 GLN cc_start: 0.8292 (mt0) cc_final: 0.7949 (mt0)
  outliers start: 82
  outliers final: 68
  residues processed: 331
  average time/residue: 0.3471
  time to fit residues: 175.2445
Evaluate side-chains
  336 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 265
  time to evaluate  : 2.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   70 ILE
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue  116 LYS
Chi-restraints excluded: chain G residue  148 CYS
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   70 ASP
Chi-restraints excluded: chain M residue   74 THR
Chi-restraints excluded: chain M residue   90 HIS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   82 LEU
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue    5 THR
Chi-restraints excluded: chain Q residue   10 THR
Chi-restraints excluded: chain Q residue   75 ILE
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   22 CYS
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   73 ASN
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain P residue   98 THR
Chi-restraints excluded: chain R residue   75 ILE
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 254 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 150 optimal weight:    8.9990
   chunk 192 optimal weight:    0.7980
   chunk 149 optimal weight:    5.9990
   chunk 222 optimal weight:    0.8980
   chunk 147 optimal weight:    5.9990
   chunk 263 optimal weight:    9.9990
   chunk 164 optimal weight:    6.9990
   chunk 160 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    2.7384

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

Flipped N/Q/H residues before XYZ refinement:
** O   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 226 GLN
K   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  22635  Z= 0.378
  Angle     :  0.642  10.890  30693  Z= 0.337
  Chirality :  0.044   0.149   3381
  Planarity :  0.005   0.078   3927
  Dihedral  :  5.438  49.677   3483
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.71 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.15), residues: 2760
  helix:  2.04 (0.26), residues: 372
  sheet:  0.01 (0.18), residues: 720
  loop : -0.59 (0.14), residues: 1668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP K 103 
 HIS   0.006   0.001   HIS A 184 
 PHE   0.018   0.002   PHE L  71 
 TYR   0.019   0.002   TYR H  32 
 ARG   0.008   0.001   ARG L  45 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 287
  time to evaluate  : 2.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8213 (t0)
REVERT: B  158 ASP cc_start: 0.8151 (t0) cc_final: 0.6770 (p0)
REVERT: C  102 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6365 (p90)
REVERT: H   64 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7106 (mmtm)
REVERT: H   72 ASP cc_start: 0.7263 (t0) cc_final: 0.7038 (t70)
REVERT: L   42 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7658 (mp-120)
REVERT: L   54 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7244 (mtp-110)
REVERT: G  158 ASP cc_start: 0.8204 (t0) cc_final: 0.6651 (p0)
REVERT: M    4 MET cc_start: 0.8940 (mmm) cc_final: 0.8533 (ttm)
REVERT: O   64 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6988 (mttp)
REVERT: O   72 ASP cc_start: 0.7726 (t0) cc_final: 0.7298 (t70)
REVERT: O  102 TYR cc_start: 0.7579 (m-80) cc_final: 0.7351 (m-80)
REVERT: Q   42 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7727 (mp10)
REVERT: Q   54 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7338 (ttm110)
REVERT: Q   61 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.6805 (mtp180)
REVERT: Q   79 GLN cc_start: 0.8127 (mt0) cc_final: 0.7744 (mt0)
REVERT: I   19 ASP cc_start: 0.6973 (p0) cc_final: 0.6749 (p0)
REVERT: I  158 ASP cc_start: 0.7987 (t0) cc_final: 0.6385 (p0)
REVERT: K   82 MET cc_start: 0.8224 (tpp) cc_final: 0.7686 (mtp)
REVERT: P   34 MET cc_start: 0.9093 (mmm) cc_final: 0.8664 (mmp)
REVERT: P   58 TYR cc_start: 0.7280 (m-80) cc_final: 0.7007 (m-80)
REVERT: P   72 ASP cc_start: 0.7412 (t0) cc_final: 0.7128 (t70)
REVERT: R   42 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7707 (mp10)
  outliers start: 69
  outliers final: 57
  residues processed: 329
  average time/residue: 0.3510
  time to fit residues: 177.0965
Evaluate side-chains
  334 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 274
  time to evaluate  : 2.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue  148 CYS
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   74 THR
Chi-restraints excluded: chain M residue   90 HIS
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   22 CYS
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain R residue   10 THR
Chi-restraints excluded: chain R residue   75 ILE
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 162 optimal weight:   20.0000
   chunk 105 optimal weight:    3.9990
   chunk 157 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 167 optimal weight:    9.9990
   chunk 179 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 206 optimal weight:    1.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
M  27 GLN
O  82AASN
K   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  22635  Z= 0.359
  Angle     :  0.643  10.989  30693  Z= 0.334
  Chirality :  0.043   0.147   3381
  Planarity :  0.005   0.075   3927
  Dihedral  :  5.365  47.363   3483
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.08 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.15), residues: 2760
  helix:  1.80 (0.26), residues: 390
  sheet: -0.03 (0.19), residues: 720
  loop : -0.68 (0.14), residues: 1650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K 103 
 HIS   0.005   0.001   HIS A 184 
 PHE   0.019   0.002   PHE L  71 
 TYR   0.019   0.002   TYR H  32 
 ARG   0.006   0.001   ARG L  45 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 286
  time to evaluate  : 2.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8203 (t0)
REVERT: B   19 ASP cc_start: 0.6860 (p0) cc_final: 0.6158 (p0)
REVERT: B  158 ASP cc_start: 0.8146 (t0) cc_final: 0.6822 (p0)
REVERT: C  102 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.6482 (p90)
REVERT: H   72 ASP cc_start: 0.7290 (t0) cc_final: 0.6970 (t70)
REVERT: L   42 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7645 (mp-120)
REVERT: L   54 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7223 (mtp-110)
REVERT: L  103 LYS cc_start: 0.8713 (tppt) cc_final: 0.8476 (tppt)
REVERT: G  158 ASP cc_start: 0.8205 (t0) cc_final: 0.6756 (p0)
REVERT: O    6 GLU cc_start: 0.5673 (mt-10) cc_final: 0.4983 (pt0)
REVERT: O   64 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7010 (mttp)
REVERT: O   72 ASP cc_start: 0.7557 (t0) cc_final: 0.7145 (t70)
REVERT: Q   42 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7703 (mp10)
REVERT: Q   54 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7531 (ttp-170)
REVERT: Q   61 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7205 (mtp180)
REVERT: Q   79 GLN cc_start: 0.8142 (mt0) cc_final: 0.7766 (mt0)
REVERT: I   19 ASP cc_start: 0.6979 (p0) cc_final: 0.6730 (p0)
REVERT: I  158 ASP cc_start: 0.8028 (t0) cc_final: 0.6482 (p0)
REVERT: K   82 MET cc_start: 0.8265 (tpp) cc_final: 0.7765 (mtp)
REVERT: P   58 TYR cc_start: 0.7261 (m-80) cc_final: 0.6861 (m-80)
REVERT: P   72 ASP cc_start: 0.7408 (t0) cc_final: 0.7062 (t70)
REVERT: R   42 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7755 (mp10)
  outliers start: 71
  outliers final: 65
  residues processed: 332
  average time/residue: 0.3474
  time to fit residues: 178.9785
Evaluate side-chains
  341 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 273
  time to evaluate  : 2.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 ILE
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   70 ILE
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue  148 CYS
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   70 ASP
Chi-restraints excluded: chain M residue   74 THR
Chi-restraints excluded: chain M residue   90 HIS
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue   75 ILE
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   37 GLN
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   22 CYS
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   75 ILE
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 239 optimal weight:    0.0070
   chunk 252 optimal weight:   10.0000
   chunk 229 optimal weight:    7.9990
   chunk 245 optimal weight:    3.9990
   chunk 147 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 192 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 221 optimal weight:    1.9990
   chunk 231 optimal weight:    6.9990
   chunk 244 optimal weight:    0.5980
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
M  27 GLN
O   3 GLN
K   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  22635  Z= 0.188
  Angle     :  0.586  10.682  30693  Z= 0.305
  Chirality :  0.041   0.142   3381
  Planarity :  0.004   0.077   3927
  Dihedral  :  5.006  43.363   3483
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.62 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.15), residues: 2760
  helix:  2.47 (0.26), residues: 372
  sheet:  0.16 (0.19), residues: 699
  loop : -0.56 (0.14), residues: 1689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  36 
 HIS   0.003   0.001   HIS G 142 
 PHE   0.014   0.001   PHE L  71 
 TYR   0.017   0.001   TYR E 105 
 ARG   0.006   0.000   ARG L  45 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 299
  time to evaluate  : 2.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8186 (t0)
REVERT: B   19 ASP cc_start: 0.6747 (p0) cc_final: 0.6087 (p0)
REVERT: B  158 ASP cc_start: 0.8122 (t0) cc_final: 0.6839 (p0)
REVERT: C  102 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6814 (p90)
REVERT: H   34 MET cc_start: 0.8550 (mmm) cc_final: 0.8226 (mmp)
REVERT: H   72 ASP cc_start: 0.7240 (t0) cc_final: 0.6925 (t70)
REVERT: L   42 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7697 (mp-120)
REVERT: L   54 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7342 (mtp-110)
REVERT: L  103 LYS cc_start: 0.8654 (tppt) cc_final: 0.8281 (tppt)
REVERT: G  158 ASP cc_start: 0.8157 (t0) cc_final: 0.6728 (p0)
REVERT: M  103 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8586 (ttpp)
REVERT: J  102 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7190 (p90)
REVERT: O   64 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6899 (mttp)
REVERT: O   72 ASP cc_start: 0.7455 (t0) cc_final: 0.7049 (t70)
REVERT: Q   54 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7543 (ttp80)
REVERT: Q   61 ARG cc_start: 0.7429 (mtp-110) cc_final: 0.7107 (mtp180)
REVERT: Q   79 GLN cc_start: 0.8268 (mt0) cc_final: 0.7926 (mt0)
REVERT: I   19 ASP cc_start: 0.6918 (p0) cc_final: 0.6683 (p0)
REVERT: I  158 ASP cc_start: 0.7968 (t0) cc_final: 0.6495 (p0)
REVERT: K   82 MET cc_start: 0.8177 (tpp) cc_final: 0.7716 (mtp)
REVERT: P   72 ASP cc_start: 0.7319 (t0) cc_final: 0.6969 (t70)
REVERT: R    4 MET cc_start: 0.7240 (tpt) cc_final: 0.6758 (tpt)
  outliers start: 60
  outliers final: 49
  residues processed: 331
  average time/residue: 0.3435
  time to fit residues: 174.7923
Evaluate side-chains
  325 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 272
  time to evaluate  : 2.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue  148 CYS
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   70 ASP
Chi-restraints excluded: chain M residue   74 THR
Chi-restraints excluded: chain M residue   90 HIS
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   56 VAL
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain I residue   15 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue   85 GLU
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   22 CYS
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain P residue   92 CYS
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 161 optimal weight:    8.9990
   chunk 259 optimal weight:   10.0000
   chunk 158 optimal weight:    0.9980
   chunk 123 optimal weight:    4.9990
   chunk 180 optimal weight:    9.9990
   chunk 271 optimal weight:    7.9990
   chunk 250 optimal weight:    4.9990
   chunk 216 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 167 optimal weight:   10.0000
   chunk 132 optimal weight:    4.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
E 231 ASN
M  27 GLN
** O   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  82AASN
Q  92 ASN
R  79 GLN
R  92 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.112  22635  Z= 0.634
  Angle     :  0.775  11.240  30693  Z= 0.405
  Chirality :  0.048   0.228   3381
  Planarity :  0.006   0.074   3927
  Dihedral  :  5.667  44.405   3483
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.04 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.42 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.15), residues: 2760
  helix:  1.48 (0.26), residues: 390
  sheet: -0.10 (0.19), residues: 711
  loop : -0.93 (0.14), residues: 1659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP C 103 
 HIS   0.009   0.001   HIS A 184 
 PHE   0.027   0.003   PHE L  71 
 TYR   0.021   0.002   TYR P  32 
 ARG   0.006   0.001   ARG R  30 

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

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

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5520 Ramachandran restraints generated.
    2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 274
  time to evaluate  : 2.764 
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: B   19 ASP cc_start: 0.6918 (p0) cc_final: 0.6571 (p0)
REVERT: D  105 GLU cc_start: 0.5210 (tm-30) cc_final: 0.4764 (tm-30)
REVERT: C    5 LEU cc_start: 0.8849 (tt) cc_final: 0.8583 (mt)
REVERT: C  102 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.6329 (p90)
REVERT: H   72 ASP cc_start: 0.7271 (t0) cc_final: 0.6952 (t70)
REVERT: L  103 LYS cc_start: 0.8713 (tppt) cc_final: 0.8338 (tppt)
REVERT: M  103 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8732 (ttpp)
REVERT: O   64 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7120 (mttt)
REVERT: O   72 ASP cc_start: 0.7522 (t0) cc_final: 0.7114 (t70)
REVERT: Q   61 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7255 (mtp180)
REVERT: Q   79 GLN cc_start: 0.8158 (mt0) cc_final: 0.7760 (mt0)
REVERT: I   19 ASP cc_start: 0.7044 (p0) cc_final: 0.6686 (p0)
REVERT: K   82 MET cc_start: 0.8354 (tpp) cc_final: 0.7867 (mtp)
REVERT: P    6 GLU cc_start: 0.5356 (mt-10) cc_final: 0.4599 (pt0)
REVERT: P   72 ASP cc_start: 0.7455 (t0) cc_final: 0.7054 (t70)
REVERT: R    4 MET cc_start: 0.7164 (tpt) cc_final: 0.6644 (tpt)
  outliers start: 62
  outliers final: 54
  residues processed: 315
  average time/residue: 0.3470
  time to fit residues: 168.8755
Evaluate side-chains
  311 residues out of total 2403 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 255
  time to evaluate  : 2.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   84 TRP
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain E residue   11 ASP
Chi-restraints excluded: chain E residue   70 ILE
Chi-restraints excluded: chain E residue   84 TRP
Chi-restraints excluded: chain E residue  277 CYS
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue  148 CYS
Chi-restraints excluded: chain M residue    5 THR
Chi-restraints excluded: chain M residue   15 VAL
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   70 ASP
Chi-restraints excluded: chain M residue   74 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   50 MET
Chi-restraints excluded: chain J residue   83 THR
Chi-restraints excluded: chain J residue  102 PHE
Chi-restraints excluded: chain O residue   24 VAL
Chi-restraints excluded: chain O residue   61 ASP
Chi-restraints excluded: chain O residue   64 LYS
Chi-restraints excluded: chain Q residue   75 ILE
Chi-restraints excluded: chain Q residue  104 VAL
Chi-restraints excluded: chain F residue   84 TRP
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   20 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue   50 MET
Chi-restraints excluded: chain K residue  102 PHE
Chi-restraints excluded: chain P residue   22 CYS
Chi-restraints excluded: chain P residue   24 VAL
Chi-restraints excluded: chain P residue   35 ASN
Chi-restraints excluded: chain P residue   61 ASP
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 172 optimal weight:    6.9990
   chunk 230 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 199 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 216 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 222 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN
** O   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  82AASN
R  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.089219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.063866 restraints weight = 54587.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.71
r_work: 0.2910 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  22635  Z= 0.222
  Angle     :  0.617  10.862  30693  Z= 0.320
  Chirality :  0.042   0.186   3381
  Planarity :  0.005   0.078   3927
  Dihedral  :  5.174  41.588   3483
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.33 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.71 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.15), residues: 2760
  helix:  1.94 (0.26), residues: 390
  sheet:  0.13 (0.19), residues: 690
  loop : -0.81 (0.14), residues: 1680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R  35 
 HIS   0.004   0.001   HIS E  18 
 PHE   0.017   0.001   PHE L  71 
 TYR   0.018   0.001   TYR E 105 
 ARG   0.007   0.001   ARG R  30 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4927.95 seconds
wall clock time: 90 minutes 40.63 seconds (5440.63 seconds total)