Starting phenix.real_space_refine
on Mon Mar 18 08:54:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dz4_27788/03_2024/8dz4_27788.pdb"
  }
  resolution = 3.2
  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=  -0.011 sd=   0.156
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      88      5.16       5
     C   12766      2.51       5
     N    3560      2.21       5
     O    3876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "I ASP   17": "OD1" <-> "OD2"
    Residue "L GLU   17": "OE1" <-> "OE2"
    Residue "L GLU   81": "OE1" <-> "OE2"
    Residue "H GLU   46": "OE1" <-> "OE2"
    Residue "H ASP   72": "OD1" <-> "OD2"
    Residue "H GLU   85": "OE1" <-> "OE2"
    Residue "H ASP   86": "OD1" <-> "OD2"
    Residue "H ASP   95": "OD1" <-> "OD2"
    Residue "H TYR   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   46": "OE1" <-> "OE2"
    Residue "A TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   46": "OE1" <-> "OE2"
    Residue "C ASP   53": "OD1" <-> "OD2"
    Residue "C TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   64": "OE1" <-> "OE2"
    Residue "C ASP   72": "OD1" <-> "OD2"
    Residue "C TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   86": "OD1" <-> "OD2"
    Residue "C TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP   82": "OD1" <-> "OD2"
    Residue "F PHE   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   61": "OD1" <-> "OD2"
    Residue "E GLU   64": "OE1" <-> "OE2"
    Residue "E ASP   72": "OD1" <-> "OD2"
    Residue "E GLU   85": "OE1" <-> "OE2"
    Residue "E ASP   86": "OD1" <-> "OD2"
    Residue "E ASP  100": "OD1" <-> "OD2"
    Residue "E TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   17": "OE1" <-> "OE2"
    Residue "N TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   81": "OE1" <-> "OE2"
    Residue "N ASP   82": "OD1" <-> "OD2"
    Residue "N ASP  105": "OD1" <-> "OD2"
    Residue "N PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP   53": "OD1" <-> "OD2"
    Residue "M ASP   61": "OD1" <-> "OD2"
    Residue "M GLU   64": "OE1" <-> "OE2"
    Residue "M TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP  100": "OD1" <-> "OD2"
    Residue "M TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P GLU   81": "OE1" <-> "OE2"
    Residue "P ASP   82": "OD1" <-> "OD2"
    Residue "P PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ASP   53": "OD1" <-> "OD2"
    Residue "O TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ASP   72": "OD1" <-> "OD2"
    Residue "O ASP   95": "OD1" <-> "OD2"
    Residue "O TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU   70": "OE1" <-> "OE2"
    Residue "R ASP   82": "OD1" <-> "OD2"
    Residue "R ASP  105": "OD1" <-> "OD2"
    Residue "R PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ASP   61": "OD1" <-> "OD2"
    Residue "Q ASP   72": "OD1" <-> "OD2"
    Residue "Q TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q GLU   85": "OE1" <-> "OE2"
    Residue "Q ASP   86": "OD1" <-> "OD2"
    Residue "Q ASP  100": "OD1" <-> "OD2"
    Residue "Q TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T GLU   17": "OE1" <-> "OE2"
    Residue "T TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T PHE   96": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ASP  105": "OD1" <-> "OD2"
    Residue "S GLU   46": "OE1" <-> "OE2"
    Residue "S ASP   53": "OD1" <-> "OD2"
    Residue "S TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ASP   61": "OD1" <-> "OD2"
    Residue "S GLU   64": "OE1" <-> "OE2"
    Residue "S TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ASP  100": "OD1" <-> "OD2"
    Residue "S TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU   17": "OE1" <-> "OE2"
    Residue "V GLU   70": "OE1" <-> "OE2"
    Residue "V ASP  105": "OD1" <-> "OD2"
    Residue "U GLU    6": "OE1" <-> "OE2"
    Residue "U GLU   46": "OE1" <-> "OE2"
    Residue "U ASP   61": "OD1" <-> "OD2"
    Residue "U TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP   95": "OD1" <-> "OD2"
    Residue "U TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X GLU   17": "OE1" <-> "OE2"
    Residue "X GLU   70": "OE1" <-> "OE2"
    Residue "X GLU   81": "OE1" <-> "OE2"
    Residue "W ASP   61": "OD1" <-> "OD2"
    Residue "W ASP   72": "OD1" <-> "OD2"
    Residue "W GLU   85": "OE1" <-> "OE2"
    Residue "W TYR   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU   46": "OE1" <-> "OE2"
    Residue "Y TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU   85": "OE1" <-> "OE2"
    Residue "Y ASP   86": "OD1" <-> "OD2"
    Residue "Y ASP   95": "OD1" <-> "OD2"
    Residue "Y PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y ASP  100": "OD1" <-> "OD2"
    Residue "Y TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 20290
  Number of models: 1
  Model: ""
    Number of chains: 23
    Chain: "I"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 622
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 22, 'TRANS': 65}
    Chain: "L"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "D"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "C"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "F"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "E"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "N"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "M"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "P"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "O"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "Q"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "T"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "S"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "V"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "U"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "X"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "W"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "Z"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "Y"
      Number of atoms: 986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 986
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
  Time building chain proxies: 10.53, per 1000 atoms: 0.52
  Number of scatterers: 20290
  At special positions: 0
  Unit cell: (147.2, 113.85, 158.7, 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      88     16.00
     O    3876      8.00
     N    3560      7.00
     C   12766      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=22, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  23 " - pdb=" SG  CYS P  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  22 " - pdb=" SG  CYS O  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  23 " - pdb=" SG  CYS R  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  22 " - pdb=" SG  CYS Q  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T  23 " - pdb=" SG  CYS T  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS V  23 " - pdb=" SG  CYS V  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS U  22 " - pdb=" SG  CYS U  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  23 " - pdb=" SG  CYS X  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS W  22 " - pdb=" SG  CYS W  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Z  23 " - pdb=" SG  CYS Z  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Y  22 " - pdb=" SG  CYS Y  92 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.45
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4708

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 66 sheets defined
      6.6% alpha, 48.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.88
  Creating SS restraints...
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.817A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.532A  pdb=" N   THR H  87 " --> pdb=" O   VAL H  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.501A  pdb=" N   ASN A  31 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 64
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 3.834A  pdb=" N   THR A  87 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.792A  pdb=" N   PHE D  83 " --> pdb=" O   SER D  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 83 through 87
      removed outlier: 3.909A  pdb=" N   THR C  87 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 83 through 87
    Processing helix  chain 'N' and resid 79 through 83
      removed outlier: 3.509A  pdb=" N   ASP N  82 " --> pdb=" O   GLN N  79 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE N  83 " --> pdb=" O   SER N  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 79 through 83'
    Processing helix  chain 'M' and resid 28 through 32
    Processing helix  chain 'M' and resid 83 through 87
    Processing helix  chain 'O' and resid 28 through 32
    Processing helix  chain 'O' and resid 61 through 64
    Processing helix  chain 'O' and resid 83 through 87
      removed outlier: 3.602A  pdb=" N   THR O  87 " --> pdb=" O   VAL O  84 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 28 through 32
      removed outlier: 3.518A  pdb=" N   ASN Q  31 " --> pdb=" O   THR Q  28 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 61 through 64
    Processing helix  chain 'Q' and resid 83 through 87
      removed outlier: 3.753A  pdb=" N   THR Q  87 " --> pdb=" O   VAL Q  84 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 79 through 83
      removed outlier: 3.526A  pdb=" N   ASP T  82 " --> pdb=" O   GLN T  79 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE T  83 " --> pdb=" O   SER T  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'T' and resid 79 through 83'
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.554A  pdb=" N   ASN S  31 " --> pdb=" O   THR S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 61 through 64
    Processing helix  chain 'S' and resid 83 through 87
    Processing helix  chain 'V' and resid 79 through 83
      removed outlier: 3.816A  pdb=" N   PHE V  83 " --> pdb=" O   SER V  80 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 28 through 32
      removed outlier: 3.508A  pdb=" N   PHE U  32 " --> pdb=" O   PHE U  29 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 61 through 64
    Processing helix  chain 'U' and resid 83 through 87
      removed outlier: 3.520A  pdb=" N   THR U  87 " --> pdb=" O   VAL U  84 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 28 through 32
      removed outlier: 3.531A  pdb=" N   PHE W  32 " --> pdb=" O   PHE W  29 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 61 through 64
    Processing helix  chain 'W' and resid 83 through 87
      removed outlier: 3.643A  pdb=" N   THR W  87 " --> pdb=" O   VAL W  84 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 79 through 83
    Processing helix  chain 'Y' and resid 28 through 32
      removed outlier: 3.516A  pdb=" N   PHE Y  32 " --> pdb=" O   PHE Y  29 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 83 through 87
      removed outlier: 3.813A  pdb=" N   THR Y  87 " --> pdb=" O   VAL Y  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.575A  pdb=" N   SER L   7 " --> pdb=" O   SER L  22 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.164A  pdb=" N   VAL L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.164A  pdb=" N   VAL L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 7.078A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.011A  pdb=" N   TYR H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.500A  pdb=" N   SER B  22 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.032A  pdb=" N   VAL B  11 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B  48 " --> pdb=" O   TRP B  35 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLN B  37 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   LEU B  46 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.032A  pdb=" N   VAL B  11 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.585A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.557A  pdb=" N   VAL A 109 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA A  88 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA A  93 " --> pdb=" O   HIS A  35 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   MET A  34 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   VAL A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.557A  pdb=" N   VAL A 109 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA A  88 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   TYR A 102 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.507A  pdb=" N   SER D   7 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.187A  pdb=" N   VAL D  11 " --> pdb=" O   ASP D 105 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE D  48 " --> pdb=" O   TRP D  35 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLN D  37 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   LEU D  46 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.187A  pdb=" N   VAL D  11 " --> pdb=" O   ASP D 105 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   THR D  97 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.596A  pdb=" N   MET C  77 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.531A  pdb=" N   GLY C  10 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.531A  pdb=" N   GLY C  10 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR C 102 " --> pdb=" O   ARG C  94 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.533A  pdb=" N   SER F   7 " --> pdb=" O   SER F  22 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER F  22 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU F  70 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.320A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12
    Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.336A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   MET E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   VAL E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.336A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 110 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR E 102 " --> pdb=" O   ARG E  94 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.620A  pdb=" N   SER N  22 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.398A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.521A  pdb=" N   THR N  97 " --> pdb=" O   GLN N  90 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.874A  pdb=" N   MET M  34 " --> pdb=" O   VAL M  50 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   VAL M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12
      removed outlier: 3.920A  pdb=" N   TYR M 102 " --> pdb=" O   ARG M  94 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'P' and resid 4 through 7
      removed outlier: 3.613A  pdb=" N   SER P  22 " --> pdb=" O   SER P   7 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU P  70 " --> pdb=" O   SER P  67 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER P  67 " --> pdb=" O   GLU P  70 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 12
      removed outlier: 3.692A  pdb=" N   ILE P  48 " --> pdb=" O   TRP P  35 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLN P  37 " --> pdb=" O   LEU P  46 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   LEU P  46 " --> pdb=" O   GLN P  37 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 12
      removed outlier: 3.504A  pdb=" N   THR P  97 " --> pdb=" O   GLN P  90 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'O' and resid 3 through 7
      removed outlier: 3.622A  pdb=" N   MET O  77 " --> pdb=" O   ASP O  72 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12
      removed outlier: 6.926A  pdb=" N   MET O  34 " --> pdb=" O   VAL O  50 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   VAL O  50 " --> pdb=" O   MET O  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TRP O  36 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'O' and resid 10 through 12
      removed outlier: 3.782A  pdb=" N   TYR O 102 " --> pdb=" O   ARG O  94 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'R' and resid 4 through 7
      removed outlier: 3.613A  pdb=" N   SER R  22 " --> pdb=" O   SER R   7 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU R  70 " --> pdb=" O   SER R  67 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'R' and resid 10 through 13
      removed outlier: 6.598A  pdb=" N   VAL R  11 " --> pdb=" O   ASP R 105 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LEU R  33 " --> pdb=" O   TYR R  49 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   TYR R  49 " --> pdb=" O   LEU R  33 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TRP R  35 " --> pdb=" O   LEU R  47 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'R' and resid 10 through 13
      removed outlier: 6.598A  pdb=" N   VAL R  11 " --> pdb=" O   ASP R 105 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR R  97 " --> pdb=" O   GLN R  90 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 7
      removed outlier: 3.568A  pdb=" N   MET Q  77 " --> pdb=" O   ASP Q  72 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12
      removed outlier: 6.407A  pdb=" N   GLY Q  10 " --> pdb=" O   THR Q 110 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   MET Q  34 " --> pdb=" O   VAL Q  50 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   VAL Q  50 " --> pdb=" O   MET Q  34 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   TRP Q  36 " --> pdb=" O   VAL Q  48 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 12
      removed outlier: 6.407A  pdb=" N   GLY Q  10 " --> pdb=" O   THR Q 110 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   TYR Q 102 " --> pdb=" O   ARG Q  94 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'T' and resid 4 through 7
      removed outlier: 3.541A  pdb=" N   SER T  22 " --> pdb=" O   SER T   7 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU T  70 " --> pdb=" O   SER T  67 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'T' and resid 10 through 12
      removed outlier: 6.385A  pdb=" N   VAL T  11 " --> pdb=" O   ASP T 105 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU T  33 " --> pdb=" O   TYR T  49 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TYR T  49 " --> pdb=" O   LEU T  33 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP T  35 " --> pdb=" O   LEU T  47 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'T' and resid 10 through 12
      removed outlier: 6.385A  pdb=" N   VAL T  11 " --> pdb=" O   ASP T 105 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.387A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 110 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   MET S  34 " --> pdb=" O   VAL S  50 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   VAL S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.387A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 110 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   TYR S 102 " --> pdb=" O   ARG S  94 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'V' and resid 4 through 7
      removed outlier: 3.506A  pdb=" N   SER V   7 " --> pdb=" O   SER V  22 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER V  22 " --> pdb=" O   SER V   7 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU V  70 " --> pdb=" O   SER V  67 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'V' and resid 10 through 12
      removed outlier: 6.604A  pdb=" N   LEU V  33 " --> pdb=" O   TYR V  49 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   TYR V  49 " --> pdb=" O   LEU V  33 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   TRP V  35 " --> pdb=" O   LEU V  47 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'V' and resid 10 through 12
    Processing sheet with id=AF7, first strand: chain 'U' and resid 3 through 7
    Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 12
      removed outlier: 6.310A  pdb=" N   GLY U  10 " --> pdb=" O   THR U 110 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA U  93 " --> pdb=" O   HIS U  35 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   MET U  34 " --> pdb=" O   VAL U  50 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   VAL U  50 " --> pdb=" O   MET U  34 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   TRP U  36 " --> pdb=" O   VAL U  48 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 12
      removed outlier: 6.310A  pdb=" N   GLY U  10 " --> pdb=" O   THR U 110 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   TYR U 102 " --> pdb=" O   ARG U  94 " (cutoff:3.500A)
    Processing sheet with id=AG1, first strand: chain 'X' and resid 4 through 7
      removed outlier: 3.536A  pdb=" N   SER X   7 " --> pdb=" O   SER X  22 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER X  22 " --> pdb=" O   SER X   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU X  70 " --> pdb=" O   SER X  67 " (cutoff:3.500A)
    Processing sheet with id=AG2, first strand: chain 'X' and resid 10 through 13
      removed outlier: 6.428A  pdb=" N   LEU X  33 " --> pdb=" O   TYR X  49 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   TYR X  49 " --> pdb=" O   LEU X  33 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   TRP X  35 " --> pdb=" O   LEU X  47 " (cutoff:3.500A)
    Processing sheet with id=AG3, first strand: chain 'X' and resid 10 through 13
      removed outlier: 3.548A  pdb=" N   THR X  97 " --> pdb=" O   GLN X  90 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'W' and resid 3 through 7
      removed outlier: 3.666A  pdb=" N   MET W  77 " --> pdb=" O   ASP W  72 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASP W  72 " --> pdb=" O   MET W  77 " (cutoff:3.500A)
    Processing sheet with id=AG5, first strand: chain 'W' and resid 10 through 12
      removed outlier: 6.479A  pdb=" N   GLY W  10 " --> pdb=" O   THR W 110 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   MET W  34 " --> pdb=" O   VAL W  50 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   VAL W  50 " --> pdb=" O   MET W  34 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TRP W  36 " --> pdb=" O   VAL W  48 " (cutoff:3.500A)
    Processing sheet with id=AG6, first strand: chain 'W' and resid 10 through 12
      removed outlier: 6.479A  pdb=" N   GLY W  10 " --> pdb=" O   THR W 110 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   TYR W 102 " --> pdb=" O   ARG W  94 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'Z' and resid 4 through 7
      removed outlier: 3.569A  pdb=" N   SER Z   7 " --> pdb=" O   SER Z  22 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER Z  22 " --> pdb=" O   SER Z   7 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU Z  70 " --> pdb=" O   SER Z  67 " (cutoff:3.500A)
    Processing sheet with id=AG8, first strand: chain 'Z' and resid 10 through 13
      removed outlier: 6.303A  pdb=" N   LEU Z  33 " --> pdb=" O   TYR Z  49 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR Z  49 " --> pdb=" O   LEU Z  33 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   TRP Z  35 " --> pdb=" O   LEU Z  47 " (cutoff:3.500A)
    Processing sheet with id=AG9, first strand: chain 'Z' and resid 10 through 13
      removed outlier: 3.566A  pdb=" N   THR Z  97 " --> pdb=" O   GLN Z  90 " (cutoff:3.500A)
    Processing sheet with id=AH1, first strand: chain 'Y' and resid 3 through 7
      removed outlier: 3.726A  pdb=" N   MET Y  77 " --> pdb=" O   ASP Y  72 " (cutoff:3.500A)
    Processing sheet with id=AH2, first strand: chain 'Y' and resid 10 through 11
      removed outlier: 6.273A  pdb=" N   GLY Y  10 " --> pdb=" O   THR Y 110 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   MET Y  34 " --> pdb=" O   VAL Y  50 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   VAL Y  50 " --> pdb=" O   MET Y  34 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   TRP Y  36 " --> pdb=" O   VAL Y  48 " (cutoff:3.500A)
    Processing sheet with id=AH3, first strand: chain 'Y' and resid 10 through 11
      removed outlier: 6.273A  pdb=" N   GLY Y  10 " --> pdb=" O   THR Y 110 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TYR Y 102 " --> pdb=" O   ARG Y  94 " (cutoff:3.500A)

    846 hydrogen bonds defined for protein.
    1947 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: 6.80

  Time building geometry restraints manager: 8.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6660
        1.34 -     1.46: 5226
        1.46 -     1.58: 8777
        1.58 -     1.69: 0
        1.69 -     1.81: 132
  Bond restraints: 20795
  Sorted by residual:
  bond pdb=" CA  GLY N  50 "
       pdb=" C   GLY N  50 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 1.04e-02 9.25e+03 2.45e+00
  bond pdb=" CA  GLY N  68 "
       pdb=" C   GLY N  68 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 1.04e-02 9.25e+03 2.40e+00
  bond pdb=" C   VAL Y  12 "
       pdb=" N   GLN Y  13 "
    ideal  model  delta    sigma   weight residual
    1.330  1.351 -0.021 1.47e-02 4.63e+03 1.97e+00
  bond pdb=" N   GLY N  68 "
       pdb=" CA  GLY N  68 "
    ideal  model  delta    sigma   weight residual
    1.464  1.449  0.016 1.12e-02 7.97e+03 1.96e+00
  bond pdb=" N   GLY N  50 "
       pdb=" CA  GLY N  50 "
    ideal  model  delta    sigma   weight residual
    1.464  1.449  0.016 1.12e-02 7.97e+03 1.93e+00
  ... (remaining 20790 not shown)

  Histogram of bond angle deviations from ideal:
      100.16 -   106.95: 592
      106.95 -   113.74: 10860
      113.74 -   120.54: 7579
      120.54 -   127.33: 8922
      127.33 -   134.12: 246
  Bond angle restraints: 28199
  Sorted by residual:
  angle pdb=" C   THR T  30 "
        pdb=" CA  THR T  30 "
        pdb=" CB  THR T  30 "
      ideal   model   delta    sigma   weight residual
     117.23  110.22    7.01 1.36e+00 5.41e-01 2.66e+01
  angle pdb=" C   THR R  30 "
        pdb=" CA  THR R  30 "
        pdb=" CB  THR R  30 "
      ideal   model   delta    sigma   weight residual
     117.23  110.23    7.00 1.36e+00 5.41e-01 2.65e+01
  angle pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
        pdb=" C   ALA L  51 "
      ideal   model   delta    sigma   weight residual
     114.62  110.41    4.21 1.14e+00 7.69e-01 1.36e+01
  angle pdb=" N   ALA Z  51 "
        pdb=" CA  ALA Z  51 "
        pdb=" C   ALA Z  51 "
      ideal   model   delta    sigma   weight residual
     114.62  110.85    3.77 1.14e+00 7.69e-01 1.10e+01
  angle pdb=" CB  LYS H  43 "
        pdb=" CG  LYS H  43 "
        pdb=" CD  LYS H  43 "
      ideal   model   delta    sigma   weight residual
     111.30  118.70   -7.40 2.30e+00 1.89e-01 1.04e+01
  ... (remaining 28194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 10847
       17.78 -    35.56: 971
       35.56 -    53.34: 249
       53.34 -    71.12: 42
       71.12 -    88.90: 15
  Dihedral angle restraints: 12124
    sinusoidal: 4689
      harmonic: 7435
  Sorted by residual:
  dihedral pdb=" CA  GLY L  50 "
           pdb=" C   GLY L  50 "
           pdb=" N   ALA L  51 "
           pdb=" CA  ALA L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.77   18.23     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  GLY Z  50 "
           pdb=" C   GLY Z  50 "
           pdb=" N   ALA Z  51 "
           pdb=" CA  ALA Z  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.90   18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  TYR W  99 "
           pdb=" C   TYR W  99 "
           pdb=" N   ASP W 100 "
           pdb=" CA  ASP W 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 12121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1949
       0.032 -    0.063: 689
       0.063 -    0.095: 189
       0.095 -    0.126: 130
       0.126 -    0.158: 16
  Chirality restraints: 2973
  Sorted by residual:
  chirality pdb=" CA  ASP X  82 "
            pdb=" N   ASP X  82 "
            pdb=" C   ASP X  82 "
            pdb=" CB  ASP X  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.21e-01
  chirality pdb=" CG  LEU X  78 "
            pdb=" CB  LEU X  78 "
            pdb=" CD1 LEU X  78 "
            pdb=" CD2 LEU X  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CB  THR Y  87 "
            pdb=" CA  THR Y  87 "
            pdb=" OG1 THR Y  87 "
            pdb=" CG2 THR Y  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.22e-01
  ... (remaining 2970 not shown)

  Planarity restraints: 3684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  58 "   -0.036 5.00e-02 4.00e+02   5.44e-02 4.73e+00
        pdb=" N   PRO R  59 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO R  59 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R  59 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE V  58 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO V  59 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO V  59 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO V  59 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C  72 "    0.008 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" CG  ASP C  72 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP C  72 "    0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP C  72 "    0.010 2.00e-02 2.50e+03
  ... (remaining 3681 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1165
        2.73 -     3.27: 18567
        3.27 -     3.82: 33581
        3.82 -     4.36: 41402
        4.36 -     4.90: 74129
  Nonbonded interactions: 168844
  Sorted by model distance:
  nonbonded pdb=" OG  SER X  14 "
            pdb=" OE2 GLU X  17 "
     model   vdw
     2.190 2.440
  nonbonded pdb=" O   SER R  77 "
            pdb=" OG  SER R  77 "
     model   vdw
     2.262 2.440
  nonbonded pdb=" OG  SER C   7 "
            pdb=" OG  SER C  21 "
     model   vdw
     2.268 2.440
  nonbonded pdb=" OG1 THR X  30 "
            pdb=" N   SER X  31 "
     model   vdw
     2.274 2.520
  nonbonded pdb=" N   GLU E   6 "
            pdb=" OE1 GLU E   6 "
     model   vdw
     2.279 2.520
  ... (remaining 168839 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 'C'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
  selection = chain 'W'
  selection = chain 'Y'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
  selection = chain 'X'
  selection = chain 'Z'
}

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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.620
  Check model and map are aligned:         0.280
  Set scattering table:                    0.160
  Process input model:                     53.100
  Find NCS groups from input model:        1.350
  Set up NCS constraints:                  0.160
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
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      :  0.002   0.036  20795  Z= 0.148
  Angle     :  0.550   8.650  28199  Z= 0.318
  Chirality :  0.040   0.158   2973
  Planarity :  0.004   0.054   3684
  Dihedral  : 14.794  88.902   7350
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 15.16 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.17), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.23 (0.14), residues: 1210
  loop :  0.21 (0.18), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP O 103 
 HIS   0.008   0.001   HIS A  52A
 PHE   0.012   0.001   PHE O  27 
 TYR   0.020   0.001   TYR O 102 
 ARG   0.009   0.001   ARG Z  61 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 353
  time to evaluate  : 2.209 
Fit side-chains
REVERT: A   77 MET cc_start: 0.7682 (mtt) cc_final: 0.7040 (mtt)
REVERT: C   13 GLN cc_start: 0.8441 (mt0) cc_final: 0.8127 (mt0)
REVERT: C   75 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8652 (mtpp)
REVERT: F  107 LYS cc_start: 0.7941 (tppt) cc_final: 0.7389 (tppp)
REVERT: P  103 LYS cc_start: 0.8477 (tppt) cc_final: 0.8276 (tptt)
REVERT: T   79 GLN cc_start: 0.8973 (mp10) cc_final: 0.8742 (mp10)
  outliers start: 2
  outliers final: 2
  residues processed: 353
  average time/residue: 0.3483
  time to fit residues: 184.1257
Evaluate side-chains
  326 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 324
  time to evaluate  : 2.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain V residue   81 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 211 optimal weight:    6.9990
   chunk 189 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 127 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 195 optimal weight:    2.9990
   chunk 75 optimal weight:    0.1980
   chunk 119 optimal weight:    9.9990
   chunk 145 optimal weight:    8.9990
   chunk 227 optimal weight:    7.9990
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
I  77 ASN
L  92 ASN
A  76 ASN
M  81 GLN
U   3 GLN
U 100CASN
W 100CASN
** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  20795  Z= 0.255
  Angle     :  0.537   6.544  28199  Z= 0.290
  Chirality :  0.043   0.163   2973
  Planarity :  0.004   0.042   3684
  Dihedral  :  4.178  27.112   2886
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.44 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.47 (0.15), residues: 1166
  loop : -0.02 (0.17), residues: 1406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S 103 
 HIS   0.006   0.001   HIS A  52A
 PHE   0.013   0.001   PHE D  98 
 TYR   0.019   0.002   TYR S  90 
 ARG   0.005   0.000   ARG H  16 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 326
  time to evaluate  : 2.633 
Fit side-chains
REVERT: H   99 TYR cc_start: 0.8625 (t80) cc_final: 0.8302 (t80)
REVERT: P  103 LYS cc_start: 0.8577 (tppt) cc_final: 0.8352 (tptt)
REVERT: X    3 VAL cc_start: 0.9060 (t) cc_final: 0.8832 (m)
REVERT: Y   34 MET cc_start: 0.8916 (tpp) cc_final: 0.8507 (mmm)
  outliers start: 43
  outliers final: 23
  residues processed: 352
  average time/residue: 0.3296
  time to fit residues: 177.2083
Evaluate side-chains
  335 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 312
  time to evaluate  : 2.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 GLN
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain E residue   28 THR
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain U residue  100 ASN
Chi-restraints excluded: chain X residue   14 SER
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   72 ASP
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Y residue    5 VAL
Chi-restraints excluded: chain Y residue   82 MET
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 188 optimal weight:    4.9990
   chunk 154 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 227 optimal weight:    8.9990
   chunk 245 optimal weight:    9.9990
   chunk 202 optimal weight:    7.9990
   chunk 225 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 182 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
I  45 ASN
B  79 GLN
B  92 ASN
A  76 ASN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 100AHIS
O 100AHIS
S 100CASN
V   1 GLN
V  79 GLN
U 100CASN
** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077  20795  Z= 0.498
  Angle     :  0.640   8.523  28199  Z= 0.342
  Chirality :  0.045   0.158   2973
  Planarity :  0.005   0.038   3684
  Dihedral  :  4.642  27.444   2881
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.27 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.14 (0.14), residues: 1210
  loop : -0.33 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP S 103 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.022   0.002   PHE Z  96 
 TYR   0.026   0.003   TYR L  91 
 ARG   0.006   0.001   ARG P  18 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 307
  time to evaluate  : 2.195 
Fit side-chains
REVERT: H   61 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8451 (t70)
REVERT: B   91 TYR cc_start: 0.7697 (p90) cc_final: 0.7456 (p90)
REVERT: A  100 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6862 (t0)
REVERT: N  103 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7982 (tttp)
REVERT: T    4 MET cc_start: 0.8384 (mmm) cc_final: 0.8182 (mtp)
REVERT: Y   34 MET cc_start: 0.8905 (tpp) cc_final: 0.8419 (mmm)
REVERT: Y   98 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.8033 (p90)
  outliers start: 70
  outliers final: 50
  residues processed: 361
  average time/residue: 0.3257
  time to fit residues: 178.6138
Evaluate side-chains
  349 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 296
  time to evaluate  : 2.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   77 ASN
Chi-restraints excluded: chain L residue    1 GLN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain A residue  100 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue   89 ILE
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain O residue   22 CYS
Chi-restraints excluded: chain O residue   63 VAL
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 MET
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue   85 VAL
Chi-restraints excluded: chain U residue   17 SER
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain U residue   89 ILE
Chi-restraints excluded: chain X residue   14 SER
Chi-restraints excluded: chain X residue   76 SER
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   21 SER
Chi-restraints excluded: chain W residue   72 ASP
Chi-restraints excluded: chain W residue   82 SER
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   73 LEU
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue    5 VAL
Chi-restraints excluded: chain Y residue   53 ASP
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   89 ILE
Chi-restraints excluded: chain Y residue   98 PHE
Chi-restraints excluded: chain Y residue  107 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 224 optimal weight:    6.9990
   chunk 170 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 152 optimal weight:    0.9980
   chunk 228 optimal weight:    7.9990
   chunk 241 optimal weight:   10.0000
   chunk 119 optimal weight:    7.9990
   chunk 216 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
B  92 ASN
A  76 ASN
D  42 GLN
D  92 ASN
F  92 ASN
W  81 GLN
Y  76 ASN
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  20795  Z= 0.195
  Angle     :  0.497   5.715  28199  Z= 0.265
  Chirality :  0.042   0.148   2973
  Planarity :  0.003   0.035   3684
  Dihedral  :  4.124  24.233   2881
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.02 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.24 (0.14), residues: 1210
  loop : -0.28 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  47 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.011   0.001   PHE Y  32 
 TYR   0.012   0.001   TYR P  91 
 ARG   0.007   0.000   ARG P  18 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 328
  time to evaluate  : 2.240 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8185 (t70)
REVERT: H   99 TYR cc_start: 0.8575 (t80) cc_final: 0.8317 (t80)
REVERT: B   91 TYR cc_start: 0.7808 (p90) cc_final: 0.7560 (p90)
REVERT: B   96 PHE cc_start: 0.8285 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  100 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6786 (t0)
REVERT: C   75 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8440 (mtmt)
REVERT: F   54 ARG cc_start: 0.8365 (mtm110) cc_final: 0.7959 (ttm-80)
REVERT: N    1 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7321 (mt0)
REVERT: O   45 LEU cc_start: 0.8769 (mm) cc_final: 0.8566 (mt)
REVERT: R   17 GLU cc_start: 0.7134 (tp30) cc_final: 0.6907 (tp30)
REVERT: Q   82 MET cc_start: 0.9178 (mtt) cc_final: 0.8782 (mtt)
REVERT: W   99 TYR cc_start: 0.7704 (t80) cc_final: 0.7183 (t80)
REVERT: Z   54 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7277 (mtm-85)
REVERT: Y   34 MET cc_start: 0.8933 (tpp) cc_final: 0.8669 (mmt)
REVERT: Y   98 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (p90)
  outliers start: 51
  outliers final: 29
  residues processed: 364
  average time/residue: 0.3275
  time to fit residues: 180.8772
Evaluate side-chains
  344 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 311
  time to evaluate  : 2.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain N residue    1 GLN
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain R residue  106 PHE
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   51 ILE
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   98 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 201 optimal weight:    4.9990
   chunk 137 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 179 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 206 optimal weight:    5.9990
   chunk 167 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 123 optimal weight:    8.9990
   chunk 216 optimal weight:    0.0980
   chunk 60 optimal weight:    9.9990
   overall best weight:    4.0188

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

Flipped N/Q/H residues before XYZ refinement:
D  42 GLN
D  92 ASN
X  38 GLN
Y  76 ASN
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  20795  Z= 0.406
  Angle     :  0.587   7.989  28199  Z= 0.310
  Chirality :  0.044   0.157   2973
  Planarity :  0.004   0.035   3684
  Dihedral  :  4.418  27.326   2881
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.89 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.65 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.15 (0.14), residues: 1210
  loop : -0.41 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP S 103 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.018   0.002   PHE Z  96 
 TYR   0.021   0.002   TYR L  91 
 ARG   0.007   0.001   ARG P  18 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 82
    poor density    : 309
  time to evaluate  : 2.266 
Fit side-chains
REVERT: H   61 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8448 (t70)
REVERT: B   91 TYR cc_start: 0.7845 (p90) cc_final: 0.7601 (p90)
REVERT: B   96 PHE cc_start: 0.8298 (m-80) cc_final: 0.8021 (m-80)
REVERT: A  100 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.6760 (t0)
REVERT: D   49 TYR cc_start: 0.8324 (p90) cc_final: 0.7946 (p90)
REVERT: E    1 GLN cc_start: 0.7484 (mt0) cc_final: 0.7242 (pt0)
REVERT: N  103 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7924 (tttp)
REVERT: V    4 MET cc_start: 0.8708 (mmm) cc_final: 0.8391 (mmm)
REVERT: Y   34 MET cc_start: 0.8949 (tpp) cc_final: 0.8671 (mmt)
REVERT: Y   98 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8088 (p90)
  outliers start: 82
  outliers final: 61
  residues processed: 370
  average time/residue: 0.3271
  time to fit residues: 183.9835
Evaluate side-chains
  366 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 302
  time to evaluate  : 2.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 GLN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain N residue   56 THR
Chi-restraints excluded: chain M residue   55 SER
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain O residue   22 CYS
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue    5 THR
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue    3 VAL
Chi-restraints excluded: chain V residue   12 SER
Chi-restraints excluded: chain V residue   85 VAL
Chi-restraints excluded: chain U residue   17 SER
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain X residue    5 THR
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   76 SER
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   21 SER
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue   82 SER
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   73 LEU
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue   53 ASP
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   89 ILE
Chi-restraints excluded: chain Y residue   98 PHE
Chi-restraints excluded: chain Y residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 217 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 141 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 241 optimal weight:    7.9990
   chunk 200 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 126 optimal weight:    0.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
H 100CASN
B  92 ASN
D  42 GLN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 105 GLN
W 100AHIS
Z   6 GLN
Y  76 ASN
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  20795  Z= 0.349
  Angle     :  0.559   6.974  28199  Z= 0.297
  Chirality :  0.043   0.162   2973
  Planarity :  0.004   0.033   3684
  Dihedral  :  4.358  25.590   2881
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.65 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.70 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.08 (0.14), residues: 1210
  loop : -0.48 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP S 103 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.015   0.002   PHE Z  96 
 TYR   0.016   0.002   TYR L  91 
 ARG   0.007   0.000   ARG P  18 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 323
  time to evaluate  : 2.270 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8424 (t70)
REVERT: B   91 TYR cc_start: 0.7915 (p90) cc_final: 0.7653 (p90)
REVERT: B   96 PHE cc_start: 0.8334 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  100 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.6820 (t0)
REVERT: D   49 TYR cc_start: 0.8379 (p90) cc_final: 0.7982 (p90)
REVERT: M    3 GLN cc_start: 0.8505 (tp40) cc_final: 0.8215 (mm-40)
REVERT: O   45 LEU cc_start: 0.8701 (mm) cc_final: 0.8419 (mt)
REVERT: X   90 GLN cc_start: 0.8716 (pp30) cc_final: 0.8444 (pp30)
REVERT: Y   34 MET cc_start: 0.8918 (tpp) cc_final: 0.8467 (mmm)
REVERT: Y   98 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8145 (p90)
  outliers start: 85
  outliers final: 70
  residues processed: 385
  average time/residue: 0.3243
  time to fit residues: 190.1895
Evaluate side-chains
  395 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 322
  time to evaluate  : 2.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 GLN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue  106 PHE
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 ASN
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain M residue   55 SER
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain O residue   22 CYS
Chi-restraints excluded: chain O residue   63 VAL
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain R residue  106 PHE
Chi-restraints excluded: chain Q residue   38 ARG
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   45 LEU
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue    5 THR
Chi-restraints excluded: chain T residue   52 SER
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue   12 SER
Chi-restraints excluded: chain V residue   81 GLU
Chi-restraints excluded: chain V residue   85 VAL
Chi-restraints excluded: chain U residue   17 SER
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain U residue  105 GLN
Chi-restraints excluded: chain X residue    5 THR
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   76 SER
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   21 SER
Chi-restraints excluded: chain W residue   40 THR
Chi-restraints excluded: chain W residue   51 ILE
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue   82 SER
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   52 SER
Chi-restraints excluded: chain Z residue   73 LEU
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue   53 ASP
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   98 PHE
Chi-restraints excluded: chain Y residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 233 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   chunk 137 optimal weight:    1.9990
   chunk 176 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   chunk 203 optimal weight:    8.9990
   chunk 135 optimal weight:    7.9990
   chunk 240 optimal weight:    9.9990
   chunk 150 optimal weight:    7.9990
   chunk 146 optimal weight:    0.4980
   chunk 111 optimal weight:    0.3980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
D  42 GLN
D  92 ASN
U 105 GLN
Y  76 ASN
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  20795  Z= 0.141
  Angle     :  0.482   7.760  28199  Z= 0.254
  Chirality :  0.041   0.162   2973
  Planarity :  0.003   0.033   3684
  Dihedral  :  3.943  23.431   2881
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  2.84 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.45 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.29 (0.14), residues: 1199
  loop : -0.39 (0.17), residues: 1373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP U 103 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.015   0.001   PHE Y  32 
 TYR   0.016   0.001   TYR U 102 
 ARG   0.007   0.000   ARG H  16 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 352
  time to evaluate  : 2.230 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8152 (t70)
REVERT: H   99 TYR cc_start: 0.8506 (t80) cc_final: 0.8174 (t80)
REVERT: B   96 PHE cc_start: 0.8311 (m-80) cc_final: 0.8022 (m-80)
REVERT: D   49 TYR cc_start: 0.8276 (p90) cc_final: 0.7922 (p90)
REVERT: C   75 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8392 (mtmt)
REVERT: F   54 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8077 (ttm-80)
REVERT: E   75 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8193 (mtmm)
REVERT: E   89 ILE cc_start: 0.8378 (mt) cc_final: 0.8175 (mt)
REVERT: O   45 LEU cc_start: 0.8635 (mm) cc_final: 0.8390 (mt)
REVERT: O  102 TYR cc_start: 0.8139 (m-10) cc_final: 0.7933 (m-10)
REVERT: T    4 MET cc_start: 0.8351 (mmm) cc_final: 0.8112 (mtp)
REVERT: S   91 TYR cc_start: 0.9039 (m-80) cc_final: 0.8719 (m-10)
REVERT: Y   34 MET cc_start: 0.8966 (tpp) cc_final: 0.8457 (mmm)
REVERT: Y   98 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8085 (p90)
  outliers start: 57
  outliers final: 43
  residues processed: 389
  average time/residue: 0.3022
  time to fit residues: 177.7007
Evaluate side-chains
  381 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 336
  time to evaluate  : 2.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain D residue   92 ASN
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain N residue   56 THR
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue  100 ASP
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain O residue  100 ASP
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue    3 VAL
Chi-restraints excluded: chain V residue   81 GLU
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain U residue  105 GLN
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   70 GLU
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   21 SER
Chi-restraints excluded: chain W residue   51 ILE
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   98 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 149 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 143 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 47 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   chunk 153 optimal weight:    7.9990
   chunk 164 optimal weight:    9.9990
   chunk 119 optimal weight:    7.9990
   chunk 22 optimal weight:    0.5980
   chunk 189 optimal weight:    7.9990
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
B  92 ASN
D  42 GLN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 105 GLN
Y 100AHIS
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  20795  Z= 0.374
  Angle     :  0.575   7.094  28199  Z= 0.304
  Chirality :  0.043   0.170   2973
  Planarity :  0.004   0.032   3684
  Dihedral  :  4.323  26.854   2881
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.81 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.22 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.13 (0.14), residues: 1210
  loop : -0.46 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP S 103 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.017   0.002   PHE Z  96 
 TYR   0.020   0.002   TYR L  91 
 ARG   0.007   0.000   ARG P  18 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  400 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 329
  time to evaluate  : 2.297 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8427 (t70)
REVERT: B   91 TYR cc_start: 0.7953 (p90) cc_final: 0.7748 (p90)
REVERT: B   96 PHE cc_start: 0.8382 (m-80) cc_final: 0.8117 (m-80)
REVERT: A  100 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6742 (t0)
REVERT: D   49 TYR cc_start: 0.8400 (p90) cc_final: 0.8066 (p90)
REVERT: E   43 LYS cc_start: 0.6766 (pttm) cc_final: 0.6546 (mttt)
REVERT: O   45 LEU cc_start: 0.8673 (mm) cc_final: 0.8385 (mt)
REVERT: V   17 GLU cc_start: 0.7403 (tt0) cc_final: 0.7154 (tt0)
REVERT: X   90 GLN cc_start: 0.8745 (pp30) cc_final: 0.8440 (pp30)
REVERT: Y   34 MET cc_start: 0.8987 (tpp) cc_final: 0.8509 (mmm)
REVERT: Y   98 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8144 (p90)
  outliers start: 71
  outliers final: 62
  residues processed: 378
  average time/residue: 0.3254
  time to fit residues: 186.3231
Evaluate side-chains
  385 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 320
  time to evaluate  : 2.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   77 ASN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  100 ASN
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain N residue   56 THR
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue  100 ASP
Chi-restraints excluded: chain M residue  108 LEU
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain Q residue   37 VAL
Chi-restraints excluded: chain Q residue   38 ARG
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue    3 VAL
Chi-restraints excluded: chain V residue   12 SER
Chi-restraints excluded: chain V residue   81 GLU
Chi-restraints excluded: chain U residue   17 SER
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain U residue  105 GLN
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   70 GLU
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   12 VAL
Chi-restraints excluded: chain W residue   51 ILE
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   52 SER
Chi-restraints excluded: chain Z residue   73 LEU
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   89 ILE
Chi-restraints excluded: chain Y residue   98 PHE
Chi-restraints excluded: chain Y residue  100 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 219 optimal weight:    2.9990
   chunk 230 optimal weight:   20.0000
   chunk 210 optimal weight:    0.3980
   chunk 224 optimal weight:    8.9990
   chunk 135 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 176 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 202 optimal weight:    9.9990
   chunk 212 optimal weight:    7.9990
   chunk 223 optimal weight:    9.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
D  42 GLN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U   3 GLN
Y 100AHIS
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  20795  Z= 0.183
  Angle     :  0.503   8.932  28199  Z= 0.265
  Chirality :  0.041   0.168   2973
  Planarity :  0.003   0.033   3684
  Dihedral  :  4.023  24.210   2881
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  2.99 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 20.00 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.44 (0.15), residues: 1155
  loop : -0.51 (0.17), residues: 1417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP U 103 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.015   0.001   PHE Y  32 
 TYR   0.025   0.001   TYR Y  99 
 ARG   0.006   0.000   ARG H  16 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 333
  time to evaluate  : 2.153 
Fit side-chains
   revert: symmetry clash
REVERT: H   61 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8356 (t70)
REVERT: B   96 PHE cc_start: 0.8391 (m-80) cc_final: 0.8117 (m-80)
REVERT: D   49 TYR cc_start: 0.8380 (p90) cc_final: 0.8017 (p90)
REVERT: C   38 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7030 (ttm170)
REVERT: C   75 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8331 (mtmt)
REVERT: F   54 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8058 (ttm-80)
REVERT: E   43 LYS cc_start: 0.6610 (pttm) cc_final: 0.6357 (mttt)
REVERT: O   75 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8578 (mtmm)
REVERT: T   81 GLU cc_start: 0.8109 (pt0) cc_final: 0.7828 (pm20)
REVERT: V   17 GLU cc_start: 0.7384 (tt0) cc_final: 0.7131 (tt0)
REVERT: Y   34 MET cc_start: 0.8990 (tpp) cc_final: 0.8487 (mmm)
REVERT: Y   98 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.8037 (p90)
  outliers start: 57
  outliers final: 46
  residues processed: 372
  average time/residue: 0.3311
  time to fit residues: 186.0474
Evaluate side-chains
  377 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 328
  time to evaluate  : 2.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue   10 THR
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain N residue   56 THR
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue  100 ASP
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain Q residue   37 VAL
Chi-restraints excluded: chain Q residue   38 ARG
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue    3 VAL
Chi-restraints excluded: chain V residue   81 GLU
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   70 GLU
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue   82 SER
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   52 SER
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   98 PHE
Chi-restraints excluded: chain Y residue  100 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 147 optimal weight:    0.8980
   chunk 237 optimal weight:    3.9990
   chunk 144 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 165 optimal weight:    2.9990
   chunk 249 optimal weight:   10.0000
   chunk 229 optimal weight:    6.9990
   chunk 198 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 153 optimal weight:    7.9990
   chunk 121 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
D  42 GLN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U   3 GLN
Y 100AHIS
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  20795  Z= 0.241
  Angle     :  0.521   8.667  28199  Z= 0.274
  Chirality :  0.042   0.168   2973
  Planarity :  0.004   0.034   3684
  Dihedral  :  4.061  25.456   2881
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.50 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.00 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.44 (0.15), residues: 1111
  loop : -0.42 (0.16), residues: 1461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S 103 
 HIS   0.007   0.001   HIS Y 100A
 PHE   0.016   0.001   PHE Y  32 
 TYR   0.023   0.002   TYR B  91 
 ARG   0.006   0.000   ARG H  16 

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

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

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5144 Ramachandran restraints generated.
    2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 320
  time to evaluate  : 2.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   77 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8701 (t0)
REVERT: H   61 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8377 (t70)
REVERT: B   96 PHE cc_start: 0.8378 (m-80) cc_final: 0.8104 (m-80)
REVERT: D   49 TYR cc_start: 0.8323 (p90) cc_final: 0.7896 (p90)
REVERT: C   38 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7067 (ttm170)
REVERT: F   54 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8061 (ttm-80)
REVERT: E   43 LYS cc_start: 0.6633 (pttm) cc_final: 0.6366 (mttt)
REVERT: Q   82 MET cc_start: 0.9099 (mtt) cc_final: 0.8737 (mtt)
REVERT: T   81 GLU cc_start: 0.8077 (pt0) cc_final: 0.7861 (pm20)
REVERT: V   17 GLU cc_start: 0.7393 (tt0) cc_final: 0.7137 (tt0)
REVERT: Y   34 MET cc_start: 0.8970 (tpp) cc_final: 0.8691 (mmt)
  outliers start: 58
  outliers final: 52
  residues processed: 361
  average time/residue: 0.3274
  time to fit residues: 178.3769
Evaluate side-chains
  373 residues out of total 2170 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 318
  time to evaluate  : 2.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   77 ASN
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   61 ASP
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain F residue   10 THR
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain N residue   56 THR
Chi-restraints excluded: chain M residue   78 ILE
Chi-restraints excluded: chain M residue  100 ASP
Chi-restraints excluded: chain O residue   78 ILE
Chi-restraints excluded: chain O residue   82 LEU
Chi-restraints excluded: chain Q residue   37 VAL
Chi-restraints excluded: chain Q residue   38 ARG
Chi-restraints excluded: chain Q residue   40 THR
Chi-restraints excluded: chain Q residue   85 GLU
Chi-restraints excluded: chain T residue    3 VAL
Chi-restraints excluded: chain T residue    5 THR
Chi-restraints excluded: chain T residue   52 SER
Chi-restraints excluded: chain T residue   78 LEU
Chi-restraints excluded: chain S residue   40 THR
Chi-restraints excluded: chain S residue   78 ILE
Chi-restraints excluded: chain V residue    3 VAL
Chi-restraints excluded: chain V residue   81 GLU
Chi-restraints excluded: chain U residue   28 THR
Chi-restraints excluded: chain U residue   61 ASP
Chi-restraints excluded: chain X residue    7 SER
Chi-restraints excluded: chain X residue   20 THR
Chi-restraints excluded: chain X residue   70 GLU
Chi-restraints excluded: chain X residue   92 ASN
Chi-restraints excluded: chain W residue    5 VAL
Chi-restraints excluded: chain W residue   51 ILE
Chi-restraints excluded: chain W residue   78 ILE
Chi-restraints excluded: chain W residue   82 SER
Chi-restraints excluded: chain W residue  110 THR
Chi-restraints excluded: chain Z residue   13 VAL
Chi-restraints excluded: chain Z residue   52 SER
Chi-restraints excluded: chain Z residue   74 THR
Chi-restraints excluded: chain Z residue   77 SER
Chi-restraints excluded: chain Z residue   81 GLU
Chi-restraints excluded: chain Y residue   69 ILE
Chi-restraints excluded: chain Y residue   82 ASN
Chi-restraints excluded: chain Y residue   89 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 157 optimal weight:    3.9990
   chunk 211 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 182 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 198 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 203 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
D  42 GLN
** D  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U   3 GLN
Y 100AHIS
** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.093015 restraints weight = 28652.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.97
r_work: 0.2993 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  20795  Z= 0.225
  Angle     :  0.512   8.540  28199  Z= 0.269
  Chirality :  0.042   0.170   2973
  Planarity :  0.003   0.034   3684
  Dihedral  :  4.008  25.245   2881
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.38 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.86 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.16), residues: 2572
  helix:  None (None), residues: 0
  sheet:  0.45 (0.15), residues: 1111
  loop : -0.40 (0.16), residues: 1461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S 103 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.015   0.001   PHE Y  32 
 TYR   0.020   0.002   TYR U 102 
 ARG   0.006   0.000   ARG H  16 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4562.86 seconds
wall clock time: 84 minutes 12.35 seconds (5052.35 seconds total)