Starting phenix.real_space_refine
on Fri Dec  8 05:36:05 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxm_27060/12_2023/8cxm_27060.pdb"
  }
  resolution = 3.21
  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=   0.002 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     110      5.16       5
     C   65835      2.51       5
     N   20130      2.21       5
     O   23485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "Z GLU  122": "OE1" <-> "OE2"
    Residue "Z GLU  464": "OE1" <-> "OE2"
    Residue "B GLU   84": "OE1" <-> "OE2"
    Residue "B PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  106": "OE1" <-> "OE2"
    Residue "D PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   84": "OE1" <-> "OE2"
    Residue "D GLU  122": "OE1" <-> "OE2"
    Residue "D ASP  458": "OD1" <-> "OD2"
    Residue "E GLU  106": "OE1" <-> "OE2"
    Residue "E PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  464": "OE1" <-> "OE2"
    Residue "F PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   84": "OE1" <-> "OE2"
    Residue "F GLU  106": "OE1" <-> "OE2"
    Residue "F GLU  122": "OE1" <-> "OE2"
    Residue "F ASP  416": "OD1" <-> "OD2"
    Residue "F ASP  458": "OD1" <-> "OD2"
    Residue "F GLU  464": "OE1" <-> "OE2"
    Residue "G GLU   79": "OE1" <-> "OE2"
    Residue "G GLU   84": "OE1" <-> "OE2"
    Residue "G GLU  115": "OE1" <-> "OE2"
    Residue "G ASP  124": "OD1" <-> "OD2"
    Residue "H GLU   30": "OE1" <-> "OE2"
    Residue "H GLU   94": "OE1" <-> "OE2"
    Residue "H GLU  106": "OE1" <-> "OE2"
    Residue "H GLU  115": "OE1" <-> "OE2"
    Residue "H GLU  122": "OE1" <-> "OE2"
    Residue "H PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU   84": "OE1" <-> "OE2"
    Residue "I GLU  115": "OE1" <-> "OE2"
    Residue "I GLU  122": "OE1" <-> "OE2"
    Residue "J GLU   84": "OE1" <-> "OE2"
    Residue "J ASP  436": "OD1" <-> "OD2"
    Residue "J TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K GLU   84": "OE1" <-> "OE2"
    Residue "K GLU  115": "OE1" <-> "OE2"
    Residue "K GLU  122": "OE1" <-> "OE2"
    Residue "K ASP  436": "OD1" <-> "OD2"
    Residue "K GLU  464": "OE1" <-> "OE2"
    Residue "L GLU  451": "OE1" <-> "OE2"
    Residue "L TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  122": "OE1" <-> "OE2"
    Residue "M GLU  451": "OE1" <-> "OE2"
    Residue "M GLU  464": "OE1" <-> "OE2"
    Residue "N GLU   30": "OE1" <-> "OE2"
    Residue "N GLU   84": "OE1" <-> "OE2"
    Residue "N GLU  106": "OE1" <-> "OE2"
    Residue "N PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU  464": "OE1" <-> "OE2"
    Residue "O GLU   30": "OE1" <-> "OE2"
    Residue "O GLU   84": "OE1" <-> "OE2"
    Residue "O GLU   94": "OE1" <-> "OE2"
    Residue "O GLU  106": "OE1" <-> "OE2"
    Residue "P GLU   84": "OE1" <-> "OE2"
    Residue "P GLU  106": "OE1" <-> "OE2"
    Residue "P ASP  121": "OD1" <-> "OD2"
    Residue "P GLU  122": "OE1" <-> "OE2"
    Residue "P ASP  422": "OD1" <-> "OD2"
    Residue "P TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q GLU  115": "OE1" <-> "OE2"
    Residue "Q PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ASP  436": "OD1" <-> "OD2"
    Residue "Q GLU  464": "OE1" <-> "OE2"
    Residue "R GLU  122": "OE1" <-> "OE2"
    Residue "R ASP  422": "OD1" <-> "OD2"
    Residue "R TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  464": "OE1" <-> "OE2"
    Residue "S PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ASP  436": "OD1" <-> "OD2"
    Residue "T GLU   79": "OE1" <-> "OE2"
    Residue "T GLU  106": "OE1" <-> "OE2"
    Residue "T GLU  122": "OE1" <-> "OE2"
    Residue "U GLU   84": "OE1" <-> "OE2"
    Residue "U ASP  171": "OD1" <-> "OD2"
    Residue "U GLU  464": "OE1" <-> "OE2"
    Residue "V GLU   84": "OE1" <-> "OE2"
    Residue "V ASP  124": "OD1" <-> "OD2"
    Residue "V PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU  451": "OE1" <-> "OE2"
    Residue "W GLU   79": "OE1" <-> "OE2"
    Residue "W GLU   94": "OE1" <-> "OE2"
    Residue "W PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X ASP   44": "OD1" <-> "OD2"
    Residue "X GLU   84": "OE1" <-> "OE2"
    Residue "X PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X GLU  464": "OE1" <-> "OE2"
    Residue "Y GLU   84": "OE1" <-> "OE2"
    Residue "Y GLU  106": "OE1" <-> "OE2"
    Residue "Y ASP  124": "OD1" <-> "OD2"
    Residue "Y ASP  436": "OD1" <-> "OD2"
    Residue "a GLU  106": "OE1" <-> "OE2"
    Residue "a GLU  122": "OE1" <-> "OE2"
    Residue "a GLU  451": "OE1" <-> "OE2"
    Residue "a GLU  464": "OE1" <-> "OE2"
    Residue "b GLU   84": "OE1" <-> "OE2"
    Residue "b ASP  124": "OD1" <-> "OD2"
    Residue "b ASP  436": "OD1" <-> "OD2"
    Residue "b TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c GLU   79": "OE1" <-> "OE2"
    Residue "c GLU   84": "OE1" <-> "OE2"
    Residue "c GLU  106": "OE1" <-> "OE2"
    Residue "c GLU  115": "OE1" <-> "OE2"
    Residue "c GLU  464": "OE1" <-> "OE2"
    Residue "d GLU   79": "OE1" <-> "OE2"
    Residue "d GLU   84": "OE1" <-> "OE2"
    Residue "d GLU  122": "OE1" <-> "OE2"
    Residue "d PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d GLU  464": "OE1" <-> "OE2"
    Residue "e GLU   84": "OE1" <-> "OE2"
    Residue "e GLU  122": "OE1" <-> "OE2"
    Residue "e GLU  464": "OE1" <-> "OE2"
    Residue "2 GLU   79": "OE1" <-> "OE2"
    Residue "2 GLU   84": "OE1" <-> "OE2"
    Residue "2 GLU  106": "OE1" <-> "OE2"
    Residue "2 GLU  115": "OE1" <-> "OE2"
    Residue "2 TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "2 GLU  464": "OE1" <-> "OE2"
    Residue "f GLU   84": "OE1" <-> "OE2"
    Residue "f ASP  114": "OD1" <-> "OD2"
    Residue "f ASP  422": "OD1" <-> "OD2"
    Residue "g PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g GLU   84": "OE1" <-> "OE2"
    Residue "g GLU  106": "OE1" <-> "OE2"
    Residue "g GLU  115": "OE1" <-> "OE2"
    Residue "g GLU  122": "OE1" <-> "OE2"
    Residue "g PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g GLU  464": "OE1" <-> "OE2"
    Residue "h PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h GLU   79": "OE1" <-> "OE2"
    Residue "h GLU  115": "OE1" <-> "OE2"
    Residue "h ASP  121": "OD1" <-> "OD2"
    Residue "h PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h ASP  458": "OD1" <-> "OD2"
    Residue "h TYR  461": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "i GLU   84": "OE1" <-> "OE2"
    Residue "i GLU  115": "OE1" <-> "OE2"
    Residue "i GLU  122": "OE1" <-> "OE2"
    Residue "i GLU  464": "OE1" <-> "OE2"
    Residue "j ASP   70": "OD1" <-> "OD2"
    Residue "j GLU   84": "OE1" <-> "OE2"
    Residue "j GLU   94": "OE1" <-> "OE2"
    Residue "j GLU  106": "OE1" <-> "OE2"
    Residue "j GLU  122": "OE1" <-> "OE2"
    Residue "k GLU  106": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A GLU  106": "OE1" <-> "OE2"
    Residue "l GLU  122": "OE1" <-> "OE2"
    Residue "m PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "m PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "n GLU  106": "OE1" <-> "OE2"
    Residue "n GLU  115": "OE1" <-> "OE2"
    Residue "n GLU  122": "OE1" <-> "OE2"
    Residue "n GLU  464": "OE1" <-> "OE2"
    Residue "o GLU   84": "OE1" <-> "OE2"
    Residue "o GLU  122": "OE1" <-> "OE2"
    Residue "p GLU  451": "OE1" <-> "OE2"
    Residue "q PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "q GLU   84": "OE1" <-> "OE2"
    Residue "q GLU   94": "OE1" <-> "OE2"
    Residue "q GLU  106": "OE1" <-> "OE2"
    Residue "q GLU  122": "OE1" <-> "OE2"
    Residue "q PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "r GLU   30": "OE1" <-> "OE2"
    Residue "r GLU  122": "OE1" <-> "OE2"
    Residue "r PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "r ASP  422": "OD1" <-> "OD2"
    Residue "r GLU  464": "OE1" <-> "OE2"
    Residue "s GLU   79": "OE1" <-> "OE2"
    Residue "s GLU  122": "OE1" <-> "OE2"
    Residue "s PHE  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "s GLU  464": "OE1" <-> "OE2"
    Residue "t GLU   84": "OE1" <-> "OE2"
    Residue "t GLU  106": "OE1" <-> "OE2"
    Residue "t GLU  122": "OE1" <-> "OE2"
    Residue "t GLU  464": "OE1" <-> "OE2"
    Residue "u GLU   84": "OE1" <-> "OE2"
    Residue "u GLU  122": "OE1" <-> "OE2"
    Residue "u ASP  436": "OD1" <-> "OD2"
    Residue "u GLU  464": "OE1" <-> "OE2"
    Residue "v GLU  115": "OE1" <-> "OE2"
    Residue "v ASP  121": "OD1" <-> "OD2"
    Residue "v GLU  451": "OE1" <-> "OE2"
    Residue "w GLU   84": "OE1" <-> "OE2"
    Residue "w GLU  106": "OE1" <-> "OE2"
    Residue "w GLU  122": "OE1" <-> "OE2"
    Residue "w GLU  464": "OE1" <-> "OE2"
    Residue "x GLU   84": "OE1" <-> "OE2"
    Residue "x GLU   94": "OE1" <-> "OE2"
    Residue "x GLU  106": "OE1" <-> "OE2"
    Residue "x PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "x GLU  464": "OE1" <-> "OE2"
    Residue "y GLU   84": "OE1" <-> "OE2"
    Residue "y GLU  106": "OE1" <-> "OE2"
    Residue "y GLU  115": "OE1" <-> "OE2"
    Residue "y PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "z GLU   79": "OE1" <-> "OE2"
    Residue "z GLU  464": "OE1" <-> "OE2"
    Residue "0 PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "0 GLU   84": "OE1" <-> "OE2"
    Residue "0 GLU  115": "OE1" <-> "OE2"
    Residue "1 GLU   84": "OE1" <-> "OE2"
    Residue "1 GLU   94": "OE1" <-> "OE2"
    Residue "1 GLU  122": "OE1" <-> "OE2"
    Residue "1 GLU  464": "OE1" <-> "OE2"
  Time to flip residues: 0.21s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 109560
  Number of models: 1
  Model: ""
    Number of chains: 55
    Chain: "Z"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "V"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "W"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "d"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "e"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "2"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "f"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "g"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "h"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "i"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "j"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "k"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "l"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "m"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "n"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "o"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "p"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "q"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "r"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "s"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "t"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "u"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "v"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "w"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "x"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "y"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "z"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "0"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
    Chain: "1"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 1992
          Classifications: {'peptide': 267}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 264}
          Chain breaks: 1
  Time building chain proxies: 38.98, per 1000 atoms: 0.36
  Number of scatterers: 109560
  At special positions: 0
  Unit cell: (139.32, 139.32, 413.64, 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     110     16.00
     O   23485      8.00
     N   20130      7.00
     C   65835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 32.62
  Conformation dependent library (CDL) restraints added in 12.9 seconds
  

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  27720

  Finding SS restraints...
    Secondary structure from input PDB file:
      440 helices and 72 sheets defined
      77.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 6.06
  Creating SS restraints...
    Processing helix  chain 'Z' and resid 8 through 35
      removed outlier: 4.154A  pdb=" N   SER Z  23 " --> pdb=" O   ASN Z  19 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ALA Z  24 " --> pdb=" O   LYS Z  20 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU Z  25 " --> pdb=" O   ASN Z  21 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 45 through 100
      removed outlier: 3.698A  pdb=" N   ASP Z  70 " --> pdb=" O   ARG Z  66 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 105 through 130
      removed outlier: 3.506A  pdb=" N   THR Z 130 " --> pdb=" O   VAL Z 126 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 136 through 140
      removed outlier: 3.596A  pdb=" N   ALA Z 139 " --> pdb=" O   ASN Z 136 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LYS Z 140 " --> pdb=" O   VAL Z 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Z' and resid 136 through 140'
    Processing helix  chain 'Z' and resid 165 through 169
      removed outlier: 3.686A  pdb=" N   GLY Z 169 " --> pdb=" O   LYS Z 166 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 409 through 458
      removed outlier: 3.505A  pdb=" N   LYS Z 423 " --> pdb=" O   ALA Z 419 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE Z 424 " --> pdb=" O   SER Z 420 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 460 through 488
    Processing helix  chain 'Z' and resid 489 through 498
      removed outlier: 4.305A  pdb=" N   LEU Z 493 " --> pdb=" O   PRO Z 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 35
      removed outlier: 4.140A  pdb=" N   SER B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ALA B  24 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU B  25 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 100
      removed outlier: 3.746A  pdb=" N   ASP B  70 " --> pdb=" O   ARG B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 130
    Processing helix  chain 'B' and resid 138 through 140
      No H-bonds generated for 'chain 'B' and resid 138 through 140'
    Processing helix  chain 'B' and resid 165 through 169
      removed outlier: 3.686A  pdb=" N   GLY B 169 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 458
      removed outlier: 3.660A  pdb=" N   PHE B 424 " --> pdb=" O   SER B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 488
    Processing helix  chain 'B' and resid 490 through 498
      removed outlier: 3.604A  pdb=" N   SER B 494 " --> pdb=" O   GLN B 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 35
      removed outlier: 4.123A  pdb=" N   SER C  23 " --> pdb=" O   ASN C  19 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ALA C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 100
      removed outlier: 3.739A  pdb=" N   ASP C  70 " --> pdb=" O   ARG C  66 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY C  71 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 130
    Processing helix  chain 'C' and resid 138 through 140
      No H-bonds generated for 'chain 'C' and resid 138 through 140'
    Processing helix  chain 'C' and resid 165 through 169
      removed outlier: 3.684A  pdb=" N   GLY C 169 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 458
      removed outlier: 3.675A  pdb=" N   PHE C 424 " --> pdb=" O   SER C 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 488
    Processing helix  chain 'C' and resid 490 through 498
      removed outlier: 3.646A  pdb=" N   SER C 494 " --> pdb=" O   GLN C 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 35
      removed outlier: 3.542A  pdb=" N   LEU D  12 " --> pdb=" O   ASN D   8 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER D  23 " --> pdb=" O   ASN D  19 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 100
      removed outlier: 3.837A  pdb=" N   ASP D  70 " --> pdb=" O   ARG D  66 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE D  72 " --> pdb=" O   ALA D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 130
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.615A  pdb=" N   ALA D 139 " --> pdb=" O   ASN D 136 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LYS D 140 " --> pdb=" O   VAL D 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 136 through 140'
    Processing helix  chain 'D' and resid 165 through 169
      removed outlier: 3.733A  pdb=" N   GLY D 169 " --> pdb=" O   LYS D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 409 through 458
      removed outlier: 3.564A  pdb=" N   PHE D 424 " --> pdb=" O   SER D 420 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN D 444 " --> pdb=" O   THR D 440 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP D 458 " --> pdb=" O   SER D 454 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 460 through 488
    Processing helix  chain 'D' and resid 490 through 498
      removed outlier: 3.590A  pdb=" N   SER D 494 " --> pdb=" O   GLN D 490 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 8 through 35
      removed outlier: 4.181A  pdb=" N   SER E  23 " --> pdb=" O   ASN E  19 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ALA E  24 " --> pdb=" O   LYS E  20 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU E  25 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 100
      removed outlier: 3.835A  pdb=" N   ASP E  70 " --> pdb=" O   ARG E  66 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY E  71 " --> pdb=" O   ASN E  67 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE E  72 " --> pdb=" O   ALA E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 130
    Processing helix  chain 'E' and resid 136 through 140
      removed outlier: 4.180A  pdb=" N   LYS E 140 " --> pdb=" O   VAL E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 165 through 169
      removed outlier: 3.698A  pdb=" N   GLY E 169 " --> pdb=" O   LYS E 166 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 409 through 458
      removed outlier: 4.110A  pdb=" N   LYS E 423 " --> pdb=" O   ALA E 419 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE E 424 " --> pdb=" O   SER E 420 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 460 through 488
    Processing helix  chain 'E' and resid 490 through 498
      removed outlier: 3.796A  pdb=" N   SER E 494 " --> pdb=" O   GLN E 490 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 8 through 35
      removed outlier: 3.931A  pdb=" N   SER F  23 " --> pdb=" O   ASN F  19 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ALA F  24 " --> pdb=" O   LYS F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 100
      removed outlier: 3.583A  pdb=" N   ASP F  70 " --> pdb=" O   ARG F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 105 through 130
    Processing helix  chain 'F' and resid 136 through 140
      removed outlier: 3.541A  pdb=" N   ALA F 139 " --> pdb=" O   ASN F 136 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LYS F 140 " --> pdb=" O   VAL F 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 136 through 140'
    Processing helix  chain 'F' and resid 165 through 169
      removed outlier: 3.731A  pdb=" N   GLY F 169 " --> pdb=" O   LYS F 166 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 409 through 458
      removed outlier: 3.531A  pdb=" N   PHE F 424 " --> pdb=" O   SER F 420 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE F 456 " --> pdb=" O   ALA F 452 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 460 through 488
    Processing helix  chain 'F' and resid 490 through 498
      removed outlier: 3.636A  pdb=" N   SER F 494 " --> pdb=" O   GLN F 490 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 35
      removed outlier: 4.209A  pdb=" N   SER G  23 " --> pdb=" O   ASN G  19 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   ALA G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU G  25 " --> pdb=" O   ASN G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 100
      removed outlier: 3.839A  pdb=" N   ASP G  70 " --> pdb=" O   ARG G  66 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY G  71 " --> pdb=" O   ASN G  67 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE G  72 " --> pdb=" O   ALA G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 105 through 130
    Processing helix  chain 'G' and resid 136 through 140
      removed outlier: 3.570A  pdb=" N   ALA G 139 " --> pdb=" O   ASN G 136 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS G 140 " --> pdb=" O   VAL G 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 136 through 140'
    Processing helix  chain 'G' and resid 165 through 169
      removed outlier: 3.622A  pdb=" N   GLY G 169 " --> pdb=" O   LYS G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 409 through 458
      removed outlier: 3.569A  pdb=" N   PHE G 424 " --> pdb=" O   SER G 420 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 460 through 488
    Processing helix  chain 'G' and resid 490 through 498
      removed outlier: 3.709A  pdb=" N   SER G 494 " --> pdb=" O   GLN G 490 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 8 through 35
      removed outlier: 4.167A  pdb=" N   SER H  23 " --> pdb=" O   ASN H  19 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   ALA H  24 " --> pdb=" O   LYS H  20 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU H  25 " --> pdb=" O   ASN H  21 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 45 through 100
      removed outlier: 3.713A  pdb=" N   ASP H  70 " --> pdb=" O   ARG H  66 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY H  71 " --> pdb=" O   ASN H  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 130
    Processing helix  chain 'H' and resid 136 through 140
      removed outlier: 3.572A  pdb=" N   ALA H 139 " --> pdb=" O   ASN H 136 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS H 140 " --> pdb=" O   VAL H 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 136 through 140'
    Processing helix  chain 'H' and resid 165 through 169
      removed outlier: 3.698A  pdb=" N   GLY H 169 " --> pdb=" O   LYS H 166 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 409 through 458
      removed outlier: 3.730A  pdb=" N   ALA H 413 " --> pdb=" O   ASP H 409 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE H 424 " --> pdb=" O   SER H 420 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 460 through 488
    Processing helix  chain 'H' and resid 490 through 498
      removed outlier: 3.692A  pdb=" N   SER H 494 " --> pdb=" O   GLN H 490 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 8 through 35
      removed outlier: 4.191A  pdb=" N   SER I  23 " --> pdb=" O   ASN I  19 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ALA I  24 " --> pdb=" O   LYS I  20 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU I  25 " --> pdb=" O   ASN I  21 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 45 through 100
      removed outlier: 3.887A  pdb=" N   ASP I  70 " --> pdb=" O   ARG I  66 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY I  71 " --> pdb=" O   ASN I  67 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE I  72 " --> pdb=" O   ALA I  68 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 105 through 130
    Processing helix  chain 'I' and resid 136 through 140
      removed outlier: 3.513A  pdb=" N   ALA I 139 " --> pdb=" O   ASN I 136 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LYS I 140 " --> pdb=" O   VAL I 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 136 through 140'
    Processing helix  chain 'I' and resid 165 through 169
      removed outlier: 3.710A  pdb=" N   GLY I 169 " --> pdb=" O   LYS I 166 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 409 through 458
      removed outlier: 3.517A  pdb=" N   ALA I 413 " --> pdb=" O   ASP I 409 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE I 424 " --> pdb=" O   SER I 420 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 460 through 488
    Processing helix  chain 'I' and resid 490 through 498
      removed outlier: 3.733A  pdb=" N   SER I 494 " --> pdb=" O   GLN I 490 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 8 through 35
      removed outlier: 3.620A  pdb=" N   LEU J  12 " --> pdb=" O   ASN J   8 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   SER J  23 " --> pdb=" O   ASN J  19 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ALA J  24 " --> pdb=" O   LYS J  20 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU J  25 " --> pdb=" O   ASN J  21 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 45 through 100
      removed outlier: 3.754A  pdb=" N   ASP J  70 " --> pdb=" O   ARG J  66 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLY J  71 " --> pdb=" O   ASN J  67 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE J  72 " --> pdb=" O   ALA J  68 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 105 through 130
    Processing helix  chain 'J' and resid 136 through 140
      removed outlier: 4.300A  pdb=" N   LYS J 140 " --> pdb=" O   VAL J 137 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 165 through 169
      removed outlier: 3.533A  pdb=" N   GLY J 169 " --> pdb=" O   LYS J 166 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 409 through 458
      removed outlier: 3.508A  pdb=" N   ALA J 413 " --> pdb=" O   ASP J 409 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE J 424 " --> pdb=" O   SER J 420 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE J 456 " --> pdb=" O   ALA J 452 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP J 458 " --> pdb=" O   SER J 454 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 460 through 488
    Processing helix  chain 'J' and resid 490 through 498
    Processing helix  chain 'K' and resid 8 through 35
      removed outlier: 4.195A  pdb=" N   SER K  23 " --> pdb=" O   ASN K  19 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   ALA K  24 " --> pdb=" O   LYS K  20 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU K  25 " --> pdb=" O   ASN K  21 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 45 through 100
      removed outlier: 3.680A  pdb=" N   ASP K  70 " --> pdb=" O   ARG K  66 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY K  71 " --> pdb=" O   ASN K  67 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 105 through 130
    Processing helix  chain 'K' and resid 136 through 140
      removed outlier: 4.329A  pdb=" N   LYS K 140 " --> pdb=" O   VAL K 137 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 165 through 169
      removed outlier: 3.671A  pdb=" N   GLY K 169 " --> pdb=" O   LYS K 166 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 409 through 458
      removed outlier: 3.564A  pdb=" N   ALA K 413 " --> pdb=" O   ASP K 409 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS K 423 " --> pdb=" O   ALA K 419 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE K 424 " --> pdb=" O   SER K 420 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE K 456 " --> pdb=" O   ALA K 452 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASP K 458 " --> pdb=" O   SER K 454 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 460 through 488
    Processing helix  chain 'K' and resid 490 through 498
      removed outlier: 3.752A  pdb=" N   SER K 494 " --> pdb=" O   GLN K 490 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 8 through 35
      removed outlier: 3.571A  pdb=" N   LEU L  12 " --> pdb=" O   ASN L   8 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER L  23 " --> pdb=" O   ASN L  19 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA L  24 " --> pdb=" O   LYS L  20 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 45 through 100
      removed outlier: 3.601A  pdb=" N   ASP L  70 " --> pdb=" O   ARG L  66 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 105 through 130
    Processing helix  chain 'L' and resid 136 through 140
      removed outlier: 4.168A  pdb=" N   LYS L 140 " --> pdb=" O   VAL L 137 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 165 through 169
      removed outlier: 3.765A  pdb=" N   GLY L 169 " --> pdb=" O   LYS L 166 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 409 through 458
      removed outlier: 3.741A  pdb=" N   PHE L 424 " --> pdb=" O   SER L 420 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 460 through 488
    Processing helix  chain 'L' and resid 490 through 498
      removed outlier: 3.784A  pdb=" N   SER L 494 " --> pdb=" O   GLN L 490 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 8 through 35
      removed outlier: 3.668A  pdb=" N   LEU M  12 " --> pdb=" O   ASN M   8 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER M  23 " --> pdb=" O   ASN M  19 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA M  24 " --> pdb=" O   LYS M  20 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 45 through 100
      removed outlier: 3.928A  pdb=" N   ASP M  70 " --> pdb=" O   ARG M  66 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLY M  71 " --> pdb=" O   ASN M  67 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE M  72 " --> pdb=" O   ALA M  68 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 130
    Processing helix  chain 'M' and resid 138 through 140
      No H-bonds generated for 'chain 'M' and resid 138 through 140'
    Processing helix  chain 'M' and resid 165 through 169
      removed outlier: 3.646A  pdb=" N   GLY M 169 " --> pdb=" O   LYS M 166 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 409 through 458
      removed outlier: 3.989A  pdb=" N   LYS M 423 " --> pdb=" O   ALA M 419 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE M 424 " --> pdb=" O   SER M 420 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 460 through 488
    Processing helix  chain 'M' and resid 490 through 498
      removed outlier: 3.694A  pdb=" N   SER M 494 " --> pdb=" O   GLN M 490 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 8 through 35
      removed outlier: 4.142A  pdb=" N   SER N  23 " --> pdb=" O   ASN N  19 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA N  24 " --> pdb=" O   LYS N  20 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 45 through 100
      removed outlier: 3.681A  pdb=" N   ASP N  70 " --> pdb=" O   ARG N  66 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 105 through 130
    Processing helix  chain 'N' and resid 136 through 140
      removed outlier: 3.641A  pdb=" N   ALA N 139 " --> pdb=" O   ASN N 136 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS N 140 " --> pdb=" O   VAL N 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 136 through 140'
    Processing helix  chain 'N' and resid 165 through 169
      removed outlier: 3.662A  pdb=" N   GLY N 169 " --> pdb=" O   LYS N 166 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 409 through 458
      removed outlier: 3.590A  pdb=" N   PHE N 424 " --> pdb=" O   SER N 420 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 460 through 488
    Processing helix  chain 'N' and resid 490 through 498
      removed outlier: 3.672A  pdb=" N   SER N 494 " --> pdb=" O   GLN N 490 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 8 through 35
      removed outlier: 3.896A  pdb=" N   SER O  23 " --> pdb=" O   ASN O  19 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA O  24 " --> pdb=" O   LYS O  20 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 45 through 100
      removed outlier: 3.624A  pdb=" N   ASP O  70 " --> pdb=" O   ARG O  66 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 105 through 130
    Processing helix  chain 'O' and resid 136 through 140
      removed outlier: 3.586A  pdb=" N   ALA O 139 " --> pdb=" O   ASN O 136 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS O 140 " --> pdb=" O   VAL O 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 136 through 140'
    Processing helix  chain 'O' and resid 165 through 169
      removed outlier: 3.779A  pdb=" N   GLY O 169 " --> pdb=" O   LYS O 166 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 409 through 458
      removed outlier: 3.534A  pdb=" N   ALA O 413 " --> pdb=" O   ASP O 409 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE O 424 " --> pdb=" O   SER O 420 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 460 through 488
    Processing helix  chain 'O' and resid 490 through 498
      removed outlier: 3.665A  pdb=" N   SER O 494 " --> pdb=" O   GLN O 490 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 8 through 35
      removed outlier: 3.512A  pdb=" N   LEU P  12 " --> pdb=" O   ASN P   8 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   SER P  23 " --> pdb=" O   ASN P  19 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ALA P  24 " --> pdb=" O   LYS P  20 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 45 through 100
      removed outlier: 3.580A  pdb=" N   ASP P  70 " --> pdb=" O   ARG P  66 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 105 through 130
    Processing helix  chain 'P' and resid 138 through 140
      No H-bonds generated for 'chain 'P' and resid 138 through 140'
    Processing helix  chain 'P' and resid 165 through 169
      removed outlier: 3.716A  pdb=" N   GLY P 169 " --> pdb=" O   LYS P 166 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 409 through 458
      removed outlier: 3.650A  pdb=" N   PHE P 424 " --> pdb=" O   SER P 420 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE P 456 " --> pdb=" O   ALA P 452 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 460 through 488
    Processing helix  chain 'P' and resid 490 through 498
      removed outlier: 3.594A  pdb=" N   SER P 494 " --> pdb=" O   GLN P 490 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 8 through 35
      removed outlier: 4.144A  pdb=" N   SER Q  23 " --> pdb=" O   ASN Q  19 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ALA Q  24 " --> pdb=" O   LYS Q  20 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU Q  25 " --> pdb=" O   ASN Q  21 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 45 through 100
      removed outlier: 3.675A  pdb=" N   ASP Q  70 " --> pdb=" O   ARG Q  66 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 105 through 130
    Processing helix  chain 'Q' and resid 136 through 140
      removed outlier: 3.522A  pdb=" N   ALA Q 139 " --> pdb=" O   ASN Q 136 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   LYS Q 140 " --> pdb=" O   VAL Q 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 136 through 140'
    Processing helix  chain 'Q' and resid 165 through 169
      removed outlier: 3.727A  pdb=" N   GLY Q 169 " --> pdb=" O   LYS Q 166 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 409 through 458
      removed outlier: 3.740A  pdb=" N   PHE Q 424 " --> pdb=" O   SER Q 420 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 460 through 488
    Processing helix  chain 'Q' and resid 490 through 498
      removed outlier: 3.779A  pdb=" N   SER Q 494 " --> pdb=" O   GLN Q 490 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 8 through 35
      removed outlier: 4.144A  pdb=" N   SER R  23 " --> pdb=" O   ASN R  19 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ALA R  24 " --> pdb=" O   LYS R  20 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU R  25 " --> pdb=" O   ASN R  21 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 45 through 100
      removed outlier: 3.652A  pdb=" N   ASP R  70 " --> pdb=" O   ARG R  66 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 130
      removed outlier: 3.505A  pdb=" N   THR R 130 " --> pdb=" O   VAL R 126 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 140
      No H-bonds generated for 'chain 'R' and resid 138 through 140'
    Processing helix  chain 'R' and resid 165 through 169
      removed outlier: 3.733A  pdb=" N   GLY R 169 " --> pdb=" O   LYS R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 409 through 458
      removed outlier: 3.589A  pdb=" N   ALA R 413 " --> pdb=" O   ASP R 409 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE R 424 " --> pdb=" O   SER R 420 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 460 through 488
    Processing helix  chain 'R' and resid 490 through 498
    Processing helix  chain 'S' and resid 8 through 35
      removed outlier: 4.106A  pdb=" N   SER S  23 " --> pdb=" O   ASN S  19 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ALA S  24 " --> pdb=" O   LYS S  20 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU S  25 " --> pdb=" O   ASN S  21 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 45 through 100
      removed outlier: 3.694A  pdb=" N   ASP S  70 " --> pdb=" O   ARG S  66 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 105 through 130
    Processing helix  chain 'S' and resid 136 through 140
      removed outlier: 4.379A  pdb=" N   LYS S 140 " --> pdb=" O   VAL S 137 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 165 through 169
      removed outlier: 3.565A  pdb=" N   GLY S 169 " --> pdb=" O   LYS S 166 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 409 through 458
      removed outlier: 3.874A  pdb=" N   ALA S 413 " --> pdb=" O   ASP S 409 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE S 424 " --> pdb=" O   SER S 420 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 460 through 488
    Processing helix  chain 'S' and resid 490 through 498
      removed outlier: 3.686A  pdb=" N   SER S 494 " --> pdb=" O   GLN S 490 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 8 through 35
      removed outlier: 4.171A  pdb=" N   SER T  23 " --> pdb=" O   ASN T  19 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ALA T  24 " --> pdb=" O   LYS T  20 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU T  25 " --> pdb=" O   ASN T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 45 through 100
      removed outlier: 3.685A  pdb=" N   ASP T  70 " --> pdb=" O   ARG T  66 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY T  71 " --> pdb=" O   ASN T  67 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 105 through 130
    Processing helix  chain 'T' and resid 136 through 140
      removed outlier: 3.582A  pdb=" N   ALA T 139 " --> pdb=" O   ASN T 136 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS T 140 " --> pdb=" O   VAL T 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'T' and resid 136 through 140'
    Processing helix  chain 'T' and resid 165 through 169
      removed outlier: 3.777A  pdb=" N   GLY T 169 " --> pdb=" O   LYS T 166 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 409 through 458
      removed outlier: 3.763A  pdb=" N   LYS T 423 " --> pdb=" O   ALA T 419 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE T 424 " --> pdb=" O   SER T 420 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 460 through 488
    Processing helix  chain 'T' and resid 490 through 498
    Processing helix  chain 'U' and resid 8 through 35
      removed outlier: 3.884A  pdb=" N   SER U  23 " --> pdb=" O   ASN U  19 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ALA U  24 " --> pdb=" O   LYS U  20 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 45 through 100
      removed outlier: 3.658A  pdb=" N   ASP U  70 " --> pdb=" O   ARG U  66 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 105 through 130
    Processing helix  chain 'U' and resid 136 through 140
      removed outlier: 3.531A  pdb=" N   ALA U 139 " --> pdb=" O   ASN U 136 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LYS U 140 " --> pdb=" O   VAL U 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'U' and resid 136 through 140'
    Processing helix  chain 'U' and resid 165 through 169
      removed outlier: 3.665A  pdb=" N   GLY U 169 " --> pdb=" O   LYS U 166 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 409 through 458
      removed outlier: 3.868A  pdb=" N   PHE U 424 " --> pdb=" O   SER U 420 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE U 456 " --> pdb=" O   ALA U 452 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 460 through 488
    Processing helix  chain 'U' and resid 490 through 498
      removed outlier: 3.707A  pdb=" N   SER U 494 " --> pdb=" O   GLN U 490 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 8 through 35
      removed outlier: 4.148A  pdb=" N   SER V  23 " --> pdb=" O   ASN V  19 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   ALA V  24 " --> pdb=" O   LYS V  20 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 45 through 100
      removed outlier: 3.639A  pdb=" N   ASP V  70 " --> pdb=" O   ARG V  66 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 105 through 130
      removed outlier: 3.635A  pdb=" N   THR V 130 " --> pdb=" O   VAL V 126 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 136 through 140
      removed outlier: 3.511A  pdb=" N   ALA V 139 " --> pdb=" O   ASN V 136 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   LYS V 140 " --> pdb=" O   VAL V 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'V' and resid 136 through 140'
    Processing helix  chain 'V' and resid 165 through 169
      removed outlier: 3.723A  pdb=" N   GLY V 169 " --> pdb=" O   LYS V 166 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 409 through 458
      removed outlier: 3.733A  pdb=" N   PHE V 424 " --> pdb=" O   SER V 420 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 460 through 488
    Processing helix  chain 'V' and resid 490 through 498
      removed outlier: 3.715A  pdb=" N   SER V 494 " --> pdb=" O   GLN V 490 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 8 through 35
      removed outlier: 4.199A  pdb=" N   SER W  23 " --> pdb=" O   ASN W  19 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ALA W  24 " --> pdb=" O   LYS W  20 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU W  25 " --> pdb=" O   ASN W  21 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 45 through 100
      removed outlier: 3.874A  pdb=" N   ASP W  70 " --> pdb=" O   ARG W  66 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY W  71 " --> pdb=" O   ASN W  67 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE W  72 " --> pdb=" O   ALA W  68 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 105 through 130
    Processing helix  chain 'W' and resid 136 through 140
      removed outlier: 4.189A  pdb=" N   LYS W 140 " --> pdb=" O   VAL W 137 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 165 through 169
      removed outlier: 3.609A  pdb=" N   GLY W 169 " --> pdb=" O   LYS W 166 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 409 through 458
      removed outlier: 3.505A  pdb=" N   LYS W 423 " --> pdb=" O   ALA W 419 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE W 424 " --> pdb=" O   SER W 420 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP W 458 " --> pdb=" O   SER W 454 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 460 through 488
    Processing helix  chain 'W' and resid 489 through 498
      removed outlier: 4.239A  pdb=" N   LEU W 493 " --> pdb=" O   PRO W 489 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 8 through 35
      removed outlier: 4.203A  pdb=" N   SER X  23 " --> pdb=" O   ASN X  19 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA X  24 " --> pdb=" O   LYS X  20 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU X  25 " --> pdb=" O   ASN X  21 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 45 through 100
      removed outlier: 3.636A  pdb=" N   ASP X  70 " --> pdb=" O   ARG X  66 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY X  71 " --> pdb=" O   ASN X  67 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 105 through 130
      removed outlier: 3.504A  pdb=" N   THR X 130 " --> pdb=" O   VAL X 126 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 136 through 140
      removed outlier: 3.510A  pdb=" N   ALA X 139 " --> pdb=" O   ASN X 136 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LYS X 140 " --> pdb=" O   VAL X 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 136 through 140'
    Processing helix  chain 'X' and resid 165 through 169
      removed outlier: 3.659A  pdb=" N   GLY X 169 " --> pdb=" O   LYS X 166 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 409 through 458
      removed outlier: 3.723A  pdb=" N   PHE X 424 " --> pdb=" O   SER X 420 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 460 through 488
    Processing helix  chain 'X' and resid 490 through 498
      removed outlier: 3.749A  pdb=" N   SER X 494 " --> pdb=" O   GLN X 490 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 8 through 35
      removed outlier: 3.990A  pdb=" N   SER Y  23 " --> pdb=" O   ASN Y  19 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ALA Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 45 through 100
      removed outlier: 3.522A  pdb=" N   ASP Y  70 " --> pdb=" O   ARG Y  66 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 105 through 130
    Processing helix  chain 'Y' and resid 136 through 140
      removed outlier: 4.272A  pdb=" N   LYS Y 140 " --> pdb=" O   VAL Y 137 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 165 through 169
      removed outlier: 3.780A  pdb=" N   GLY Y 169 " --> pdb=" O   LYS Y 166 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 409 through 458
      removed outlier: 3.596A  pdb=" N   ALA Y 413 " --> pdb=" O   ASP Y 409 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE Y 424 " --> pdb=" O   SER Y 420 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP Y 458 " --> pdb=" O   SER Y 454 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 460 through 488
    Processing helix  chain 'Y' and resid 490 through 498
      removed outlier: 3.611A  pdb=" N   SER Y 494 " --> pdb=" O   GLN Y 490 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 8 through 35
      removed outlier: 4.193A  pdb=" N   SER a  23 " --> pdb=" O   ASN a  19 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA a  24 " --> pdb=" O   LYS a  20 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU a  25 " --> pdb=" O   ASN a  21 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 45 through 100
      removed outlier: 3.656A  pdb=" N   ASP a  70 " --> pdb=" O   ARG a  66 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 105 through 130
    Processing helix  chain 'a' and resid 136 through 140
      removed outlier: 3.620A  pdb=" N   ALA a 139 " --> pdb=" O   ASN a 136 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LYS a 140 " --> pdb=" O   VAL a 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 136 through 140'
    Processing helix  chain 'a' and resid 165 through 169
      removed outlier: 3.721A  pdb=" N   GLY a 169 " --> pdb=" O   LYS a 166 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 409 through 458
      removed outlier: 3.596A  pdb=" N   LYS a 423 " --> pdb=" O   ALA a 419 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE a 424 " --> pdb=" O   SER a 420 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE a 456 " --> pdb=" O   ALA a 452 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 460 through 488
    Processing helix  chain 'a' and resid 490 through 498
      removed outlier: 3.568A  pdb=" N   SER a 494 " --> pdb=" O   GLN a 490 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 8 through 35
      removed outlier: 3.553A  pdb=" N   LEU b  12 " --> pdb=" O   ASN b   8 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   SER b  23 " --> pdb=" O   ASN b  19 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ALA b  24 " --> pdb=" O   LYS b  20 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 45 through 100
      removed outlier: 3.787A  pdb=" N   ASP b  70 " --> pdb=" O   ARG b  66 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY b  71 " --> pdb=" O   ASN b  67 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE b  72 " --> pdb=" O   ALA b  68 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 105 through 130
      removed outlier: 3.542A  pdb=" N   THR b 130 " --> pdb=" O   VAL b 126 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 136 through 140
      removed outlier: 4.254A  pdb=" N   LYS b 140 " --> pdb=" O   VAL b 137 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 165 through 169
      removed outlier: 3.694A  pdb=" N   GLY b 169 " --> pdb=" O   LYS b 166 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 409 through 458
      removed outlier: 4.074A  pdb=" N   LYS b 423 " --> pdb=" O   ALA b 419 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE b 424 " --> pdb=" O   SER b 420 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 460 through 488
    Processing helix  chain 'b' and resid 490 through 498
      removed outlier: 3.844A  pdb=" N   SER b 494 " --> pdb=" O   GLN b 490 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 8 through 35
      removed outlier: 3.946A  pdb=" N   SER c  23 " --> pdb=" O   ASN c  19 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ALA c  24 " --> pdb=" O   LYS c  20 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 45 through 100
      removed outlier: 3.776A  pdb=" N   ASP c  70 " --> pdb=" O   ARG c  66 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY c  71 " --> pdb=" O   ASN c  67 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE c  72 " --> pdb=" O   ALA c  68 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 105 through 130
    Processing helix  chain 'c' and resid 136 through 140
      removed outlier: 4.232A  pdb=" N   LYS c 140 " --> pdb=" O   VAL c 137 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 164 through 169
      removed outlier: 3.677A  pdb=" N   GLY c 169 " --> pdb=" O   LYS c 166 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 409 through 458
      removed outlier: 3.726A  pdb=" N   PHE c 424 " --> pdb=" O   SER c 420 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 460 through 488
    Processing helix  chain 'c' and resid 490 through 498
      removed outlier: 3.830A  pdb=" N   SER c 494 " --> pdb=" O   GLN c 490 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 8 through 35
      removed outlier: 3.569A  pdb=" N   LEU d  12 " --> pdb=" O   ASN d   8 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER d  23 " --> pdb=" O   ASN d  19 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ALA d  24 " --> pdb=" O   LYS d  20 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 45 through 100
      removed outlier: 3.652A  pdb=" N   ASP d  70 " --> pdb=" O   ARG d  66 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 105 through 130
    Processing helix  chain 'd' and resid 136 through 140
      removed outlier: 4.317A  pdb=" N   LYS d 140 " --> pdb=" O   VAL d 137 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 165 through 169
      removed outlier: 3.695A  pdb=" N   GLY d 169 " --> pdb=" O   LYS d 166 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 409 through 458
      removed outlier: 3.897A  pdb=" N   LYS d 423 " --> pdb=" O   ALA d 419 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   PHE d 424 " --> pdb=" O   SER d 420 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE d 456 " --> pdb=" O   ALA d 452 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 460 through 488
    Processing helix  chain 'd' and resid 490 through 498
      removed outlier: 3.848A  pdb=" N   SER d 494 " --> pdb=" O   GLN d 490 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 8 through 35
      removed outlier: 4.115A  pdb=" N   SER e  23 " --> pdb=" O   ASN e  19 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ALA e  24 " --> pdb=" O   LYS e  20 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 45 through 100
      removed outlier: 3.911A  pdb=" N   ASP e  70 " --> pdb=" O   ARG e  66 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLY e  71 " --> pdb=" O   ASN e  67 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE e  72 " --> pdb=" O   ALA e  68 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 105 through 130
    Processing helix  chain 'e' and resid 138 through 140
      No H-bonds generated for 'chain 'e' and resid 138 through 140'
    Processing helix  chain 'e' and resid 165 through 169
      removed outlier: 3.650A  pdb=" N   GLY e 169 " --> pdb=" O   LYS e 166 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 409 through 458
      removed outlier: 3.577A  pdb=" N   ALA e 413 " --> pdb=" O   ASP e 409 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE e 424 " --> pdb=" O   SER e 420 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 460 through 488
    Processing helix  chain 'e' and resid 490 through 498
      removed outlier: 3.634A  pdb=" N   SER e 494 " --> pdb=" O   GLN e 490 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 8 through 35
      removed outlier: 4.020A  pdb=" N   SER 2  23 " --> pdb=" O   ASN 2  19 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ALA 2  24 " --> pdb=" O   LYS 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 46 through 100
      removed outlier: 3.984A  pdb=" N   GLU 2  84 " --> pdb=" O   GLY 2  80 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 105 through 130
      removed outlier: 3.582A  pdb=" N   SER 2 110 " --> pdb=" O   GLU 2 106 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 138 through 140
      No H-bonds generated for 'chain '2' and resid 138 through 140'
    Processing helix  chain '2' and resid 165 through 169
      removed outlier: 3.721A  pdb=" N   GLY 2 169 " --> pdb=" O   LYS 2 166 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 409 through 458
      removed outlier: 3.539A  pdb=" N   LYS 2 423 " --> pdb=" O   ALA 2 419 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   PHE 2 424 " --> pdb=" O   SER 2 420 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE 2 456 " --> pdb=" O   ALA 2 452 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 460 through 486
      removed outlier: 3.656A  pdb=" N   SER 2 466 " --> pdb=" O   ALA 2 462 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 489 through 498
      removed outlier: 4.015A  pdb=" N   LEU 2 493 " --> pdb=" O   PRO 2 489 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER 2 494 " --> pdb=" O   GLN 2 490 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 8 through 35
      removed outlier: 3.529A  pdb=" N   LEU f  12 " --> pdb=" O   ASN f   8 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER f  23 " --> pdb=" O   ASN f  19 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA f  24 " --> pdb=" O   LYS f  20 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 45 through 100
      removed outlier: 3.822A  pdb=" N   ASP f  70 " --> pdb=" O   ARG f  66 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY f  71 " --> pdb=" O   ASN f  67 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE f  72 " --> pdb=" O   ALA f  68 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 105 through 130
    Processing helix  chain 'f' and resid 136 through 140
      removed outlier: 3.521A  pdb=" N   ALA f 139 " --> pdb=" O   ASN f 136 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS f 140 " --> pdb=" O   VAL f 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'f' and resid 136 through 140'
    Processing helix  chain 'f' and resid 165 through 169
      removed outlier: 3.740A  pdb=" N   GLY f 169 " --> pdb=" O   LYS f 166 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 409 through 458
      removed outlier: 3.672A  pdb=" N   PHE f 424 " --> pdb=" O   SER f 420 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN f 444 " --> pdb=" O   THR f 440 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASP f 458 " --> pdb=" O   SER f 454 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 460 through 488
    Processing helix  chain 'f' and resid 490 through 498
      removed outlier: 3.676A  pdb=" N   SER f 494 " --> pdb=" O   GLN f 490 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 8 through 35
      removed outlier: 3.915A  pdb=" N   SER g  23 " --> pdb=" O   ASN g  19 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA g  24 " --> pdb=" O   LYS g  20 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 45 through 100
      removed outlier: 4.056A  pdb=" N   ASP g  70 " --> pdb=" O   ARG g  66 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY g  71 " --> pdb=" O   ASN g  67 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE g  72 " --> pdb=" O   ALA g  68 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 105 through 130
    Processing helix  chain 'g' and resid 138 through 140
      No H-bonds generated for 'chain 'g' and resid 138 through 140'
    Processing helix  chain 'g' and resid 165 through 169
      removed outlier: 3.538A  pdb=" N   LEU g 168 " --> pdb=" O   ALA g 165 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY g 169 " --> pdb=" O   LYS g 166 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'g' and resid 165 through 169'
    Processing helix  chain 'g' and resid 409 through 458
      removed outlier: 3.515A  pdb=" N   ALA g 413 " --> pdb=" O   ASP g 409 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE g 424 " --> pdb=" O   SER g 420 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE g 456 " --> pdb=" O   ALA g 452 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 460 through 488
    Processing helix  chain 'g' and resid 490 through 498
      removed outlier: 3.868A  pdb=" N   SER g 494 " --> pdb=" O   GLN g 490 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 8 through 35
      removed outlier: 3.942A  pdb=" N   SER h  23 " --> pdb=" O   ASN h  19 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA h  24 " --> pdb=" O   LYS h  20 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 45 through 100
      removed outlier: 3.802A  pdb=" N   ASP h  70 " --> pdb=" O   ARG h  66 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLY h  71 " --> pdb=" O   ASN h  67 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 105 through 130
    Processing helix  chain 'h' and resid 136 through 140
      removed outlier: 4.214A  pdb=" N   LYS h 140 " --> pdb=" O   VAL h 137 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 165 through 169
      removed outlier: 3.540A  pdb=" N   GLY h 169 " --> pdb=" O   LYS h 166 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 409 through 458
      removed outlier: 3.668A  pdb=" N   PHE h 424 " --> pdb=" O   SER h 420 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE h 456 " --> pdb=" O   ALA h 452 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP h 458 " --> pdb=" O   SER h 454 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 460 through 488
    Processing helix  chain 'h' and resid 490 through 498
      removed outlier: 3.822A  pdb=" N   SER h 494 " --> pdb=" O   GLN h 490 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 8 through 35
      removed outlier: 4.106A  pdb=" N   SER i  23 " --> pdb=" O   ASN i  19 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ALA i  24 " --> pdb=" O   LYS i  20 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU i  25 " --> pdb=" O   ASN i  21 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 45 through 100
      removed outlier: 3.690A  pdb=" N   ASP i  70 " --> pdb=" O   ARG i  66 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 105 through 130
    Processing helix  chain 'i' and resid 138 through 140
      No H-bonds generated for 'chain 'i' and resid 138 through 140'
    Processing helix  chain 'i' and resid 165 through 169
      removed outlier: 3.672A  pdb=" N   GLY i 169 " --> pdb=" O   LYS i 166 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 409 through 458
      removed outlier: 3.526A  pdb=" N   ALA i 413 " --> pdb=" O   ASP i 409 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE i 424 " --> pdb=" O   SER i 420 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 460 through 488
    Processing helix  chain 'i' and resid 490 through 498
      removed outlier: 3.825A  pdb=" N   SER i 494 " --> pdb=" O   GLN i 490 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 8 through 35
      removed outlier: 4.113A  pdb=" N   SER j  23 " --> pdb=" O   ASN j  19 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ALA j  24 " --> pdb=" O   LYS j  20 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 45 through 100
      removed outlier: 3.907A  pdb=" N   ASP j  70 " --> pdb=" O   ARG j  66 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY j  71 " --> pdb=" O   ASN j  67 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE j  72 " --> pdb=" O   ALA j  68 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 105 through 130
    Processing helix  chain 'j' and resid 136 through 140
      removed outlier: 3.573A  pdb=" N   ALA j 139 " --> pdb=" O   ASN j 136 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LYS j 140 " --> pdb=" O   VAL j 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'j' and resid 136 through 140'
    Processing helix  chain 'j' and resid 165 through 169
      removed outlier: 3.778A  pdb=" N   GLY j 169 " --> pdb=" O   LYS j 166 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 409 through 458
      removed outlier: 3.721A  pdb=" N   PHE j 424 " --> pdb=" O   SER j 420 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 460 through 488
    Processing helix  chain 'j' and resid 490 through 498
      removed outlier: 3.819A  pdb=" N   SER j 494 " --> pdb=" O   GLN j 490 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 8 through 35
      removed outlier: 3.649A  pdb=" N   LEU k  12 " --> pdb=" O   ASN k   8 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER k  23 " --> pdb=" O   ASN k  19 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ALA k  24 " --> pdb=" O   LYS k  20 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 45 through 100
      removed outlier: 3.722A  pdb=" N   ASP k  70 " --> pdb=" O   ARG k  66 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 105 through 130
    Processing helix  chain 'k' and resid 136 through 140
      removed outlier: 3.617A  pdb=" N   ALA k 139 " --> pdb=" O   ASN k 136 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LYS k 140 " --> pdb=" O   VAL k 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'k' and resid 136 through 140'
    Processing helix  chain 'k' and resid 165 through 169
      removed outlier: 3.775A  pdb=" N   GLY k 169 " --> pdb=" O   LYS k 166 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 409 through 458
      removed outlier: 3.556A  pdb=" N   ALA k 413 " --> pdb=" O   ASP k 409 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS k 423 " --> pdb=" O   ALA k 419 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE k 424 " --> pdb=" O   SER k 420 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 460 through 488
    Processing helix  chain 'k' and resid 490 through 498
      removed outlier: 3.655A  pdb=" N   SER k 494 " --> pdb=" O   GLN k 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 35
      removed outlier: 4.159A  pdb=" N   SER A  23 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A  25 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 100
      removed outlier: 3.821A  pdb=" N   ASP A  70 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY A  71 " --> pdb=" O   ASN A  67 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 130
    Processing helix  chain 'A' and resid 138 through 140
      No H-bonds generated for 'chain 'A' and resid 138 through 140'
    Processing helix  chain 'A' and resid 165 through 169
      removed outlier: 3.805A  pdb=" N   GLY A 169 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 458
      removed outlier: 3.532A  pdb=" N   LYS A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 488
    Processing helix  chain 'A' and resid 490 through 498
      removed outlier: 3.557A  pdb=" N   SER A 494 " --> pdb=" O   GLN A 490 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 8 through 35
      removed outlier: 3.633A  pdb=" N   LEU l  12 " --> pdb=" O   ASN l   8 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER l  23 " --> pdb=" O   ASN l  19 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ALA l  24 " --> pdb=" O   LYS l  20 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 45 through 100
      removed outlier: 3.648A  pdb=" N   ASP l  70 " --> pdb=" O   ARG l  66 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 105 through 130
    Processing helix  chain 'l' and resid 136 through 140
      removed outlier: 3.597A  pdb=" N   ALA l 139 " --> pdb=" O   ASN l 136 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LYS l 140 " --> pdb=" O   VAL l 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'l' and resid 136 through 140'
    Processing helix  chain 'l' and resid 165 through 169
      removed outlier: 3.703A  pdb=" N   GLY l 169 " --> pdb=" O   LYS l 166 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 409 through 458
      removed outlier: 3.555A  pdb=" N   LYS l 423 " --> pdb=" O   ALA l 419 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE l 424 " --> pdb=" O   SER l 420 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 460 through 488
    Processing helix  chain 'l' and resid 490 through 498
      removed outlier: 3.710A  pdb=" N   SER l 494 " --> pdb=" O   GLN l 490 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 8 through 35
      removed outlier: 3.632A  pdb=" N   LEU m  12 " --> pdb=" O   ASN m   8 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER m  23 " --> pdb=" O   ASN m  19 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ALA m  24 " --> pdb=" O   LYS m  20 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 45 through 100
      removed outlier: 3.786A  pdb=" N   ASP m  70 " --> pdb=" O   ARG m  66 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY m  71 " --> pdb=" O   ASN m  67 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 105 through 130
    Processing helix  chain 'm' and resid 136 through 140
      removed outlier: 3.579A  pdb=" N   ALA m 139 " --> pdb=" O   ASN m 136 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS m 140 " --> pdb=" O   VAL m 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 136 through 140'
    Processing helix  chain 'm' and resid 165 through 169
      removed outlier: 3.510A  pdb=" N   LEU m 168 " --> pdb=" O   ALA m 165 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY m 169 " --> pdb=" O   LYS m 166 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 165 through 169'
    Processing helix  chain 'm' and resid 409 through 458
      removed outlier: 3.520A  pdb=" N   ALA m 413 " --> pdb=" O   ASP m 409 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS m 423 " --> pdb=" O   ALA m 419 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE m 424 " --> pdb=" O   SER m 420 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE m 456 " --> pdb=" O   ALA m 452 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 460 through 488
    Processing helix  chain 'm' and resid 490 through 498
      removed outlier: 3.993A  pdb=" N   SER m 494 " --> pdb=" O   GLN m 490 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 8 through 35
      removed outlier: 4.389A  pdb=" N   SER n  23 " --> pdb=" O   ASN n  19 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ALA n  24 " --> pdb=" O   LYS n  20 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU n  25 " --> pdb=" O   ASN n  21 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 45 through 100
      removed outlier: 3.601A  pdb=" N   ASP n  70 " --> pdb=" O   ARG n  66 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 105 through 130
    Processing helix  chain 'n' and resid 136 through 140
      removed outlier: 3.529A  pdb=" N   ALA n 139 " --> pdb=" O   ASN n 136 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS n 140 " --> pdb=" O   VAL n 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'n' and resid 136 through 140'
    Processing helix  chain 'n' and resid 165 through 169
      removed outlier: 3.578A  pdb=" N   GLY n 169 " --> pdb=" O   LYS n 166 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 409 through 458
      removed outlier: 3.639A  pdb=" N   PHE n 424 " --> pdb=" O   SER n 420 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 460 through 488
    Processing helix  chain 'n' and resid 490 through 498
      removed outlier: 3.815A  pdb=" N   SER n 494 " --> pdb=" O   GLN n 490 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 8 through 35
      removed outlier: 4.184A  pdb=" N   SER o  23 " --> pdb=" O   ASN o  19 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ALA o  24 " --> pdb=" O   LYS o  20 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU o  25 " --> pdb=" O   ASN o  21 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 45 through 100
      removed outlier: 3.820A  pdb=" N   ASP o  70 " --> pdb=" O   ARG o  66 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY o  71 " --> pdb=" O   ASN o  67 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE o  72 " --> pdb=" O   ALA o  68 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 105 through 130
    Processing helix  chain 'o' and resid 136 through 140
      removed outlier: 3.583A  pdb=" N   ALA o 139 " --> pdb=" O   ASN o 136 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   LYS o 140 " --> pdb=" O   VAL o 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'o' and resid 136 through 140'
    Processing helix  chain 'o' and resid 165 through 169
      removed outlier: 3.650A  pdb=" N   GLY o 169 " --> pdb=" O   LYS o 166 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 409 through 458
      removed outlier: 3.595A  pdb=" N   ALA o 413 " --> pdb=" O   ASP o 409 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE o 424 " --> pdb=" O   SER o 420 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 460 through 488
    Processing helix  chain 'o' and resid 490 through 498
      removed outlier: 3.704A  pdb=" N   SER o 494 " --> pdb=" O   GLN o 490 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 8 through 35
      removed outlier: 4.111A  pdb=" N   SER p  23 " --> pdb=" O   ASN p  19 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ALA p  24 " --> pdb=" O   LYS p  20 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 45 through 100
      removed outlier: 3.602A  pdb=" N   ASP p  70 " --> pdb=" O   ARG p  66 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 105 through 130
    Processing helix  chain 'p' and resid 138 through 140
      No H-bonds generated for 'chain 'p' and resid 138 through 140'
    Processing helix  chain 'p' and resid 165 through 169
      removed outlier: 3.734A  pdb=" N   GLY p 169 " --> pdb=" O   LYS p 166 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 409 through 458
      removed outlier: 3.509A  pdb=" N   ALA p 413 " --> pdb=" O   ASP p 409 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE p 424 " --> pdb=" O   SER p 420 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 460 through 488
    Processing helix  chain 'p' and resid 490 through 498
      removed outlier: 3.734A  pdb=" N   SER p 494 " --> pdb=" O   GLN p 490 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 8 through 35
      removed outlier: 4.105A  pdb=" N   SER q  23 " --> pdb=" O   ASN q  19 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ALA q  24 " --> pdb=" O   LYS q  20 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 45 through 100
      removed outlier: 3.580A  pdb=" N   ASP q  70 " --> pdb=" O   ARG q  66 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 105 through 130
    Processing helix  chain 'q' and resid 136 through 140
      removed outlier: 4.191A  pdb=" N   LYS q 140 " --> pdb=" O   VAL q 137 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 165 through 169
      removed outlier: 3.724A  pdb=" N   GLY q 169 " --> pdb=" O   LYS q 166 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 409 through 458
      removed outlier: 3.655A  pdb=" N   PHE q 424 " --> pdb=" O   SER q 420 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE q 456 " --> pdb=" O   ALA q 452 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP q 458 " --> pdb=" O   SER q 454 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 460 through 488
    Processing helix  chain 'q' and resid 490 through 498
      removed outlier: 3.757A  pdb=" N   SER q 494 " --> pdb=" O   GLN q 490 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 8 through 35
      removed outlier: 4.202A  pdb=" N   SER r  23 " --> pdb=" O   ASN r  19 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ALA r  24 " --> pdb=" O   LYS r  20 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU r  25 " --> pdb=" O   ASN r  21 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 45 through 100
      removed outlier: 3.685A  pdb=" N   ASP r  70 " --> pdb=" O   ARG r  66 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 105 through 130
    Processing helix  chain 'r' and resid 138 through 140
      No H-bonds generated for 'chain 'r' and resid 138 through 140'
    Processing helix  chain 'r' and resid 165 through 169
      removed outlier: 3.768A  pdb=" N   GLY r 169 " --> pdb=" O   LYS r 166 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 409 through 458
      removed outlier: 3.578A  pdb=" N   ALA r 413 " --> pdb=" O   ASP r 409 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   PHE r 424 " --> pdb=" O   SER r 420 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 460 through 488
    Processing helix  chain 'r' and resid 490 through 498
      removed outlier: 3.570A  pdb=" N   SER r 494 " --> pdb=" O   GLN r 490 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 8 through 35
      removed outlier: 4.105A  pdb=" N   SER s  23 " --> pdb=" O   ASN s  19 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   ALA s  24 " --> pdb=" O   LYS s  20 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 45 through 100
      removed outlier: 3.906A  pdb=" N   ASP s  70 " --> pdb=" O   ARG s  66 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY s  71 " --> pdb=" O   ASN s  67 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE s  72 " --> pdb=" O   ALA s  68 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 105 through 130
    Processing helix  chain 's' and resid 138 through 140
      No H-bonds generated for 'chain 's' and resid 138 through 140'
    Processing helix  chain 's' and resid 165 through 169
      removed outlier: 3.689A  pdb=" N   GLY s 169 " --> pdb=" O   LYS s 166 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 409 through 458
      removed outlier: 3.516A  pdb=" N   ALA s 413 " --> pdb=" O   ASP s 409 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE s 424 " --> pdb=" O   SER s 420 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 460 through 488
    Processing helix  chain 's' and resid 490 through 498
      removed outlier: 3.648A  pdb=" N   SER s 494 " --> pdb=" O   GLN s 490 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 8 through 35
      removed outlier: 4.113A  pdb=" N   SER t  23 " --> pdb=" O   ASN t  19 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ALA t  24 " --> pdb=" O   LYS t  20 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU t  25 " --> pdb=" O   ASN t  21 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 45 through 100
      removed outlier: 3.616A  pdb=" N   ASP t  70 " --> pdb=" O   ARG t  66 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 105 through 130
    Processing helix  chain 't' and resid 138 through 140
      No H-bonds generated for 'chain 't' and resid 138 through 140'
    Processing helix  chain 't' and resid 165 through 169
      removed outlier: 3.735A  pdb=" N   GLY t 169 " --> pdb=" O   LYS t 166 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 409 through 458
      removed outlier: 3.507A  pdb=" N   ALA t 413 " --> pdb=" O   ASP t 409 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE t 424 " --> pdb=" O   SER t 420 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE t 456 " --> pdb=" O   ALA t 452 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 460 through 488
    Processing helix  chain 't' and resid 490 through 498
      removed outlier: 3.771A  pdb=" N   SER t 494 " --> pdb=" O   GLN t 490 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 8 through 35
      removed outlier: 3.742A  pdb=" N   LEU u  12 " --> pdb=" O   ASN u   8 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER u  23 " --> pdb=" O   ASN u  19 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA u  24 " --> pdb=" O   LYS u  20 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 45 through 100
      removed outlier: 3.793A  pdb=" N   ASP u  70 " --> pdb=" O   ARG u  66 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY u  71 " --> pdb=" O   ASN u  67 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE u  72 " --> pdb=" O   ALA u  68 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 105 through 130
    Processing helix  chain 'u' and resid 136 through 140
      removed outlier: 3.572A  pdb=" N   ALA u 139 " --> pdb=" O   ASN u 136 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LYS u 140 " --> pdb=" O   VAL u 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'u' and resid 136 through 140'
    Processing helix  chain 'u' and resid 165 through 169
      removed outlier: 3.678A  pdb=" N   GLY u 169 " --> pdb=" O   LYS u 166 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 409 through 458
      removed outlier: 3.770A  pdb=" N   PHE u 424 " --> pdb=" O   SER u 420 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE u 456 " --> pdb=" O   ALA u 452 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 460 through 488
    Processing helix  chain 'u' and resid 490 through 498
      removed outlier: 3.603A  pdb=" N   SER u 494 " --> pdb=" O   GLN u 490 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 8 through 35
      removed outlier: 3.837A  pdb=" N   SER v  23 " --> pdb=" O   ASN v  19 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA v  24 " --> pdb=" O   LYS v  20 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 45 through 100
      removed outlier: 3.677A  pdb=" N   ASP v  70 " --> pdb=" O   ARG v  66 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 105 through 130
    Processing helix  chain 'v' and resid 138 through 140
      No H-bonds generated for 'chain 'v' and resid 138 through 140'
    Processing helix  chain 'v' and resid 165 through 169
      removed outlier: 3.811A  pdb=" N   GLY v 169 " --> pdb=" O   LYS v 166 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 409 through 458
      removed outlier: 3.597A  pdb=" N   ALA v 413 " --> pdb=" O   ASP v 409 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE v 424 " --> pdb=" O   SER v 420 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 460 through 488
    Processing helix  chain 'v' and resid 490 through 498
      removed outlier: 3.680A  pdb=" N   SER v 494 " --> pdb=" O   GLN v 490 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 8 through 35
      removed outlier: 3.510A  pdb=" N   LEU w  12 " --> pdb=" O   ASN w   8 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   SER w  23 " --> pdb=" O   ASN w  19 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ALA w  24 " --> pdb=" O   LYS w  20 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 45 through 100
      removed outlier: 3.769A  pdb=" N   ASP w  70 " --> pdb=" O   ARG w  66 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY w  71 " --> pdb=" O   ASN w  67 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE w  72 " --> pdb=" O   ALA w  68 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 105 through 130
    Processing helix  chain 'w' and resid 136 through 140
      removed outlier: 3.565A  pdb=" N   ALA w 139 " --> pdb=" O   ASN w 136 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS w 140 " --> pdb=" O   VAL w 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'w' and resid 136 through 140'
    Processing helix  chain 'w' and resid 165 through 169
      removed outlier: 3.724A  pdb=" N   GLY w 169 " --> pdb=" O   LYS w 166 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 409 through 458
      removed outlier: 3.747A  pdb=" N   PHE w 424 " --> pdb=" O   SER w 420 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 460 through 488
    Processing helix  chain 'w' and resid 490 through 498
      removed outlier: 3.832A  pdb=" N   SER w 494 " --> pdb=" O   GLN w 490 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 8 through 35
      removed outlier: 3.859A  pdb=" N   SER x  23 " --> pdb=" O   ASN x  19 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA x  24 " --> pdb=" O   LYS x  20 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 45 through 100
      removed outlier: 3.697A  pdb=" N   ASP x  70 " --> pdb=" O   ARG x  66 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY x  71 " --> pdb=" O   ASN x  67 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE x  72 " --> pdb=" O   ALA x  68 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 105 through 130
    Processing helix  chain 'x' and resid 136 through 140
      removed outlier: 4.295A  pdb=" N   LYS x 140 " --> pdb=" O   VAL x 137 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 165 through 169
      removed outlier: 3.556A  pdb=" N   GLY x 169 " --> pdb=" O   LYS x 166 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 409 through 458
      removed outlier: 3.549A  pdb=" N   ALA x 413 " --> pdb=" O   ASP x 409 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE x 424 " --> pdb=" O   SER x 420 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE x 456 " --> pdb=" O   ALA x 452 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 460 through 488
    Processing helix  chain 'x' and resid 490 through 498
      removed outlier: 3.767A  pdb=" N   SER x 494 " --> pdb=" O   GLN x 490 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 8 through 35
      removed outlier: 3.900A  pdb=" N   SER y  23 " --> pdb=" O   ASN y  19 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA y  24 " --> pdb=" O   LYS y  20 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 45 through 100
      removed outlier: 3.627A  pdb=" N   ASP y  70 " --> pdb=" O   ARG y  66 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 105 through 130
    Processing helix  chain 'y' and resid 138 through 140
      No H-bonds generated for 'chain 'y' and resid 138 through 140'
    Processing helix  chain 'y' and resid 165 through 169
      removed outlier: 3.734A  pdb=" N   GLY y 169 " --> pdb=" O   LYS y 166 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 409 through 458
      removed outlier: 3.576A  pdb=" N   ALA y 413 " --> pdb=" O   ASP y 409 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS y 423 " --> pdb=" O   ALA y 419 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE y 424 " --> pdb=" O   SER y 420 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 460 through 488
    Processing helix  chain 'y' and resid 490 through 498
      removed outlier: 3.727A  pdb=" N   SER y 494 " --> pdb=" O   GLN y 490 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 8 through 35
      removed outlier: 4.119A  pdb=" N   SER z  23 " --> pdb=" O   ASN z  19 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ALA z  24 " --> pdb=" O   LYS z  20 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU z  25 " --> pdb=" O   ASN z  21 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 45 through 100
      removed outlier: 3.673A  pdb=" N   ASP z  70 " --> pdb=" O   ARG z  66 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 105 through 130
    Processing helix  chain 'z' and resid 136 through 140
      removed outlier: 4.302A  pdb=" N   LYS z 140 " --> pdb=" O   VAL z 137 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 165 through 169
      removed outlier: 3.627A  pdb=" N   GLY z 169 " --> pdb=" O   LYS z 166 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 409 through 458
      removed outlier: 3.718A  pdb=" N   ALA z 413 " --> pdb=" O   ASP z 409 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   PHE z 424 " --> pdb=" O   SER z 420 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 460 through 488
    Processing helix  chain 'z' and resid 490 through 498
      removed outlier: 3.678A  pdb=" N   SER z 494 " --> pdb=" O   GLN z 490 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 8 through 35
      removed outlier: 3.914A  pdb=" N   SER 0  23 " --> pdb=" O   ASN 0  19 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ALA 0  24 " --> pdb=" O   LYS 0  20 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 45 through 100
      removed outlier: 3.640A  pdb=" N   ASP 0  70 " --> pdb=" O   ARG 0  66 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 105 through 130
    Processing helix  chain '0' and resid 138 through 140
      No H-bonds generated for 'chain '0' and resid 138 through 140'
    Processing helix  chain '0' and resid 165 through 169
      removed outlier: 3.656A  pdb=" N   GLY 0 169 " --> pdb=" O   LYS 0 166 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 409 through 458
      removed outlier: 3.589A  pdb=" N   PHE 0 424 " --> pdb=" O   SER 0 420 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE 0 456 " --> pdb=" O   ALA 0 452 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 460 through 488
    Processing helix  chain '0' and resid 490 through 498
      removed outlier: 3.829A  pdb=" N   SER 0 494 " --> pdb=" O   GLN 0 490 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 8 through 35
      removed outlier: 3.690A  pdb=" N   LEU 1  12 " --> pdb=" O   ASN 1   8 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   SER 1  23 " --> pdb=" O   ASN 1  19 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ALA 1  24 " --> pdb=" O   LYS 1  20 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 45 through 100
      removed outlier: 3.779A  pdb=" N   ASP 1  70 " --> pdb=" O   ARG 1  66 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY 1  71 " --> pdb=" O   ASN 1  67 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE 1  72 " --> pdb=" O   ALA 1  68 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 105 through 130
    Processing helix  chain '1' and resid 136 through 140
      removed outlier: 4.186A  pdb=" N   LYS 1 140 " --> pdb=" O   VAL 1 137 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 165 through 169
      removed outlier: 3.683A  pdb=" N   GLY 1 169 " --> pdb=" O   LYS 1 166 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 409 through 458
      removed outlier: 3.687A  pdb=" N   PHE 1 424 " --> pdb=" O   SER 1 420 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE 1 456 " --> pdb=" O   ALA 1 452 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 460 through 488
    Processing helix  chain '1' and resid 490 through 498
      removed outlier: 3.822A  pdb=" N   SER 1 494 " --> pdb=" O   GLN 1 490 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Z' and resid 142 through 147
    Processing sheet with id=AA2, first strand: chain 'B' and resid 131 through 132
    Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 147
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
    Processing sheet with id=AA5, first strand: chain 'C' and resid 142 through 147
    Processing sheet with id=AA6, first strand: chain 'D' and resid 142 through 147
    Processing sheet with id=AA7, first strand: chain 'E' and resid 142 through 147
    Processing sheet with id=AA8, first strand: chain 'F' and resid 142 through 147
    Processing sheet with id=AA9, first strand: chain 'G' and resid 142 through 147
    Processing sheet with id=AB1, first strand: chain 'H' and resid 142 through 147
    Processing sheet with id=AB2, first strand: chain 'I' and resid 142 through 147
    Processing sheet with id=AB3, first strand: chain 'J' and resid 142 through 147
    Processing sheet with id=AB4, first strand: chain 'K' and resid 142 through 147
    Processing sheet with id=AB5, first strand: chain 'L' and resid 142 through 147
    Processing sheet with id=AB6, first strand: chain 'M' and resid 131 through 132
    Processing sheet with id=AB7, first strand: chain 'M' and resid 142 through 147
    Processing sheet with id=AB8, first strand: chain 'N' and resid 142 through 147
    Processing sheet with id=AB9, first strand: chain 'O' and resid 142 through 147
    Processing sheet with id=AC1, first strand: chain 'P' and resid 131 through 132
    Processing sheet with id=AC2, first strand: chain 'P' and resid 142 through 147
    Processing sheet with id=AC3, first strand: chain 'Q' and resid 142 through 147
    Processing sheet with id=AC4, first strand: chain 'R' and resid 131 through 132
    Processing sheet with id=AC5, first strand: chain 'R' and resid 142 through 147
    Processing sheet with id=AC6, first strand: chain 'S' and resid 142 through 147
    Processing sheet with id=AC7, first strand: chain 'T' and resid 142 through 147
    Processing sheet with id=AC8, first strand: chain 'U' and resid 142 through 147
    Processing sheet with id=AC9, first strand: chain 'V' and resid 142 through 147
    Processing sheet with id=AD1, first strand: chain 'W' and resid 142 through 147
    Processing sheet with id=AD2, first strand: chain 'X' and resid 142 through 147
    Processing sheet with id=AD3, first strand: chain 'Y' and resid 142 through 147
    Processing sheet with id=AD4, first strand: chain 'a' and resid 142 through 147
    Processing sheet with id=AD5, first strand: chain 'b' and resid 142 through 147
    Processing sheet with id=AD6, first strand: chain 'c' and resid 142 through 147
    Processing sheet with id=AD7, first strand: chain 'd' and resid 142 through 147
    Processing sheet with id=AD8, first strand: chain 'e' and resid 131 through 132
    Processing sheet with id=AD9, first strand: chain 'e' and resid 142 through 147
    Processing sheet with id=AE1, first strand: chain '2' and resid 131 through 132
    Processing sheet with id=AE2, first strand: chain '2' and resid 142 through 147
    Processing sheet with id=AE3, first strand: chain 'f' and resid 142 through 147
    Processing sheet with id=AE4, first strand: chain 'g' and resid 131 through 132
    Processing sheet with id=AE5, first strand: chain 'g' and resid 142 through 147
    Processing sheet with id=AE6, first strand: chain 'h' and resid 142 through 147
    Processing sheet with id=AE7, first strand: chain 'i' and resid 131 through 132
    Processing sheet with id=AE8, first strand: chain 'i' and resid 142 through 147
    Processing sheet with id=AE9, first strand: chain 'j' and resid 142 through 147
    Processing sheet with id=AF1, first strand: chain 'k' and resid 142 through 147
    Processing sheet with id=AF2, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AF3, first strand: chain 'A' and resid 142 through 147
    Processing sheet with id=AF4, first strand: chain 'l' and resid 142 through 147
    Processing sheet with id=AF5, first strand: chain 'm' and resid 142 through 147
    Processing sheet with id=AF6, first strand: chain 'n' and resid 142 through 147
    Processing sheet with id=AF7, first strand: chain 'o' and resid 142 through 147
    Processing sheet with id=AF8, first strand: chain 'p' and resid 131 through 132
    Processing sheet with id=AF9, first strand: chain 'p' and resid 142 through 147
    Processing sheet with id=AG1, first strand: chain 'q' and resid 142 through 147
    Processing sheet with id=AG2, first strand: chain 'r' and resid 131 through 132
    Processing sheet with id=AG3, first strand: chain 'r' and resid 142 through 147
    Processing sheet with id=AG4, first strand: chain 's' and resid 131 through 132
    Processing sheet with id=AG5, first strand: chain 's' and resid 142 through 147
    Processing sheet with id=AG6, first strand: chain 't' and resid 131 through 132
    Processing sheet with id=AG7, first strand: chain 't' and resid 142 through 147
    Processing sheet with id=AG8, first strand: chain 'u' and resid 142 through 147
    Processing sheet with id=AG9, first strand: chain 'v' and resid 131 through 132
    Processing sheet with id=AH1, first strand: chain 'v' and resid 142 through 147
    Processing sheet with id=AH2, first strand: chain 'w' and resid 142 through 147
    Processing sheet with id=AH3, first strand: chain 'x' and resid 142 through 147
    Processing sheet with id=AH4, first strand: chain 'y' and resid 131 through 132
    Processing sheet with id=AH5, first strand: chain 'y' and resid 142 through 147
    Processing sheet with id=AH6, first strand: chain 'z' and resid 142 through 147
    Processing sheet with id=AH7, first strand: chain '0' and resid 131 through 132
    Processing sheet with id=AH8, first strand: chain '0' and resid 142 through 147
    Processing sheet with id=AH9, first strand: chain '1' and resid 142 through 147

    9576 hydrogen bonds defined for protein.
    28305 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: 37.70

  Time building geometry restraints manager: 35.75 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: 37767
        1.34 -     1.45: 7365
        1.45 -     1.57: 64483
        1.57 -     1.69: 0
        1.69 -     1.80: 220
  Bond restraints: 109835
  Sorted by residual:
  bond pdb=" N   VAL R   4 "
       pdb=" CA  VAL R   4 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.11e-02 8.12e+03 1.14e+01
  bond pdb=" C   VAL R 488 "
       pdb=" N   PRO R 489 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.08e-02 8.57e+03 4.46e+00
  bond pdb=" CA  VAL o 488 "
       pdb=" CB  VAL o 488 "
    ideal  model  delta    sigma   weight residual
    1.534  1.548 -0.013 6.80e-03 2.16e+04 3.80e+00
  bond pdb=" CA  VAL a 488 "
       pdb=" CB  VAL a 488 "
    ideal  model  delta    sigma   weight residual
    1.537  1.546 -0.009 5.00e-03 4.00e+04 3.07e+00
  bond pdb=" C   VAL t 488 "
       pdb=" N   PRO t 489 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.016 9.80e-03 1.04e+04 2.78e+00
  ... (remaining 109830 not shown)

  Histogram of bond angle deviations from ideal:
       98.88 -   104.98: 484
      104.98 -   111.08: 44836
      111.08 -   117.19: 37569
      117.19 -   123.29: 63784
      123.29 -   129.40: 1882
  Bond angle restraints: 148555
  Sorted by residual:
  angle pdb=" C   ASP q  44 "
        pdb=" N   ALA q  45 "
        pdb=" CA  ALA q  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.40   -7.86 1.91e+00 2.74e-01 1.69e+01
  angle pdb=" C   ASP u  44 "
        pdb=" N   ALA u  45 "
        pdb=" CA  ALA u  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" C   ASP F  44 "
        pdb=" N   ALA F  45 "
        pdb=" CA  ALA F  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" C   ASP w  44 "
        pdb=" N   ALA w  45 "
        pdb=" CA  ALA w  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.03   -7.49 1.91e+00 2.74e-01 1.54e+01
  angle pdb=" CA  VAL R   4 "
        pdb=" C   VAL R   4 "
        pdb=" O   VAL R   4 "
      ideal   model   delta    sigma   weight residual
     121.67  117.55    4.12 1.05e+00 9.07e-01 1.54e+01
  ... (remaining 148550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 62111
       17.98 -    35.96: 5262
       35.96 -    53.94: 898
       53.94 -    71.91: 342
       71.91 -    89.89: 137
  Dihedral angle restraints: 68750
    sinusoidal: 26400
      harmonic: 42350
  Sorted by residual:
  dihedral pdb=" CA  GLN q 154 "
           pdb=" C   GLN q 154 "
           pdb=" N   THR q 155 "
           pdb=" CA  THR q 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.11  -20.89     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  GLN u   3 "
           pdb=" C   GLN u   3 "
           pdb=" N   VAL u   4 "
           pdb=" CA  VAL u   4 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  GLN i 154 "
           pdb=" C   GLN i 154 "
           pdb=" N   THR i 155 "
           pdb=" CA  THR i 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.57  -20.43     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 68747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 13026
       0.030 -    0.059: 3699
       0.059 -    0.089: 1182
       0.089 -    0.119: 331
       0.119 -    0.148: 132
  Chirality restraints: 18370
  Sorted by residual:
  chirality pdb=" CA  VAL R   4 "
            pdb=" N   VAL R   4 "
            pdb=" C   VAL R   4 "
            pdb=" CB  VAL R   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  PRO Z 489 "
            pdb=" N   PRO Z 489 "
            pdb=" C   PRO Z 489 "
            pdb=" CB  PRO Z 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CB  THR d 130 "
            pdb=" CA  THR d 130 "
            pdb=" OG1 THR d 130 "
            pdb=" CG2 THR d 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 18367 not shown)

  Planarity restraints: 20020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL o 488 "    0.075 5.00e-02 4.00e+02   1.12e-01 2.02e+01
        pdb=" N   PRO o 489 "   -0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO o 489 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO o 489 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE 0  54 "    0.019 2.00e-02 2.50e+03   2.07e-02 7.47e+00
        pdb=" CG  PHE 0  54 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE 0  54 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE 0  54 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE 0  54 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE 0  54 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE 0  54 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL 0 488 "   -0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO 0 489 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO 0 489 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO 0 489 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 20017 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 1710
        2.65 -     3.22: 112344
        3.22 -     3.78: 178364
        3.78 -     4.34: 222572
        4.34 -     4.90: 384922
  Nonbonded interactions: 899912
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN e 154 "
            pdb=" OE1 GLN 2 129 "
     model   vdw
     2.093 2.520
  nonbonded pdb=" OE2 GLU f  94 "
            pdb=" NZ  LYS w  59 "
     model   vdw
     2.116 2.520
  nonbonded pdb=" OE1 GLN C 129 "
            pdb=" NE2 GLN v 154 "
     model   vdw
     2.140 2.520
  nonbonded pdb=" OE1 GLN Z 129 "
            pdb=" NE2 GLN A 154 "
     model   vdw
     2.150 2.520
  nonbonded pdb=" OG  SER m 437 "
            pdb=" OE2 GLU p  84 "
     model   vdw
     2.154 2.440
  ... (remaining 899907 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 '0'
  selection = chain '1'
  selection = chain '2'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
  selection = chain 'Z'
  selection = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
  selection = chain 'e'
  selection = chain 'f'
  selection = chain 'g'
  selection = chain 'h'
  selection = chain 'i'
  selection = chain 'j'
  selection = chain 'k'
  selection = chain 'l'
  selection = chain 'm'
  selection = chain 'n'
  selection = chain 'o'
  selection = chain 'p'
  selection = chain 'q'
  selection = chain 'r'
  selection = chain 's'
  selection = chain 't'
  selection = chain 'u'
  selection = chain 'v'
  selection = chain 'w'
  selection = chain 'x'
  selection = chain 'y'
  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:             4.690
  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:             0.070
  Extract box with map and model:          28.760
  Check model and map are aligned:         1.170
  Set scattering table:                    0.690
  Process input model:                     201.560
  Find NCS groups from input model:        5.180
  Set up NCS constraints:                  1.220
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  245.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
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      :  0.003   0.044 109835  Z= 0.175
  Angle     :  0.503   8.234 148555  Z= 0.293
  Chirality :  0.034   0.148  18370
  Planarity :  0.004   0.112  20020
  Dihedral  : 14.839  89.892  41030
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.38 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.68 (0.07), residues: 14465
  helix:  3.84 (0.05), residues: 10890
  sheet: -1.26 (0.15), residues: 990
  loop : -2.83 (0.10), residues: 2585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.048   0.002   PHE 0  54 
   TYR   0.012   0.002   TYR 1 461 
   ARG   0.014   0.001   ARG N 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1586 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 1578
  time to evaluate  : 9.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 1
  residues processed: 1582
  average time/residue: 0.8329
  time to fit residues: 2367.3982
Evaluate side-chains
  1069 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 1068
  time to evaluate  : 9.216 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.7105
  time to fit residues: 13.5985
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 1207 optimal weight:    7.9990
   chunk 1083 optimal weight:    0.3980
   chunk 601 optimal weight:    8.9990
   chunk 370 optimal weight:    5.9990
   chunk 731 optimal weight:    9.9990
   chunk 579 optimal weight:    0.9980
   chunk 1120 optimal weight:    4.9990
   chunk 433 optimal weight:    0.0050
   chunk 681 optimal weight:   10.0000
   chunk 834 optimal weight:    0.9980
   chunk 1298 optimal weight:    2.9990
   overall best weight:    1.0796

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

Flipped N/Q/H residues before XYZ refinement:
** Z  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  63 GLN
Z  67 ASN
B  22 GLN
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 GLN
B  67 ASN
B 475 GLN
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 131 GLN
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 486 ASN
G  22 GLN
G 475 GLN
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 432 GLN
I   6 ASN
I  39 ASN
** I  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  17 ASN
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  63 GLN
L  67 ASN
L 475 GLN
M  39 ASN
N  16 ASN
N  17 ASN
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  22 GLN
** Q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  63 GLN
R  67 ASN
R  76 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 GLN
R 147 GLN
S   6 ASN
S 497 GLN
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  63 GLN
U  67 ASN
** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  22 GLN
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 475 GLN
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  22 GLN
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  21 ASN
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
2 472 GLN
f  52 ASN
g  15 GLN
g  39 ASN
** g  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
i  76 GLN
** i  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
k  76 GLN
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  86 ASN
l  15 GLN
l  22 GLN
** m  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n  21 ASN
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
n  63 GLN
n  67 ASN
** n  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p   3 GLN
p 491 GLN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  21 ASN
** s 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
u 487 GLN
v  63 GLN
v  67 ASN
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x  15 GLN
y  76 GLN
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  63 GLN
z  67 ASN
z 491 GLN
0  63 GLN
0 441 ASN
** 1  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 60

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040 109835  Z= 0.175
  Angle     :  0.471   7.768 148555  Z= 0.268
  Chirality :  0.034   0.195  18370
  Planarity :  0.003   0.073  20020
  Dihedral  :  4.387  78.974  15290
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.00 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.14 (0.07), residues: 14465
  helix:  4.14 (0.05), residues: 10835
  sheet: -0.85 (0.16), residues: 990
  loop : -2.49 (0.10), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.048   0.002   PHE Y  54 
   TYR   0.015   0.002   TYR J 461 
   ARG   0.006   0.001   ARG g 119 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1296 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 92
    poor density    : 1204
  time to evaluate  : 8.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 92
  outliers final: 56
  residues processed: 1253
  average time/residue: 0.8515
  time to fit residues: 1921.1345
Evaluate side-chains
  1125 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 1069
  time to evaluate  : 9.332 
Switching outliers to nearest non-outliers
  outliers start: 56
  outliers final: 0
  residues processed: 56
  average time/residue: 0.7731
  time to fit residues: 94.4719
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 721 optimal weight:    0.9980
   chunk 403 optimal weight:    9.9990
   chunk 1080 optimal weight:    8.9990
   chunk 884 optimal weight:    8.9990
   chunk 358 optimal weight:   10.0000
   chunk 1300 optimal weight:    0.1980
   chunk 1405 optimal weight:    5.9990
   chunk 1158 optimal weight:    2.9990
   chunk 1290 optimal weight:    7.9990
   chunk 443 optimal weight:    4.9990
   chunk 1043 optimal weight:    9.9990
   overall best weight:    3.0386

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

Flipped N/Q/H residues before XYZ refinement:
Z  52 ASN
B  22 GLN
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 ASN
B  76 GLN
B 475 GLN
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 147 GLN
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 147 GLN
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 147 GLN
** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  22 GLN
** K  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  22 GLN
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 475 GLN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 151 ASN
** M 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  17 ASN
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  63 GLN
P  67 ASN
Q  63 GLN
Q  67 ASN
Q 497 GLN
R  67 ASN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 487 GLN
S   8 ASN
S  22 GLN
S 147 GLN
S 475 GLN
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  22 GLN
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 147 GLN
W 154 GLN
W 475 GLN
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  63 GLN
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 147 GLN
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 147 GLN
b 154 GLN
c   3 GLN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 453 GLN
** e  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
e 147 GLN
2  21 ASN
** 2  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
2 147 GLN
** 2 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 432 GLN
f 487 GLN
g  15 GLN
h  21 ASN
j  76 GLN
k  15 GLN
** k  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  86 ASN
A 147 GLN
l  15 GLN
** l  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
o  86 ASN
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 486 ASN
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
q 490 GLN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r  63 GLN
r  67 ASN
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 147 GLN
** s 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
t 147 GLN
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
w  39 ASN
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
x  15 GLN
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z 147 GLN
0  39 ASN
1  21 ASN
** 1  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 131 GLN
1 476 GLN

Total number of N/Q/H flips: 61

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054 109835  Z= 0.294
  Angle     :  0.508  10.098 148555  Z= 0.286
  Chirality :  0.036   0.214  18370
  Planarity :  0.003   0.057  20020
  Dihedral  :  4.313  79.131  15290
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.46 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.24 (0.07), residues: 14465
  helix:  4.17 (0.05), residues: 10835
  sheet: -0.57 (0.16), residues: 990
  loop : -2.33 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.023   0.002   PHE Y  54 
   TYR   0.019   0.003   TYR O 461 
   ARG   0.009   0.001   ARG e 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1161 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 109
    poor density    : 1052
  time to evaluate  : 9.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 109
  outliers final: 67
  residues processed: 1121
  average time/residue: 0.8522
  time to fit residues: 1726.3230
Evaluate side-chains
  1055 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 988
  time to evaluate  : 10.521
Switching outliers to nearest non-outliers
  outliers start: 67
  outliers final: 0
  residues processed: 67
  average time/residue: 0.7273
  time to fit residues: 105.5334
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 1285 optimal weight:    3.9990
   chunk 978 optimal weight:    6.9990
   chunk 675 optimal weight:    5.9990
   chunk 144 optimal weight:    5.9990
   chunk 620 optimal weight:    1.9990
   chunk 873 optimal weight:    6.9990
   chunk 1305 optimal weight:    6.9990
   chunk 1382 optimal weight:    4.9990
   chunk 682 optimal weight:    4.9990
   chunk 1237 optimal weight:    7.9990
   chunk 372 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
Z  67 ASN
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  67 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  15 GLN
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  63 GLN
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  22 GLN
K  15 GLN
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  67 ASN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 491 GLN
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  17 ASN
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 486 ASN
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 491 GLN
Q 147 GLN
Q 497 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 147 GLN
U  39 ASN
U  67 ASN
U 136 ASN
** V  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  63 GLN
W  67 ASN
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 448 ASN
a  15 GLN
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 131 GLN
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 ASN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c 448 ASN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  19 ASN
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
e  69 ASN
e 497 GLN
f 131 GLN
f 147 GLN
f 432 GLN
g 147 GLN
h  21 ASN
h 147 GLN
i  63 GLN
** k  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 GLN
m  15 GLN
m  69 ASN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
o  86 ASN
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
q  17 ASN
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r  67 ASN
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  16 ASN
** s 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
v  67 ASN
v 147 GLN
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
w 154 GLN
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  15 GLN
z  22 GLN
z  67 ASN
z 475 GLN
0  39 ASN
0 441 ASN
0 448 ASN

Total number of N/Q/H flips: 51

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074 109835  Z= 0.393
  Angle     :  0.556   7.305 148555  Z= 0.313
  Chirality :  0.038   0.187  18370
  Planarity :  0.004   0.048  20020
  Dihedral  :  4.390  80.636  15290
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.51 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.09 (0.07), residues: 14465
  helix:  4.06 (0.05), residues: 10725
  sheet: -0.49 (0.17), residues: 990
  loop : -2.15 (0.11), residues: 2750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.019   0.002   PHE Y  54 
   TYR   0.025   0.003   TYR c 461 
   ARG   0.014   0.001   ARG y 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1124 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 114
    poor density    : 1010
  time to evaluate  : 9.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 114
  outliers final: 60
  residues processed: 1084
  average time/residue: 0.8383
  time to fit residues: 1638.5160
Evaluate side-chains
  1019 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 959
  time to evaluate  : 9.425 
Switching outliers to nearest non-outliers
  outliers start: 60
  outliers final: 0
  residues processed: 60
  average time/residue: 0.7855
  time to fit residues: 102.8753
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 1151 optimal weight:    0.9980
   chunk 784 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 1029 optimal weight:    7.9990
   chunk 570 optimal weight:    4.9990
   chunk 1179 optimal weight:    0.9980
   chunk 955 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 705 optimal weight:    0.9980
   chunk 1240 optimal weight:    0.9980
   chunk 348 optimal weight:    4.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 GLN
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 490 GLN
G  22 GLN
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 475 GLN
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  67 ASN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 154 GLN
** N  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  15 GLN
** Q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 497 GLN
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 136 ASN
** V  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W   3 GLN
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 432 GLN
c  15 GLN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c 154 GLN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 487 GLN
** e  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 487 GLN
h  21 ASN
** j  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  86 ASN
l  39 ASN
m  15 GLN
m  69 ASN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
q 154 GLN
r  15 GLN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r 486 ASN
s 154 GLN
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  67 ASN
** 1  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 154 GLN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053 109835  Z= 0.180
  Angle     :  0.458  14.450 148555  Z= 0.261
  Chirality :  0.034   0.214  18370
  Planarity :  0.003   0.045  20020
  Dihedral  :  4.271  80.880  15290
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 11.48 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.47 (0.07), residues: 14465
  helix:  4.30 (0.05), residues: 10835
  sheet: -0.31 (0.17), residues: 990
  loop : -2.18 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.014   0.001   PHE h 173 
   TYR   0.022   0.002   TYR u 461 
   ARG   0.006   0.000   ARG e 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1176 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 1101
  time to evaluate  : 9.497 
Fit side-chains
   revert: symmetry clash
  outliers start: 75
  outliers final: 32
  residues processed: 1146
  average time/residue: 0.8752
  time to fit residues: 1805.5397
Evaluate side-chains
  1031 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 999
  time to evaluate  : 9.388 
Switching outliers to nearest non-outliers
  outliers start: 32
  outliers final: 0
  residues processed: 32
  average time/residue: 0.7677
  time to fit residues: 59.1057
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 465 optimal weight:    3.9990
   chunk 1244 optimal weight:    5.9990
   chunk 273 optimal weight:   10.0000
   chunk 811 optimal weight:    0.9990
   chunk 341 optimal weight:   10.0000
   chunk 1383 optimal weight:   10.0000
   chunk 1148 optimal weight:    7.9990
   chunk 640 optimal weight:    8.9990
   chunk 115 optimal weight:    8.9990
   chunk 457 optimal weight:   10.0000
   chunk 726 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  15 GLN
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  22 GLN
G 147 GLN
G 475 GLN
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 154 GLN
J  39 ASN
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  63 GLN
L  67 ASN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  16 ASN
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  63 GLN
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  69 ASN
P  15 GLN
Q  15 GLN
Q 497 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 487 GLN
U 136 ASN
** V  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  69 ASN
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c 136 ASN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 453 GLN
d 487 GLN
e  63 GLN
2  21 ASN
f 487 GLN
h  21 ASN
** i 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
j  63 GLN
** k  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
m  69 ASN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 131 GLN
o  39 ASN
** o  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 147 GLN
r   8 ASN
r  15 GLN
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
u 487 GLN
** v 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
w  39 ASN
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
w  69 ASN
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  67 ASN
1  21 ASN
1 453 GLN

Total number of N/Q/H flips: 39

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062 109835  Z= 0.435
  Angle     :  0.592   8.730 148555  Z= 0.330
  Chirality :  0.039   0.212  18370
  Planarity :  0.004   0.043  20020
  Dihedral  :  4.359  80.178  15290
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.91 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.15 (0.07), residues: 14465
  helix:  4.06 (0.05), residues: 10725
  sheet: -0.33 (0.17), residues: 990
  loop : -1.97 (0.11), residues: 2750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.020   0.002   PHE g 424 
   TYR   0.031   0.004   TYR c 461 
   ARG   0.009   0.001   ARG o 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1093 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 119
    poor density    : 974
  time to evaluate  : 9.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 119
  outliers final: 81
  residues processed: 1057
  average time/residue: 0.9745
  time to fit residues: 1862.1305
Evaluate side-chains
  1029 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 81
    poor density    : 948
  time to evaluate  : 9.382 
Switching outliers to nearest non-outliers
  outliers start: 81
  outliers final: 0
  residues processed: 81
  average time/residue: 0.8237
  time to fit residues: 141.0688
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 1333 optimal weight:    3.9990
   chunk 155 optimal weight:    5.9990
   chunk 788 optimal weight:    3.9990
   chunk 1010 optimal weight:    6.9990
   chunk 782 optimal weight:    6.9990
   chunk 1164 optimal weight:    0.9990
   chunk 772 optimal weight:    1.9990
   chunk 1378 optimal weight:    0.2980
   chunk 862 optimal weight:    5.9990
   chunk 840 optimal weight:    2.9990
   chunk 636 optimal weight:    5.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
Z  39 ASN
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 487 GLN
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 131 GLN
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 136 ASN
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  15 GLN
** Q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 131 GLN
Q 497 GLN
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 151 ASN
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  52 ASN
** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c 475 GLN
c 479 ASN
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
f 154 GLN
f 487 GLN
g  39 ASN
h  21 ASN
** k  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
n  86 ASN
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r   8 ASN
r  15 GLN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s   8 ASN
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
t  63 GLN
t  67 ASN
t 154 GLN
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040 109835  Z= 0.220
  Angle     :  0.484   8.065 148555  Z= 0.276
  Chirality :  0.034   0.190  18370
  Planarity :  0.003   0.047  20020
  Dihedral  :  4.286  79.775  15290
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 13.49 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.46 (0.07), residues: 14465
  helix:  4.26 (0.05), residues: 10835
  sheet: -0.24 (0.17), residues: 990
  loop : -2.04 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.014   0.001   PHE z 173 
   TYR   0.025   0.002   TYR c 461 
   ARG   0.006   0.000   ARG U 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1095 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 1021
  time to evaluate  : 9.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 74
  outliers final: 31
  residues processed: 1068
  average time/residue: 0.9572
  time to fit residues: 1848.6561
Evaluate side-chains
  998 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 967
  time to evaluate  : 9.333 
Switching outliers to nearest non-outliers
  outliers start: 31
  outliers final: 0
  residues processed: 31
  average time/residue: 0.8118
  time to fit residues: 60.5830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 852 optimal weight:    6.9990
   chunk 550 optimal weight:    3.9990
   chunk 823 optimal weight:    2.9990
   chunk 415 optimal weight:    1.9990
   chunk 270 optimal weight:    0.9980
   chunk 267 optimal weight:    2.9990
   chunk 876 optimal weight:    7.9990
   chunk 939 optimal weight:    0.0030
   chunk 681 optimal weight:    4.9990
   chunk 128 optimal weight:    3.9990
   chunk 1083 optimal weight:    4.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  67 ASN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 136 ASN
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 497 GLN
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 487 GLN
e 479 ASN
2  21 ASN
f 131 GLN
h  21 ASN
** h  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r   6 ASN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
u 487 GLN
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  67 ASN
** 0 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044 109835  Z= 0.210
  Angle     :  0.480  10.304 148555  Z= 0.272
  Chirality :  0.034   0.211  18370
  Planarity :  0.003   0.044  20020
  Dihedral  :  4.185  77.765  15290
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 14.13 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.58 (0.07), residues: 14465
  helix:  4.34 (0.04), residues: 10835
  sheet: -0.13 (0.17), residues: 990
  loop : -1.96 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.015   0.001   PHE z 173 
   TYR   0.021   0.002   TYR c 461 
   ARG   0.006   0.000   ARG C  66 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1070 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 1025
  time to evaluate  : 9.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 45
  outliers final: 20
  residues processed: 1055
  average time/residue: 0.8734
  time to fit residues: 1663.3251
Evaluate side-chains
  1011 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 991
  time to evaluate  : 9.355 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.7599
  time to fit residues: 41.6012
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 1253 optimal weight:    4.9990
   chunk 1320 optimal weight:    0.9990
   chunk 1204 optimal weight:    5.9990
   chunk 1284 optimal weight:    6.9990
   chunk 773 optimal weight:    1.9990
   chunk 559 optimal weight:    5.9990
   chunk 1008 optimal weight:    8.9990
   chunk 394 optimal weight:    7.9990
   chunk 1160 optimal weight:    3.9990
   chunk 1214 optimal weight:    1.9990
   chunk 1279 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 487 GLN
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 497 GLN
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  22 GLN
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 475 GLN
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 487 GLN
2  21 ASN
h  21 ASN
** h  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
k  63 GLN
k  67 ASN
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** l  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p   8 ASN
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
r   6 ASN
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 0 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043 109835  Z= 0.275
  Angle     :  0.508  15.340 148555  Z= 0.286
  Chirality :  0.035   0.294  18370
  Planarity :  0.003   0.044  20020
  Dihedral  :  4.156  75.899  15290
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.46 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.54 (0.07), residues: 14465
  helix:  4.29 (0.04), residues: 10835
  sheet: -0.11 (0.17), residues: 990
  loop : -1.93 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.015   0.001   PHE h 173 
   TYR   0.027   0.003   TYR u 461 
   ARG   0.007   0.000   ARG U 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1045 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 1006
  time to evaluate  : 9.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 39
  outliers final: 23
  residues processed: 1027
  average time/residue: 0.9096
  time to fit residues: 1677.4899
Evaluate side-chains
  1003 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 980
  time to evaluate  : 8.574 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 0
  residues processed: 23
  average time/residue: 0.7799
  time to fit residues: 45.9527
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 843 optimal weight:    4.9990
   chunk 1358 optimal weight:    5.9990
   chunk 828 optimal weight:   10.0000
   chunk 644 optimal weight:    6.9990
   chunk 944 optimal weight:    3.9990
   chunk 1424 optimal weight:    4.9990
   chunk 1311 optimal weight:    4.9990
   chunk 1134 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 876 optimal weight:    7.9990
   chunk 695 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  67 ASN
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 497 GLN
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
d 487 GLN
e 497 GLN
** 2  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
h  21 ASN
** h  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
i 479 ASN
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
o  86 ASN
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
v   8 ASN
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  67 ASN
** 0 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 147 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050 109835  Z= 0.363
  Angle     :  0.560  13.465 148555  Z= 0.315
  Chirality :  0.037   0.244  18370
  Planarity :  0.003   0.046  20020
  Dihedral  :  4.234  73.734  15290
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 14.73 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.37 (0.07), residues: 14465
  helix:  4.19 (0.04), residues: 10725
  sheet: -0.16 (0.17), residues: 990
  loop : -1.80 (0.12), residues: 2750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.015   0.002   PHE z 173 
   TYR   0.026   0.003   TYR c 461 
   ARG   0.009   0.001   ARG U 455 

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

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

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  28930 Ramachandran restraints generated.
    14465 Oldfield, 0 Emsley, 14465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  992 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 974
  time to evaluate  : 9.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 9
  residues processed: 985
  average time/residue: 0.8758
  time to fit residues: 1551.8412
Evaluate side-chains
  968 residues out of total 12375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 959
  time to evaluate  : 9.333 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.7587
  time to fit residues: 25.2487
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1430
   random chunks:
   chunk 901 optimal weight:    3.9990
   chunk 1208 optimal weight:    0.9990
   chunk 347 optimal weight:    4.9990
   chunk 1046 optimal weight:    1.9990
   chunk 167 optimal weight:    3.9990
   chunk 315 optimal weight:   10.0000
   chunk 1136 optimal weight:    6.9990
   chunk 475 optimal weight:    2.9990
   chunk 1166 optimal weight:    0.6980
   chunk 143 optimal weight:    5.9990
   chunk 209 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 487 GLN
** E  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 497 GLN
** R  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 136 ASN
** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  15 GLN
** c 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** k  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  15 GLN
** m 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
o  86 ASN
** o 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p   8 ASN
** p  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** q  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s   8 ASN
** t  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** u  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** v  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** v  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** w  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
y  86 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.076569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.065791 restraints weight = 249563.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.68
r_work: 0.3133 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052 109835  Z= 0.199
  Angle     :  0.486  13.807 148555  Z= 0.275
  Chirality :  0.034   0.284  18370
  Planarity :  0.003   0.047  20020
  Dihedral  :  4.134  71.166  15290
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 14.80 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.62 (0.07), residues: 14465
  helix:  4.35 (0.04), residues: 10835
  sheet: -0.09 (0.17), residues: 990
  loop : -1.87 (0.11), residues: 2640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.015   0.001   PHE h 173 
   TYR   0.020   0.002   TYR c 461 
   ARG   0.004   0.000   ARG B  37 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 26864.69 seconds
wall clock time: 470 minutes 48.87 seconds (28248.87 seconds total)