Starting phenix.real_space_refine
on Thu Nov 16 13:18:51 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1s_15086/11_2023/8a1s_15086_updated.pdb"
  }
  resolution = 4.0
  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=   0.000 sd=   0.005
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     432      5.16       5
     C   42912      2.51       5
     N   11008      2.21       5
     O   12800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  122": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  244": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  580": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   95": "OE1" <-> "OE2"
    Residue "B TYR  107": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  218": "OE1" <-> "OE2"
    Residue "B PHE  244": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   95": "OE1" <-> "OE2"
    Residue "C PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  166": "OE1" <-> "OE2"
    Residue "C TYR  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  228": "OD1" <-> "OD2"
    Residue "C ASP  304": "OD1" <-> "OD2"
    Residue "C PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  448": "OD1" <-> "OD2"
    Residue "C PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  573": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  580": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   95": "OE1" <-> "OE2"
    Residue "D GLU  102": "OE1" <-> "OE2"
    Residue "D PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  166": "OE1" <-> "OE2"
    Residue "D PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  476": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  580": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  218": "OE1" <-> "OE2"
    Residue "E ASP  219": "OD1" <-> "OD2"
    Residue "E TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  448": "OD1" <-> "OD2"
    Residue "E PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  166": "OE1" <-> "OE2"
    Residue "F PHE  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  312": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  219": "OD1" <-> "OD2"
    Residue "G TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  304": "OD1" <-> "OD2"
    Residue "G PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  456": "OE1" <-> "OE2"
    Residue "G PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  580": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU   95": "OE1" <-> "OE2"
    Residue "H PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ASP  228": "OD1" <-> "OD2"
    Residue "I PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J GLU   95": "OE1" <-> "OE2"
    Residue "J TYR  107": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  244": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  341": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K GLU   95": "OE1" <-> "OE2"
    Residue "K PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ASP  448": "OD1" <-> "OD2"
    Residue "K TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  122": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  407": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  476": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  580": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  102": "OE1" <-> "OE2"
    Residue "M PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  218": "OE1" <-> "OE2"
    Residue "M ASP  219": "OD1" <-> "OD2"
    Residue "M ASP  304": "OD1" <-> "OD2"
    Residue "M PHE  312": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP  448": "OD1" <-> "OD2"
    Residue "N PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU  166": "OE1" <-> "OE2"
    Residue "N PHE  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  312": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR  341": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  521": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ASP  219": "OD1" <-> "OD2"
    Residue "O ASP  304": "OD1" <-> "OD2"
    Residue "O PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O PHE  504": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P GLU   95": "OE1" <-> "OE2"
    Residue "P PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ASP  448": "OD1" <-> "OD2"
    Residue "P TYR  593": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.19s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 67152
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "K"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "M"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "O"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 4148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4148
          Classifications: {'peptide': 533}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 503}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "J"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "K"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "L"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "M"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "N"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "O"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'MA4': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 26.95, per 1000 atoms: 0.40
  Number of scatterers: 67152
  At special positions: 0
  Unit cell: (212.541, 214.635, 157.05, 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     432     16.00
     O   12800      8.00
     N   11008      7.00
     C   42912      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=128, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  34 " - pdb=" SG  CYS A  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 409 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 432 " - pdb=" SG  CYS A 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 436 " - pdb=" SG  CYS A 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 554 " - pdb=" SG  CYS A 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  70 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 385 " - pdb=" SG  CYS B 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 409 " - pdb=" SG  CYS B 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 432 " - pdb=" SG  CYS B 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 436 " - pdb=" SG  CYS B 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 494 " - pdb=" SG  CYS B 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 531 " - pdb=" SG  CYS B 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 554 " - pdb=" SG  CYS B 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  34 " - pdb=" SG  CYS C  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 385 " - pdb=" SG  CYS C 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 409 " - pdb=" SG  CYS C 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 432 " - pdb=" SG  CYS C 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 436 " - pdb=" SG  CYS C 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 494 " - pdb=" SG  CYS C 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 531 " - pdb=" SG  CYS C 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 554 " - pdb=" SG  CYS C 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  34 " - pdb=" SG  CYS D  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 385 " - pdb=" SG  CYS D 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 409 " - pdb=" SG  CYS D 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 432 " - pdb=" SG  CYS D 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 436 " - pdb=" SG  CYS D 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 494 " - pdb=" SG  CYS D 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 531 " - pdb=" SG  CYS D 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 554 " - pdb=" SG  CYS D 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  34 " - pdb=" SG  CYS E  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 385 " - pdb=" SG  CYS E 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 409 " - pdb=" SG  CYS E 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 432 " - pdb=" SG  CYS E 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 436 " - pdb=" SG  CYS E 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 494 " - pdb=" SG  CYS E 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 531 " - pdb=" SG  CYS E 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 554 " - pdb=" SG  CYS E 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  34 " - pdb=" SG  CYS F  70 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 385 " - pdb=" SG  CYS F 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 409 " - pdb=" SG  CYS F 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 432 " - pdb=" SG  CYS F 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 436 " - pdb=" SG  CYS F 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 494 " - pdb=" SG  CYS F 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 531 " - pdb=" SG  CYS F 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 554 " - pdb=" SG  CYS F 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  34 " - pdb=" SG  CYS G  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 385 " - pdb=" SG  CYS G 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 409 " - pdb=" SG  CYS G 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 432 " - pdb=" SG  CYS G 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 436 " - pdb=" SG  CYS G 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 494 " - pdb=" SG  CYS G 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 531 " - pdb=" SG  CYS G 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 554 " - pdb=" SG  CYS G 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  34 " - pdb=" SG  CYS H  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 385 " - pdb=" SG  CYS H 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 409 " - pdb=" SG  CYS H 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 432 " - pdb=" SG  CYS H 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 436 " - pdb=" SG  CYS H 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 494 " - pdb=" SG  CYS H 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 531 " - pdb=" SG  CYS H 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 554 " - pdb=" SG  CYS H 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  34 " - pdb=" SG  CYS I  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 385 " - pdb=" SG  CYS I 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 409 " - pdb=" SG  CYS I 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 432 " - pdb=" SG  CYS I 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 436 " - pdb=" SG  CYS I 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 494 " - pdb=" SG  CYS I 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 531 " - pdb=" SG  CYS I 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 554 " - pdb=" SG  CYS I 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  34 " - pdb=" SG  CYS J  70 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J 385 " - pdb=" SG  CYS J 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 409 " - pdb=" SG  CYS J 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 432 " - pdb=" SG  CYS J 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 436 " - pdb=" SG  CYS J 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 494 " - pdb=" SG  CYS J 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 531 " - pdb=" SG  CYS J 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 554 " - pdb=" SG  CYS J 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  34 " - pdb=" SG  CYS K  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 385 " - pdb=" SG  CYS K 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 409 " - pdb=" SG  CYS K 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 432 " - pdb=" SG  CYS K 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 436 " - pdb=" SG  CYS K 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 494 " - pdb=" SG  CYS K 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 531 " - pdb=" SG  CYS K 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 554 " - pdb=" SG  CYS K 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  34 " - pdb=" SG  CYS L  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 385 " - pdb=" SG  CYS L 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 409 " - pdb=" SG  CYS L 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 432 " - pdb=" SG  CYS L 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 436 " - pdb=" SG  CYS L 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 494 " - pdb=" SG  CYS L 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 531 " - pdb=" SG  CYS L 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 554 " - pdb=" SG  CYS L 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  34 " - pdb=" SG  CYS M  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 385 " - pdb=" SG  CYS M 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 409 " - pdb=" SG  CYS M 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 432 " - pdb=" SG  CYS M 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 436 " - pdb=" SG  CYS M 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 494 " - pdb=" SG  CYS M 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 531 " - pdb=" SG  CYS M 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 554 " - pdb=" SG  CYS M 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  34 " - pdb=" SG  CYS N  70 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 385 " - pdb=" SG  CYS N 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 409 " - pdb=" SG  CYS N 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 432 " - pdb=" SG  CYS N 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 436 " - pdb=" SG  CYS N 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 494 " - pdb=" SG  CYS N 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 531 " - pdb=" SG  CYS N 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 554 " - pdb=" SG  CYS N 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  34 " - pdb=" SG  CYS O  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 385 " - pdb=" SG  CYS O 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 409 " - pdb=" SG  CYS O 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 432 " - pdb=" SG  CYS O 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 436 " - pdb=" SG  CYS O 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 494 " - pdb=" SG  CYS O 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 531 " - pdb=" SG  CYS O 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 554 " - pdb=" SG  CYS O 574 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  34 " - pdb=" SG  CYS P  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 385 " - pdb=" SG  CYS P 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 409 " - pdb=" SG  CYS P 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 432 " - pdb=" SG  CYS P 446 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 436 " - pdb=" SG  CYS P 442 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 494 " - pdb=" SG  CYS P 510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 531 " - pdb=" SG  CYS P 569 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 554 " - pdb=" SG  CYS P 574 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 269 "
      " NAG B 701 " - " ASN B 269 "
      " NAG C 701 " - " ASN C 269 "
      " NAG D 701 " - " ASN D 269 "
      " NAG E 701 " - " ASN E 269 "
      " NAG F 701 " - " ASN F 269 "
      " NAG G 701 " - " ASN G 269 "
      " NAG H 701 " - " ASN H 269 "
      " NAG I 701 " - " ASN I 269 "
      " NAG J 701 " - " ASN J 269 "
      " NAG K 701 " - " ASN K 269 "
      " NAG L 701 " - " ASN L 269 "
      " NAG M 701 " - " ASN M 269 "
      " NAG N 701 " - " ASN N 269 "
      " NAG O 701 " - " ASN O 269 "
      " NAG P 701 " - " ASN P 269 "
  Time building additional restraints: 19.87
  Conformation dependent library (CDL) restraints added in 8.7 seconds
  

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  15808

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      146 helices and 97 sheets defined
      15.4% alpha, 48.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 9.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 169 through 183
    Processing helix  chain 'A' and resid 187 through 201
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 310 through 313
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 324 through 344
    Processing helix  chain 'A' and resid 394 through 397
      No H-bonds generated for 'chain 'A' and resid 394 through 397'
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'B' and resid 32 through 38
    Processing helix  chain 'B' and resid 169 through 183
    Processing helix  chain 'B' and resid 187 through 201
    Processing helix  chain 'B' and resid 289 through 295
    Processing helix  chain 'B' and resid 310 through 312
      No H-bonds generated for 'chain 'B' and resid 310 through 312'
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 324 through 344
    Processing helix  chain 'B' and resid 394 through 397
      No H-bonds generated for 'chain 'B' and resid 394 through 397'
    Processing helix  chain 'B' and resid 437 through 439
      No H-bonds generated for 'chain 'B' and resid 437 through 439'
    Processing helix  chain 'B' and resid 515 through 520
    Processing helix  chain 'C' and resid 32 through 38
    Processing helix  chain 'C' and resid 169 through 183
    Processing helix  chain 'C' and resid 187 through 201
      removed outlier: 3.702A  pdb=" N   THR C 191 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR C 192 " --> pdb=" O   LYS C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 295
    Processing helix  chain 'C' and resid 310 through 313
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 324 through 344
    Processing helix  chain 'C' and resid 393 through 395
      No H-bonds generated for 'chain 'C' and resid 393 through 395'
    Processing helix  chain 'C' and resid 515 through 521
    Processing helix  chain 'D' and resid 32 through 38
    Processing helix  chain 'D' and resid 169 through 183
    Processing helix  chain 'D' and resid 187 through 201
      removed outlier: 3.738A  pdb=" N   THR D 191 " --> pdb=" O   THR D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 289 through 295
    Processing helix  chain 'D' and resid 310 through 313
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 324 through 344
    Processing helix  chain 'D' and resid 393 through 395
      No H-bonds generated for 'chain 'D' and resid 393 through 395'
    Processing helix  chain 'D' and resid 515 through 521
    Processing helix  chain 'E' and resid 32 through 38
    Processing helix  chain 'E' and resid 169 through 183
    Processing helix  chain 'E' and resid 187 through 201
    Processing helix  chain 'E' and resid 289 through 295
    Processing helix  chain 'E' and resid 310 through 313
      No H-bonds generated for 'chain 'E' and resid 310 through 313'
    Processing helix  chain 'E' and resid 324 through 344
    Processing helix  chain 'E' and resid 393 through 397
      removed outlier: 3.992A  pdb=" N   ASN E 396 " --> pdb=" O   LEU E 393 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU E 397 " --> pdb=" O   CYS E 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 393 through 397'
    Processing helix  chain 'E' and resid 515 through 521
    Processing helix  chain 'F' and resid 32 through 38
    Processing helix  chain 'F' and resid 169 through 183
    Processing helix  chain 'F' and resid 187 through 201
      removed outlier: 3.541A  pdb=" N   THR F 191 " --> pdb=" O   THR F 187 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR F 192 " --> pdb=" O   LYS F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 289 through 295
    Processing helix  chain 'F' and resid 310 through 313
    Processing helix  chain 'F' and resid 316 through 318
      No H-bonds generated for 'chain 'F' and resid 316 through 318'
    Processing helix  chain 'F' and resid 324 through 344
    Processing helix  chain 'F' and resid 393 through 395
      No H-bonds generated for 'chain 'F' and resid 393 through 395'
    Processing helix  chain 'F' and resid 515 through 520
    Processing helix  chain 'G' and resid 32 through 38
    Processing helix  chain 'G' and resid 169 through 183
    Processing helix  chain 'G' and resid 187 through 201
      removed outlier: 3.554A  pdb=" N   THR G 191 " --> pdb=" O   THR G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 289 through 295
    Processing helix  chain 'G' and resid 310 through 313
    Processing helix  chain 'G' and resid 316 through 318
      No H-bonds generated for 'chain 'G' and resid 316 through 318'
    Processing helix  chain 'G' and resid 324 through 344
    Processing helix  chain 'G' and resid 394 through 397
      No H-bonds generated for 'chain 'G' and resid 394 through 397'
    Processing helix  chain 'G' and resid 437 through 439
      No H-bonds generated for 'chain 'G' and resid 437 through 439'
    Processing helix  chain 'G' and resid 515 through 521
    Processing helix  chain 'H' and resid 32 through 38
    Processing helix  chain 'H' and resid 169 through 183
    Processing helix  chain 'H' and resid 187 through 201
    Processing helix  chain 'H' and resid 289 through 295
    Processing helix  chain 'H' and resid 310 through 313
    Processing helix  chain 'H' and resid 316 through 318
      No H-bonds generated for 'chain 'H' and resid 316 through 318'
    Processing helix  chain 'H' and resid 324 through 344
    Processing helix  chain 'H' and resid 393 through 395
      No H-bonds generated for 'chain 'H' and resid 393 through 395'
    Processing helix  chain 'H' and resid 515 through 520
    Processing helix  chain 'I' and resid 32 through 38
    Processing helix  chain 'I' and resid 169 through 183
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.587A  pdb=" N   THR I 191 " --> pdb=" O   THR I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 289 through 295
    Processing helix  chain 'I' and resid 310 through 313
    Processing helix  chain 'I' and resid 316 through 318
      No H-bonds generated for 'chain 'I' and resid 316 through 318'
    Processing helix  chain 'I' and resid 324 through 344
    Processing helix  chain 'I' and resid 394 through 397
      No H-bonds generated for 'chain 'I' and resid 394 through 397'
    Processing helix  chain 'I' and resid 515 through 519
    Processing helix  chain 'J' and resid 32 through 38
    Processing helix  chain 'J' and resid 169 through 183
    Processing helix  chain 'J' and resid 187 through 201
      removed outlier: 3.624A  pdb=" N   THR J 191 " --> pdb=" O   THR J 187 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 289 through 295
    Processing helix  chain 'J' and resid 310 through 312
      No H-bonds generated for 'chain 'J' and resid 310 through 312'
    Processing helix  chain 'J' and resid 316 through 318
      No H-bonds generated for 'chain 'J' and resid 316 through 318'
    Processing helix  chain 'J' and resid 324 through 344
    Processing helix  chain 'J' and resid 394 through 397
      No H-bonds generated for 'chain 'J' and resid 394 through 397'
    Processing helix  chain 'J' and resid 437 through 439
      No H-bonds generated for 'chain 'J' and resid 437 through 439'
    Processing helix  chain 'J' and resid 515 through 520
    Processing helix  chain 'K' and resid 32 through 38
    Processing helix  chain 'K' and resid 169 through 183
    Processing helix  chain 'K' and resid 187 through 201
      removed outlier: 3.761A  pdb=" N   THR K 191 " --> pdb=" O   THR K 187 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR K 192 " --> pdb=" O   LYS K 188 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 289 through 295
    Processing helix  chain 'K' and resid 310 through 313
    Processing helix  chain 'K' and resid 316 through 318
      No H-bonds generated for 'chain 'K' and resid 316 through 318'
    Processing helix  chain 'K' and resid 324 through 344
    Processing helix  chain 'K' and resid 393 through 395
      No H-bonds generated for 'chain 'K' and resid 393 through 395'
    Processing helix  chain 'K' and resid 515 through 521
    Processing helix  chain 'L' and resid 32 through 38
    Processing helix  chain 'L' and resid 169 through 183
    Processing helix  chain 'L' and resid 187 through 201
      removed outlier: 3.676A  pdb=" N   THR L 191 " --> pdb=" O   THR L 187 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 289 through 295
    Processing helix  chain 'L' and resid 310 through 313
    Processing helix  chain 'L' and resid 316 through 318
      No H-bonds generated for 'chain 'L' and resid 316 through 318'
    Processing helix  chain 'L' and resid 324 through 344
    Processing helix  chain 'L' and resid 393 through 395
      No H-bonds generated for 'chain 'L' and resid 393 through 395'
    Processing helix  chain 'L' and resid 515 through 521
    Processing helix  chain 'M' and resid 32 through 38
    Processing helix  chain 'M' and resid 169 through 183
    Processing helix  chain 'M' and resid 187 through 201
      removed outlier: 3.588A  pdb=" N   TYR M 192 " --> pdb=" O   LYS M 188 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 289 through 295
    Processing helix  chain 'M' and resid 310 through 313
    Processing helix  chain 'M' and resid 324 through 344
    Processing helix  chain 'M' and resid 393 through 397
      removed outlier: 4.019A  pdb=" N   ASN M 396 " --> pdb=" O   LEU M 393 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU M 397 " --> pdb=" O   CYS M 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 393 through 397'
    Processing helix  chain 'M' and resid 515 through 520
    Processing helix  chain 'N' and resid 32 through 38
    Processing helix  chain 'N' and resid 169 through 183
    Processing helix  chain 'N' and resid 187 through 201
      removed outlier: 3.557A  pdb=" N   TYR N 192 " --> pdb=" O   LYS N 188 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 289 through 295
    Processing helix  chain 'N' and resid 310 through 313
    Processing helix  chain 'N' and resid 316 through 318
      No H-bonds generated for 'chain 'N' and resid 316 through 318'
    Processing helix  chain 'N' and resid 324 through 344
    Processing helix  chain 'N' and resid 393 through 395
      No H-bonds generated for 'chain 'N' and resid 393 through 395'
    Processing helix  chain 'N' and resid 437 through 439
      No H-bonds generated for 'chain 'N' and resid 437 through 439'
    Processing helix  chain 'N' and resid 515 through 520
    Processing helix  chain 'O' and resid 32 through 38
    Processing helix  chain 'O' and resid 169 through 183
    Processing helix  chain 'O' and resid 187 through 201
      removed outlier: 3.527A  pdb=" N   THR O 191 " --> pdb=" O   THR O 187 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 289 through 295
    Processing helix  chain 'O' and resid 310 through 313
    Processing helix  chain 'O' and resid 324 through 344
    Processing helix  chain 'O' and resid 394 through 397
      No H-bonds generated for 'chain 'O' and resid 394 through 397'
    Processing helix  chain 'O' and resid 437 through 439
      No H-bonds generated for 'chain 'O' and resid 437 through 439'
    Processing helix  chain 'O' and resid 515 through 521
    Processing helix  chain 'P' and resid 32 through 38
    Processing helix  chain 'P' and resid 169 through 183
    Processing helix  chain 'P' and resid 187 through 201
    Processing helix  chain 'P' and resid 289 through 295
    Processing helix  chain 'P' and resid 310 through 313
    Processing helix  chain 'P' and resid 316 through 318
      No H-bonds generated for 'chain 'P' and resid 316 through 318'
    Processing helix  chain 'P' and resid 324 through 344
    Processing helix  chain 'P' and resid 393 through 395
      No H-bonds generated for 'chain 'P' and resid 393 through 395'
    Processing helix  chain 'P' and resid 515 through 521
    Processing sheet with id=  A, first strand: chain 'A' and resid 84 through 88
      removed outlier: 6.708A  pdb=" N   ALA A 211 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   THR A 158 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A 209 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 91 through 121
    Processing sheet with id=  C, first strand: chain 'A' and resid 479 through 481
    Processing sheet with id=  D, first strand: chain 'A' and resid 528 through 530
      removed outlier: 3.520A  pdb=" N   PHE A 529 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   TYR A 573 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   LEU A 562 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   VAL A 575 " --> pdb=" O   GLN A 560 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   GLN A 560 " --> pdb=" O   VAL A 575 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 204 through 209
      removed outlier: 6.768A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'A' and resid 378 through 387
      removed outlier: 5.631A  pdb=" N   CYS A 462 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL A 381 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TYR A 460 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLN A 383 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   ARG A 458 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS A 385 " --> pdb=" O   GLU A 456 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLU A 456 " --> pdb=" O   CYS A 385 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   GLU A 387 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LYS A 454 " --> pdb=" O   GLU A 387 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   TRP A 461 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   HIS A 417 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL A 463 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 84 through 88
      removed outlier: 6.626A  pdb=" N   ALA B 211 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   THR B 158 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL B 209 " --> pdb=" O   THR B 158 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 91 through 121
    Processing sheet with id=  I, first strand: chain 'B' and resid 479 through 481
    Processing sheet with id=  J, first strand: chain 'B' and resid 204 through 209
      removed outlier: 6.764A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 207 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 378 through 387
      removed outlier: 5.704A  pdb=" N   CYS B 462 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   VAL B 381 " --> pdb=" O   TYR B 460 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TYR B 460 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLN B 383 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ARG B 458 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   CYS B 385 " --> pdb=" O   GLU B 456 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU B 456 " --> pdb=" O   CYS B 385 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   GLU B 387 " --> pdb=" O   LYS B 454 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   LYS B 454 " --> pdb=" O   GLU B 387 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   TRP B 461 " --> pdb=" O   HIS B 417 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   HIS B 417 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   VAL B 463 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 525 through 529
      removed outlier: 6.349A  pdb=" N   CYS B 574 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE B 528 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   SER B 572 " --> pdb=" O   PHE B 528 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   TYR B 573 " --> pdb=" O   LEU B 562 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   LEU B 562 " --> pdb=" O   TYR B 573 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   VAL B 575 " --> pdb=" O   GLN B 560 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   GLN B 560 " --> pdb=" O   VAL B 575 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'C' and resid 84 through 88
      removed outlier: 6.615A  pdb=" N   ALA C 211 " --> pdb=" O   ILE C 156 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR C 158 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   VAL C 209 " --> pdb=" O   THR C 158 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'C' and resid 91 through 121
    Processing sheet with id=  O, first strand: chain 'C' and resid 498 through 502
    Processing sheet with id=  P, first strand: chain 'C' and resid 49 through 52
      removed outlier: 5.194A  pdb=" N   GLY C  60 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   ASP C  52 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ASP C  58 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'C' and resid 204 through 210
      removed outlier: 6.837A  pdb=" N   ALA C 306 " --> pdb=" O   THR C 207 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   VAL C 209 " --> pdb=" O   ASP C 304 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ASP C 304 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'C' and resid 378 through 387
      removed outlier: 5.954A  pdb=" N   CYS C 462 " --> pdb=" O   GLY C 379 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   VAL C 381 " --> pdb=" O   TYR C 460 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR C 460 " --> pdb=" O   VAL C 381 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   GLN C 383 " --> pdb=" O   ARG C 458 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   ARG C 458 " --> pdb=" O   GLN C 383 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   CYS C 385 " --> pdb=" O   GLU C 456 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLU C 456 " --> pdb=" O   CYS C 385 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   GLU C 387 " --> pdb=" O   LYS C 454 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   LYS C 454 " --> pdb=" O   GLU C 387 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   TRP C 461 " --> pdb=" O   HIS C 417 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   HIS C 417 " --> pdb=" O   TRP C 461 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL C 463 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'C' and resid 525 through 529
      removed outlier: 6.365A  pdb=" N   CYS C 574 " --> pdb=" O   GLY C 526 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   PHE C 528 " --> pdb=" O   SER C 572 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   SER C 572 " --> pdb=" O   PHE C 528 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   TYR C 573 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   LEU C 562 " --> pdb=" O   TYR C 573 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   VAL C 575 " --> pdb=" O   GLN C 560 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   GLN C 560 " --> pdb=" O   VAL C 575 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'D' and resid 84 through 88
      removed outlier: 6.642A  pdb=" N   ALA D 211 " --> pdb=" O   ILE D 156 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   THR D 158 " --> pdb=" O   VAL D 209 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL D 209 " --> pdb=" O   THR D 158 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'D' and resid 91 through 121
    Processing sheet with id=  V, first strand: chain 'D' and resid 498 through 502
    Processing sheet with id=  W, first strand: chain 'D' and resid 204 through 210
      removed outlier: 6.824A  pdb=" N   ALA D 306 " --> pdb=" O   THR D 207 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL D 209 " --> pdb=" O   ASP D 304 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP D 304 " --> pdb=" O   VAL D 209 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'D' and resid 378 through 387
      removed outlier: 5.810A  pdb=" N   CYS D 462 " --> pdb=" O   GLY D 379 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL D 381 " --> pdb=" O   TYR D 460 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   TYR D 460 " --> pdb=" O   VAL D 381 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   GLN D 383 " --> pdb=" O   ARG D 458 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ARG D 458 " --> pdb=" O   GLN D 383 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   CYS D 385 " --> pdb=" O   GLU D 456 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLU D 456 " --> pdb=" O   CYS D 385 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   GLU D 387 " --> pdb=" O   LYS D 454 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LYS D 454 " --> pdb=" O   GLU D 387 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   TRP D 461 " --> pdb=" O   HIS D 417 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   HIS D 417 " --> pdb=" O   TRP D 461 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL D 463 " --> pdb=" O   PRO D 415 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'D' and resid 558 through 566
      removed outlier: 3.559A  pdb=" N   HIS D 561 " --> pdb=" O   TYR D 573 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL D 571 " --> pdb=" O   ALA D 563 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ILE D 565 " --> pdb=" O   CYS D 569 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   CYS D 569 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'E' and resid 84 through 88
      removed outlier: 6.690A  pdb=" N   ALA E 211 " --> pdb=" O   ILE E 156 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   THR E 158 " --> pdb=" O   VAL E 209 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   VAL E 209 " --> pdb=" O   THR E 158 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'E' and resid 91 through 121
    Processing sheet with id= AB, first strand: chain 'E' and resid 498 through 502
    Processing sheet with id= AC, first strand: chain 'E' and resid 204 through 209
      removed outlier: 6.745A  pdb=" N   ALA E 306 " --> pdb=" O   THR E 207 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'E' and resid 378 through 387
      removed outlier: 6.020A  pdb=" N   CYS E 462 " --> pdb=" O   GLY E 379 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   VAL E 381 " --> pdb=" O   TYR E 460 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   TYR E 460 " --> pdb=" O   VAL E 381 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLN E 383 " --> pdb=" O   ARG E 458 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   ARG E 458 " --> pdb=" O   GLN E 383 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   CYS E 385 " --> pdb=" O   GLU E 456 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   GLU E 456 " --> pdb=" O   CYS E 385 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLU E 387 " --> pdb=" O   LYS E 454 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   LYS E 454 " --> pdb=" O   GLU E 387 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   TRP E 461 " --> pdb=" O   HIS E 417 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   HIS E 417 " --> pdb=" O   TRP E 461 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL E 463 " --> pdb=" O   PRO E 415 " (cutoff:3.500A)
    Processing sheet with id= AE, first strand: chain 'E' and resid 558 through 566
      removed outlier: 3.711A  pdb=" N   HIS E 561 " --> pdb=" O   TYR E 573 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR E 573 " --> pdb=" O   HIS E 561 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   VAL E 571 " --> pdb=" O   ALA E 563 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ILE E 565 " --> pdb=" O   CYS E 569 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   CYS E 569 " --> pdb=" O   ILE E 565 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'F' and resid 84 through 88
      removed outlier: 6.720A  pdb=" N   ALA F 211 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   THR F 158 " --> pdb=" O   VAL F 209 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   VAL F 209 " --> pdb=" O   THR F 158 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'F' and resid 91 through 121
    Processing sheet with id= AH, first strand: chain 'F' and resid 383 through 387
      removed outlier: 6.520A  pdb=" N   TRP F 461 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   HIS F 417 " --> pdb=" O   TRP F 461 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL F 463 " --> pdb=" O   PRO F 415 " (cutoff:3.500A)
    Processing sheet with id= AI, first strand: chain 'F' and resid 498 through 502
    Processing sheet with id= AJ, first strand: chain 'F' and resid 204 through 209
      removed outlier: 6.750A  pdb=" N   ALA F 306 " --> pdb=" O   THR F 207 " (cutoff:3.500A)
    Processing sheet with id= AK, first strand: chain 'F' and resid 558 through 566
      removed outlier: 3.644A  pdb=" N   HIS F 561 " --> pdb=" O   TYR F 573 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR F 573 " --> pdb=" O   HIS F 561 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL F 571 " --> pdb=" O   ALA F 563 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ILE F 565 " --> pdb=" O   CYS F 569 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   CYS F 569 " --> pdb=" O   ILE F 565 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'G' and resid 84 through 88
      removed outlier: 6.643A  pdb=" N   ALA G 211 " --> pdb=" O   ILE G 156 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   THR G 158 " --> pdb=" O   VAL G 209 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL G 209 " --> pdb=" O   THR G 158 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'G' and resid 91 through 121
    Processing sheet with id= AN, first strand: chain 'G' and resid 498 through 502
    Processing sheet with id= AO, first strand: chain 'G' and resid 204 through 209
      removed outlier: 6.829A  pdb=" N   ALA G 306 " --> pdb=" O   THR G 207 " (cutoff:3.500A)
    Processing sheet with id= AP, first strand: chain 'G' and resid 378 through 387
      removed outlier: 5.642A  pdb=" N   CYS G 462 " --> pdb=" O   GLY G 379 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   VAL G 381 " --> pdb=" O   TYR G 460 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TYR G 460 " --> pdb=" O   VAL G 381 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   GLN G 383 " --> pdb=" O   ARG G 458 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ARG G 458 " --> pdb=" O   GLN G 383 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   CYS G 385 " --> pdb=" O   GLU G 456 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU G 456 " --> pdb=" O   CYS G 385 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLU G 387 " --> pdb=" O   LYS G 454 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   LYS G 454 " --> pdb=" O   GLU G 387 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   TRP G 461 " --> pdb=" O   HIS G 417 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   HIS G 417 " --> pdb=" O   TRP G 461 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL G 463 " --> pdb=" O   PRO G 415 " (cutoff:3.500A)
    Processing sheet with id= AQ, first strand: chain 'G' and resid 525 through 529
      removed outlier: 6.562A  pdb=" N   CYS G 574 " --> pdb=" O   GLY G 526 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   PHE G 528 " --> pdb=" O   SER G 572 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER G 572 " --> pdb=" O   PHE G 528 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   TYR G 573 " --> pdb=" O   LEU G 562 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LEU G 562 " --> pdb=" O   TYR G 573 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   VAL G 575 " --> pdb=" O   GLN G 560 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLN G 560 " --> pdb=" O   VAL G 575 " (cutoff:3.500A)
    Processing sheet with id= AR, first strand: chain 'H' and resid 84 through 88
      removed outlier: 6.704A  pdb=" N   ALA H 211 " --> pdb=" O   ILE H 156 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   THR H 158 " --> pdb=" O   VAL H 209 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL H 209 " --> pdb=" O   THR H 158 " (cutoff:3.500A)
    Processing sheet with id= AS, first strand: chain 'H' and resid 91 through 121
    Processing sheet with id= AT, first strand: chain 'H' and resid 479 through 481
    Processing sheet with id= AU, first strand: chain 'H' and resid 204 through 209
      removed outlier: 6.813A  pdb=" N   ALA H 306 " --> pdb=" O   THR H 207 " (cutoff:3.500A)
    Processing sheet with id= AV, first strand: chain 'H' and resid 378 through 387
      removed outlier: 5.762A  pdb=" N   CYS H 462 " --> pdb=" O   GLY H 379 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   VAL H 381 " --> pdb=" O   TYR H 460 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   TYR H 460 " --> pdb=" O   VAL H 381 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLN H 383 " --> pdb=" O   ARG H 458 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   ARG H 458 " --> pdb=" O   GLN H 383 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   CYS H 385 " --> pdb=" O   GLU H 456 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   GLU H 456 " --> pdb=" O   CYS H 385 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   GLU H 387 " --> pdb=" O   LYS H 454 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   LYS H 454 " --> pdb=" O   GLU H 387 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   TRP H 461 " --> pdb=" O   HIS H 417 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   HIS H 417 " --> pdb=" O   TRP H 461 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL H 463 " --> pdb=" O   PRO H 415 " (cutoff:3.500A)
    Processing sheet with id= AW, first strand: chain 'H' and resid 525 through 530
      removed outlier: 6.381A  pdb=" N   CYS H 574 " --> pdb=" O   GLY H 526 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   PHE H 528 " --> pdb=" O   SER H 572 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   SER H 572 " --> pdb=" O   PHE H 528 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   SER H 530 " --> pdb=" O   GLN H 570 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   GLN H 570 " --> pdb=" O   SER H 530 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   TYR H 573 " --> pdb=" O   LEU H 562 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   LEU H 562 " --> pdb=" O   TYR H 573 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   VAL H 575 " --> pdb=" O   GLN H 560 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   GLN H 560 " --> pdb=" O   VAL H 575 " (cutoff:3.500A)
    Processing sheet with id= AX, first strand: chain 'I' and resid 84 through 88
      removed outlier: 6.662A  pdb=" N   ALA I 211 " --> pdb=" O   ILE I 156 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   THR I 158 " --> pdb=" O   VAL I 209 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL I 209 " --> pdb=" O   THR I 158 " (cutoff:3.500A)
    Processing sheet with id= AY, first strand: chain 'I' and resid 91 through 121
    Processing sheet with id= AZ, first strand: chain 'I' and resid 479 through 481
    Processing sheet with id= BA, first strand: chain 'I' and resid 204 through 209
      removed outlier: 6.778A  pdb=" N   ALA I 306 " --> pdb=" O   THR I 207 " (cutoff:3.500A)
    Processing sheet with id= BB, first strand: chain 'I' and resid 378 through 387
      removed outlier: 5.602A  pdb=" N   CYS I 462 " --> pdb=" O   GLY I 379 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   VAL I 381 " --> pdb=" O   TYR I 460 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   TYR I 460 " --> pdb=" O   VAL I 381 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLN I 383 " --> pdb=" O   ARG I 458 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   ARG I 458 " --> pdb=" O   GLN I 383 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   CYS I 385 " --> pdb=" O   GLU I 456 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLU I 456 " --> pdb=" O   CYS I 385 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLU I 387 " --> pdb=" O   LYS I 454 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   LYS I 454 " --> pdb=" O   GLU I 387 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   TRP I 461 " --> pdb=" O   HIS I 417 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   HIS I 417 " --> pdb=" O   TRP I 461 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL I 463 " --> pdb=" O   PRO I 415 " (cutoff:3.500A)
    Processing sheet with id= BC, first strand: chain 'I' and resid 525 through 530
      removed outlier: 6.279A  pdb=" N   CYS I 574 " --> pdb=" O   GLY I 526 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   PHE I 528 " --> pdb=" O   SER I 572 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   SER I 572 " --> pdb=" O   PHE I 528 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   SER I 530 " --> pdb=" O   GLN I 570 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN I 570 " --> pdb=" O   SER I 530 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   TYR I 573 " --> pdb=" O   LEU I 562 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   LEU I 562 " --> pdb=" O   TYR I 573 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   VAL I 575 " --> pdb=" O   GLN I 560 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLN I 560 " --> pdb=" O   VAL I 575 " (cutoff:3.500A)
    Processing sheet with id= BD, first strand: chain 'J' and resid 84 through 88
      removed outlier: 6.651A  pdb=" N   ALA J 211 " --> pdb=" O   ILE J 156 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR J 158 " --> pdb=" O   VAL J 209 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL J 209 " --> pdb=" O   THR J 158 " (cutoff:3.500A)
    Processing sheet with id= BE, first strand: chain 'J' and resid 91 through 121
    Processing sheet with id= BF, first strand: chain 'J' and resid 479 through 481
    Processing sheet with id= BG, first strand: chain 'J' and resid 204 through 210
      removed outlier: 6.743A  pdb=" N   ALA J 306 " --> pdb=" O   THR J 207 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   VAL J 209 " --> pdb=" O   ASP J 304 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASP J 304 " --> pdb=" O   VAL J 209 " (cutoff:3.500A)
    Processing sheet with id= BH, first strand: chain 'J' and resid 378 through 387
      removed outlier: 5.716A  pdb=" N   CYS J 462 " --> pdb=" O   GLY J 379 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   VAL J 381 " --> pdb=" O   TYR J 460 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   TYR J 460 " --> pdb=" O   VAL J 381 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   GLN J 383 " --> pdb=" O   ARG J 458 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ARG J 458 " --> pdb=" O   GLN J 383 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   CYS J 385 " --> pdb=" O   GLU J 456 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU J 456 " --> pdb=" O   CYS J 385 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   GLU J 387 " --> pdb=" O   LYS J 454 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   LYS J 454 " --> pdb=" O   GLU J 387 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   TRP J 461 " --> pdb=" O   HIS J 417 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   HIS J 417 " --> pdb=" O   TRP J 461 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   VAL J 463 " --> pdb=" O   PRO J 415 " (cutoff:3.500A)
    Processing sheet with id= BI, first strand: chain 'J' and resid 525 through 529
      removed outlier: 6.349A  pdb=" N   CYS J 574 " --> pdb=" O   GLY J 526 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   PHE J 528 " --> pdb=" O   SER J 572 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER J 572 " --> pdb=" O   PHE J 528 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   TYR J 573 " --> pdb=" O   LEU J 562 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   LEU J 562 " --> pdb=" O   TYR J 573 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   VAL J 575 " --> pdb=" O   GLN J 560 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   GLN J 560 " --> pdb=" O   VAL J 575 " (cutoff:3.500A)
    Processing sheet with id= BJ, first strand: chain 'K' and resid 84 through 88
      removed outlier: 6.623A  pdb=" N   ALA K 211 " --> pdb=" O   ILE K 156 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   THR K 158 " --> pdb=" O   VAL K 209 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL K 209 " --> pdb=" O   THR K 158 " (cutoff:3.500A)
    Processing sheet with id= BK, first strand: chain 'K' and resid 91 through 121
    Processing sheet with id= BL, first strand: chain 'K' and resid 498 through 502
    Processing sheet with id= BM, first strand: chain 'K' and resid 204 through 210
      removed outlier: 6.881A  pdb=" N   ALA K 306 " --> pdb=" O   THR K 207 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   VAL K 209 " --> pdb=" O   ASP K 304 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASP K 304 " --> pdb=" O   VAL K 209 " (cutoff:3.500A)
    Processing sheet with id= BN, first strand: chain 'K' and resid 378 through 387
      removed outlier: 5.914A  pdb=" N   CYS K 462 " --> pdb=" O   GLY K 379 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   VAL K 381 " --> pdb=" O   TYR K 460 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TYR K 460 " --> pdb=" O   VAL K 381 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   GLN K 383 " --> pdb=" O   ARG K 458 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   ARG K 458 " --> pdb=" O   GLN K 383 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS K 385 " --> pdb=" O   GLU K 456 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLU K 456 " --> pdb=" O   CYS K 385 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   GLU K 387 " --> pdb=" O   LYS K 454 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   LYS K 454 " --> pdb=" O   GLU K 387 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TRP K 461 " --> pdb=" O   HIS K 417 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   HIS K 417 " --> pdb=" O   TRP K 461 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL K 463 " --> pdb=" O   PRO K 415 " (cutoff:3.500A)
    Processing sheet with id= BO, first strand: chain 'K' and resid 525 through 529
      removed outlier: 6.353A  pdb=" N   CYS K 574 " --> pdb=" O   GLY K 526 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   PHE K 528 " --> pdb=" O   SER K 572 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   SER K 572 " --> pdb=" O   PHE K 528 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   TYR K 573 " --> pdb=" O   LEU K 562 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   LEU K 562 " --> pdb=" O   TYR K 573 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   VAL K 575 " --> pdb=" O   GLN K 560 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   GLN K 560 " --> pdb=" O   VAL K 575 " (cutoff:3.500A)
    Processing sheet with id= BP, first strand: chain 'L' and resid 84 through 87
      removed outlier: 6.676A  pdb=" N   ALA L 211 " --> pdb=" O   ILE L 156 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   THR L 158 " --> pdb=" O   VAL L 209 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL L 209 " --> pdb=" O   THR L 158 " (cutoff:3.500A)
    Processing sheet with id= BQ, first strand: chain 'L' and resid 91 through 121
    Processing sheet with id= BR, first strand: chain 'L' and resid 498 through 502
    Processing sheet with id= BS, first strand: chain 'L' and resid 204 through 210
      removed outlier: 6.814A  pdb=" N   ALA L 306 " --> pdb=" O   THR L 207 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL L 209 " --> pdb=" O   ASP L 304 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP L 304 " --> pdb=" O   VAL L 209 " (cutoff:3.500A)
    Processing sheet with id= BT, first strand: chain 'L' and resid 378 through 387
      removed outlier: 5.795A  pdb=" N   CYS L 462 " --> pdb=" O   GLY L 379 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   VAL L 381 " --> pdb=" O   TYR L 460 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   TYR L 460 " --> pdb=" O   VAL L 381 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLN L 383 " --> pdb=" O   ARG L 458 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   ARG L 458 " --> pdb=" O   GLN L 383 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   CYS L 385 " --> pdb=" O   GLU L 456 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLU L 456 " --> pdb=" O   CYS L 385 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   GLU L 387 " --> pdb=" O   LYS L 454 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   LYS L 454 " --> pdb=" O   GLU L 387 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   TRP L 461 " --> pdb=" O   HIS L 417 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   HIS L 417 " --> pdb=" O   TRP L 461 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL L 463 " --> pdb=" O   PRO L 415 " (cutoff:3.500A)
    Processing sheet with id= BU, first strand: chain 'L' and resid 558 through 566
      removed outlier: 3.592A  pdb=" N   HIS L 561 " --> pdb=" O   TYR L 573 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL L 571 " --> pdb=" O   ALA L 563 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ILE L 565 " --> pdb=" O   CYS L 569 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   CYS L 569 " --> pdb=" O   ILE L 565 " (cutoff:3.500A)
    Processing sheet with id= BV, first strand: chain 'M' and resid 84 through 88
      removed outlier: 6.720A  pdb=" N   ALA M 211 " --> pdb=" O   ILE M 156 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR M 158 " --> pdb=" O   VAL M 209 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL M 209 " --> pdb=" O   THR M 158 " (cutoff:3.500A)
    Processing sheet with id= BW, first strand: chain 'M' and resid 91 through 121
    Processing sheet with id= BX, first strand: chain 'M' and resid 498 through 502
    Processing sheet with id= BY, first strand: chain 'M' and resid 204 through 210
      removed outlier: 6.761A  pdb=" N   ALA M 306 " --> pdb=" O   THR M 207 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   VAL M 209 " --> pdb=" O   ASP M 304 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ASP M 304 " --> pdb=" O   VAL M 209 " (cutoff:3.500A)
    Processing sheet with id= BZ, first strand: chain 'M' and resid 378 through 387
      removed outlier: 6.023A  pdb=" N   CYS M 462 " --> pdb=" O   GLY M 379 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   VAL M 381 " --> pdb=" O   TYR M 460 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   TYR M 460 " --> pdb=" O   VAL M 381 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN M 383 " --> pdb=" O   ARG M 458 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   ARG M 458 " --> pdb=" O   GLN M 383 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   CYS M 385 " --> pdb=" O   GLU M 456 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLU M 456 " --> pdb=" O   CYS M 385 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   GLU M 387 " --> pdb=" O   LYS M 454 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   LYS M 454 " --> pdb=" O   GLU M 387 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   TRP M 461 " --> pdb=" O   HIS M 417 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   HIS M 417 " --> pdb=" O   TRP M 461 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   VAL M 463 " --> pdb=" O   PRO M 415 " (cutoff:3.500A)
    Processing sheet with id= CA, first strand: chain 'M' and resid 558 through 566
      removed outlier: 3.747A  pdb=" N   HIS M 561 " --> pdb=" O   TYR M 573 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TYR M 573 " --> pdb=" O   HIS M 561 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   VAL M 571 " --> pdb=" O   ALA M 563 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ILE M 565 " --> pdb=" O   CYS M 569 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   CYS M 569 " --> pdb=" O   ILE M 565 " (cutoff:3.500A)
    Processing sheet with id= CB, first strand: chain 'N' and resid 84 through 88
      removed outlier: 6.720A  pdb=" N   ALA N 211 " --> pdb=" O   ILE N 156 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   THR N 158 " --> pdb=" O   VAL N 209 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL N 209 " --> pdb=" O   THR N 158 " (cutoff:3.500A)
    Processing sheet with id= CC, first strand: chain 'N' and resid 91 through 121
    Processing sheet with id= CD, first strand: chain 'N' and resid 383 through 387
      removed outlier: 6.500A  pdb=" N   TRP N 461 " --> pdb=" O   HIS N 417 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   HIS N 417 " --> pdb=" O   TRP N 461 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL N 463 " --> pdb=" O   PRO N 415 " (cutoff:3.500A)
    Processing sheet with id= CE, first strand: chain 'N' and resid 498 through 502
    Processing sheet with id= CF, first strand: chain 'N' and resid 204 through 209
      removed outlier: 6.727A  pdb=" N   ALA N 306 " --> pdb=" O   THR N 207 " (cutoff:3.500A)
    Processing sheet with id= CG, first strand: chain 'N' and resid 558 through 566
      removed outlier: 3.945A  pdb=" N   HIS N 561 " --> pdb=" O   TYR N 573 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR N 573 " --> pdb=" O   HIS N 561 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL N 571 " --> pdb=" O   ALA N 563 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ILE N 565 " --> pdb=" O   CYS N 569 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   CYS N 569 " --> pdb=" O   ILE N 565 " (cutoff:3.500A)
    Processing sheet with id= CH, first strand: chain 'O' and resid 84 through 88
      removed outlier: 6.654A  pdb=" N   ALA O 211 " --> pdb=" O   ILE O 156 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   THR O 158 " --> pdb=" O   VAL O 209 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL O 209 " --> pdb=" O   THR O 158 " (cutoff:3.500A)
    Processing sheet with id= CI, first strand: chain 'O' and resid 91 through 121
    Processing sheet with id= CJ, first strand: chain 'O' and resid 499 through 502
    Processing sheet with id= CK, first strand: chain 'O' and resid 204 through 210
      removed outlier: 6.823A  pdb=" N   ALA O 306 " --> pdb=" O   THR O 207 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   VAL O 209 " --> pdb=" O   ASP O 304 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ASP O 304 " --> pdb=" O   VAL O 209 " (cutoff:3.500A)
    Processing sheet with id= CL, first strand: chain 'O' and resid 378 through 387
      removed outlier: 5.661A  pdb=" N   CYS O 462 " --> pdb=" O   GLY O 379 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL O 381 " --> pdb=" O   TYR O 460 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   TYR O 460 " --> pdb=" O   VAL O 381 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN O 383 " --> pdb=" O   ARG O 458 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   ARG O 458 " --> pdb=" O   GLN O 383 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   CYS O 385 " --> pdb=" O   GLU O 456 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   GLU O 456 " --> pdb=" O   CYS O 385 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   GLU O 387 " --> pdb=" O   LYS O 454 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LYS O 454 " --> pdb=" O   GLU O 387 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   TRP O 461 " --> pdb=" O   HIS O 417 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   HIS O 417 " --> pdb=" O   TRP O 461 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL O 463 " --> pdb=" O   PRO O 415 " (cutoff:3.500A)
    Processing sheet with id= CM, first strand: chain 'O' and resid 525 through 529
      removed outlier: 6.547A  pdb=" N   CYS O 574 " --> pdb=" O   GLY O 526 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   PHE O 528 " --> pdb=" O   SER O 572 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   SER O 572 " --> pdb=" O   PHE O 528 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   TYR O 573 " --> pdb=" O   LEU O 562 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   LEU O 562 " --> pdb=" O   TYR O 573 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   VAL O 575 " --> pdb=" O   GLN O 560 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   GLN O 560 " --> pdb=" O   VAL O 575 " (cutoff:3.500A)
    Processing sheet with id= CN, first strand: chain 'P' and resid 84 through 88
      removed outlier: 6.733A  pdb=" N   ALA P 211 " --> pdb=" O   ILE P 156 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   THR P 158 " --> pdb=" O   VAL P 209 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL P 209 " --> pdb=" O   THR P 158 " (cutoff:3.500A)
    Processing sheet with id= CO, first strand: chain 'P' and resid 91 through 121
    Processing sheet with id= CP, first strand: chain 'P' and resid 479 through 481
    Processing sheet with id= CQ, first strand: chain 'P' and resid 204 through 210
      removed outlier: 6.802A  pdb=" N   ALA P 306 " --> pdb=" O   THR P 207 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL P 209 " --> pdb=" O   ASP P 304 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ASP P 304 " --> pdb=" O   VAL P 209 " (cutoff:3.500A)
    Processing sheet with id= CR, first strand: chain 'P' and resid 378 through 387
      removed outlier: 5.757A  pdb=" N   CYS P 462 " --> pdb=" O   GLY P 379 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   VAL P 381 " --> pdb=" O   TYR P 460 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   TYR P 460 " --> pdb=" O   VAL P 381 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLN P 383 " --> pdb=" O   ARG P 458 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ARG P 458 " --> pdb=" O   GLN P 383 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   CYS P 385 " --> pdb=" O   GLU P 456 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   GLU P 456 " --> pdb=" O   CYS P 385 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   GLU P 387 " --> pdb=" O   LYS P 454 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   LYS P 454 " --> pdb=" O   GLU P 387 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TRP P 461 " --> pdb=" O   HIS P 417 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   HIS P 417 " --> pdb=" O   TRP P 461 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL P 463 " --> pdb=" O   PRO P 415 " (cutoff:3.500A)
    Processing sheet with id= CS, first strand: chain 'P' and resid 525 through 530
      removed outlier: 6.370A  pdb=" N   CYS P 574 " --> pdb=" O   GLY P 526 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   PHE P 528 " --> pdb=" O   SER P 572 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER P 572 " --> pdb=" O   PHE P 528 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   SER P 530 " --> pdb=" O   GLN P 570 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   GLN P 570 " --> pdb=" O   SER P 530 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   TYR P 573 " --> pdb=" O   LEU P 562 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   LEU P 562 " --> pdb=" O   TYR P 573 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL P 575 " --> pdb=" O   GLN P 560 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   GLN P 560 " --> pdb=" O   VAL P 575 " (cutoff:3.500A)

    2847 hydrogen bonds defined for protein.
    8325 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: 21.12

  Time building geometry restraints manager: 21.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 20981
        1.33 -     1.46: 12946
        1.46 -     1.58: 34101
        1.58 -     1.70: 4
        1.70 -     1.82: 592
  Bond restraints: 68624
  Sorted by residual:
  bond pdb=" CB  PRO E 500 "
       pdb=" CG  PRO E 500 "
    ideal  model  delta    sigma   weight residual
    1.492  1.634 -0.142 5.00e-02 4.00e+02 8.07e+00
  bond pdb=" CB  PRO M 500 "
       pdb=" CG  PRO M 500 "
    ideal  model  delta    sigma   weight residual
    1.492  1.634 -0.142 5.00e-02 4.00e+02 8.02e+00
  bond pdb=" CA  ILE E 499 "
       pdb=" C   ILE E 499 "
    ideal  model  delta    sigma   weight residual
    1.524  1.543 -0.019 8.30e-03 1.45e+04 5.27e+00
  bond pdb=" CB  PRO H 592 "
       pdb=" CG  PRO H 592 "
    ideal  model  delta    sigma   weight residual
    1.506  1.586 -0.080 3.90e-02 6.57e+02 4.22e+00
  bond pdb=" CB  PRO P 592 "
       pdb=" CG  PRO P 592 "
    ideal  model  delta    sigma   weight residual
    1.506  1.586 -0.080 3.90e-02 6.57e+02 4.19e+00
  ... (remaining 68619 not shown)

  Histogram of bond angle deviations from ideal:
       98.87 -   105.89: 1703
      105.89 -   112.91: 38039
      112.91 -   119.93: 21695
      119.93 -   126.95: 30981
      126.95 -   133.97: 718
  Bond angle restraints: 93136
  Sorted by residual:
  angle pdb=" N   VAL O 588 "
        pdb=" CA  VAL O 588 "
        pdb=" C   VAL O 588 "
      ideal   model   delta    sigma   weight residual
     111.91  103.63    8.28 8.90e-01 1.26e+00 8.65e+01
  angle pdb=" CA  PRO E 500 "
        pdb=" N   PRO E 500 "
        pdb=" CD  PRO E 500 "
      ideal   model   delta    sigma   weight residual
     112.00  100.43   11.57 1.40e+00 5.10e-01 6.83e+01
  angle pdb=" CA  PRO M 500 "
        pdb=" N   PRO M 500 "
        pdb=" CD  PRO M 500 "
      ideal   model   delta    sigma   weight residual
     112.00  100.74   11.26 1.40e+00 5.10e-01 6.47e+01
  angle pdb=" CA  PRO P 592 "
        pdb=" N   PRO P 592 "
        pdb=" CD  PRO P 592 "
      ideal   model   delta    sigma   weight residual
     111.50  103.16    8.34 1.40e+00 5.10e-01 3.55e+01
  angle pdb=" CA  PRO H 592 "
        pdb=" N   PRO H 592 "
        pdb=" CD  PRO H 592 "
      ideal   model   delta    sigma   weight residual
     111.50  103.18    8.32 1.40e+00 5.10e-01 3.53e+01
  ... (remaining 93131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 39308
       17.97 -    35.94: 1474
       35.94 -    53.91: 287
       53.91 -    71.88: 52
       71.88 -    89.85: 15
  Dihedral angle restraints: 41136
    sinusoidal: 16528
      harmonic: 24608
  Sorted by residual:
  dihedral pdb=" CA  MET F 533 "
           pdb=" C   MET F 533 "
           pdb=" N   GLY F 534 "
           pdb=" CA  GLY F 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  MET N 533 "
           pdb=" C   MET N 533 "
           pdb=" N   GLY N 534 "
           pdb=" CA  GLY N 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.77   26.23     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  LEU G 590 "
           pdb=" C   LEU G 590 "
           pdb=" N   PRO G 591 "
           pdb=" CA  PRO G 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.30   23.70     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 41133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 8336
       0.049 -    0.099: 1944
       0.099 -    0.148: 500
       0.148 -    0.197: 5
       0.197 -    0.247: 31
  Chirality restraints: 10816
  Sorted by residual:
  chirality pdb=" C1  NAG I 701 "
            pdb=" ND2 ASN I 269 "
            pdb=" C2  NAG I 701 "
            pdb=" O5  NAG I 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 269 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C1  NAG D 701 "
            pdb=" ND2 ASN D 269 "
            pdb=" C2  NAG D 701 "
            pdb=" O5  NAG D 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 10813 not shown)

  Planarity restraints: 11808
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M 499 "    0.071 5.00e-02 4.00e+02   9.95e-02 1.58e+01
        pdb=" N   PRO M 500 "   -0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO M 500 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO M 500 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 499 "    0.071 5.00e-02 4.00e+02   9.94e-02 1.58e+01
        pdb=" N   PRO E 500 "   -0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 590 "    0.044 5.00e-02 4.00e+02   6.60e-02 6.97e+00
        pdb=" N   PRO D 591 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO D 591 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 591 "    0.037 5.00e-02 4.00e+02
  ... (remaining 11805 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 728
        2.57 -     3.15: 53431
        3.15 -     3.74: 100650
        3.74 -     4.32: 144760
        4.32 -     4.90: 245515
  Nonbonded interactions: 545084
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN M 345 "
            pdb=" OH  TYR M 593 "
     model   vdw
     1.988 2.440
  nonbonded pdb=" O   MET A  59 "
            pdb=" OH  TYR B  85 "
     model   vdw
     1.999 2.440
  nonbonded pdb=" OD1 ASN E 345 "
            pdb=" OH  TYR E 593 "
     model   vdw
     2.001 2.440
  nonbonded pdb=" O   MET J  59 "
            pdb=" OH  TYR K  85 "
     model   vdw
     2.005 2.440
  nonbonded pdb=" O   MET N  59 "
            pdb=" OH  TYR O  85 "
     model   vdw
     2.013 2.440
  ... (remaining 545079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.270
  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:             0.050
  Extract box with map and model:          12.090
  Check model and map are aligned:         0.910
  Set scattering table:                    0.570
  Process input model:                     132.990
  Find NCS groups from input model:        3.600
  Set up NCS constraints:                  0.570
  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:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  155.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0024
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      :  0.008   0.142  68624  Z= 0.493
  Angle     :  0.739  12.560  93136  Z= 0.392
  Chirality :  0.046   0.247  10816
  Planarity :  0.004   0.100  11792
  Dihedral  : 10.007  89.851  24944
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.87 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.93 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.09), residues: 8432
  helix:  1.59 (0.15), residues: 1232
  sheet: -0.02 (0.09), residues: 3744
  loop : -0.85 (0.11), residues: 3456

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  761 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 688
  time to evaluate  : 5.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 73
  outliers final: 17
  residues processed: 752
  average time/residue: 0.6365
  time to fit residues: 811.4998
Evaluate side-chains
  446 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 429
  time to evaluate  : 5.279 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.4930
  time to fit residues: 23.8219
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 716 optimal weight:    0.8980
   chunk 642 optimal weight:    0.5980
   chunk 356 optimal weight:    0.4980
   chunk 219 optimal weight:   10.0000
   chunk 433 optimal weight:   30.0000
   chunk 343 optimal weight:    6.9990
   chunk 664 optimal weight:    0.0270
   chunk 257 optimal weight:   40.0000
   chunk 404 optimal weight:    3.9990
   chunk 494 optimal weight:    0.1980
   chunk 770 optimal weight:    4.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
A 276 GLN
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 234 ASN
B 467 GLN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 311 HIS
C 467 GLN
C 570 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 276 GLN
D 467 GLN
D 570 GLN
E  32 GLN
E 276 GLN
E 467 GLN
E 570 GLN
F 220 HIS
F 259 GLN
F 276 GLN
F 340 HIS
F 383 GLN
** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 467 GLN
F 561 HIS
F 570 GLN
** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 276 GLN
G 383 GLN
G 401 ASN
G 467 GLN
H 134 GLN
H 181 GLN
** H 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 231 ASN
H 234 ASN
H 276 GLN
H 345 ASN
** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 467 GLN
I 186 GLN
I 276 GLN
J  89 GLN
J 220 HIS
J 311 HIS
J 340 HIS
J 467 GLN
K 204 HIS
K 276 GLN
K 311 HIS
K 383 GLN
K 467 GLN
K 560 GLN
K 570 GLN
L 181 GLN
L 186 GLN
L 204 HIS
L 276 GLN
L 467 GLN
L 570 GLN
M  32 GLN
M 276 GLN
M 311 HIS
** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 570 GLN
N 204 HIS
N 276 GLN
N 467 GLN
N 570 GLN
O  69 ASN
** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 276 GLN
O 383 GLN
O 467 GLN
O 570 GLN
P  77 GLN
P 181 GLN
** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 276 GLN
P 467 GLN
P 490 ASN

Total number of N/Q/H flips: 73

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0151
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060  68624  Z= 0.156
  Angle     :  0.580  16.789  93136  Z= 0.289
  Chirality :  0.044   0.233  10816
  Planarity :  0.004   0.061  11792
  Dihedral  :  4.644  59.213   9216
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.47 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.12 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.09), residues: 8432
  helix:  1.11 (0.14), residues: 1376
  sheet:  0.23 (0.09), residues: 3744
  loop : -0.90 (0.11), residues: 3312

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  611 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 130
    poor density    : 481
  time to evaluate  : 5.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 130
  outliers final: 47
  residues processed: 586
  average time/residue: 0.6349
  time to fit residues: 645.2507
Evaluate side-chains
  445 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 398
  time to evaluate  : 5.360 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 47
  outliers final: 1
  residues processed: 47
  average time/residue: 0.5118
  time to fit residues: 53.2629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 427 optimal weight:    8.9990
   chunk 238 optimal weight:   50.0000
   chunk 640 optimal weight:    5.9990
   chunk 524 optimal weight:    4.9990
   chunk 212 optimal weight:   90.0000
   chunk 771 optimal weight:    5.9990
   chunk 833 optimal weight:   20.0000
   chunk 687 optimal weight:    0.0170
   chunk 765 optimal weight:    0.9980
   chunk 263 optimal weight:    0.0970
   chunk 618 optimal weight:    0.0170
   overall best weight:    1.2256

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

Flipped N/Q/H residues before XYZ refinement:
A 126 ASN
A 383 GLN
A 401 ASN
B 186 GLN
C 144 GLN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 561 HIS
F 217 GLN
** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 570 GLN
H 144 GLN
H 229 ASN
H 383 GLN
I 144 GLN
** I 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 217 GLN
J 234 ASN
J 570 GLN
L 108 GLN
L 154 ASN
L 181 GLN
L 293 GLN
L 383 GLN
L 401 ASN
L 561 HIS
M 217 GLN
M 220 HIS
M 272 ASN
** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 186 GLN
N 217 GLN
N 220 HIS
N 234 ASN
N 299 HIS
** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 217 GLN
O 561 HIS
P 108 GLN
P 144 GLN
P 154 ASN
P 181 GLN
P 233 GLN
P 293 GLN
P 399 GLN

Total number of N/Q/H flips: 40

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0478
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090  68624  Z= 0.176
  Angle     :  0.600  12.924  93136  Z= 0.299
  Chirality :  0.045   0.429  10816
  Planarity :  0.005   0.060  11792
  Dihedral  :  4.595  59.491   9216
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.95 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.74 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.01 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.09), residues: 8432
  helix:  0.88 (0.14), residues: 1376
  sheet:  0.35 (0.09), residues: 3712
  loop : -0.86 (0.11), residues: 3344

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  599 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 119
    poor density    : 480
  time to evaluate  : 5.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 119
  outliers final: 51
  residues processed: 577
  average time/residue: 0.6274
  time to fit residues: 622.1748
Evaluate side-chains
  465 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 414
  time to evaluate  : 5.251 
Switching outliers to nearest non-outliers
  outliers start: 51
  outliers final: 0
  residues processed: 51
  average time/residue: 0.4997
  time to fit residues: 55.4716
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 762 optimal weight:   20.0000
   chunk 580 optimal weight:    0.9990
   chunk 400 optimal weight:    0.0050
   chunk 85 optimal weight:   20.0000
   chunk 368 optimal weight:   20.0000
   chunk 518 optimal weight:    4.9990
   chunk 774 optimal weight:    0.9980
   chunk 819 optimal weight:    4.9990
   chunk 404 optimal weight:   20.0000
   chunk 733 optimal weight:    0.5980
   chunk 220 optimal weight:   20.0000
   overall best weight:    1.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 340 HIS
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 570 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 345 ASN
E 561 HIS
** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 401 ASN
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 570 GLN
** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  77 GLN
L  97 ASN
L 311 HIS
** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 561 HIS
M 249 ASN
** M 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 401 ASN
N  69 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 231 ASN
** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 311 HIS
P  32 GLN
** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 259 GLN
** P 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0700
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096  68624  Z= 0.193
  Angle     :  0.612  12.681  93136  Z= 0.308
  Chirality :  0.046   0.353  10816
  Planarity :  0.005   0.084  11792
  Dihedral  :  4.702  59.781   9216
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.78 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.23 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.09), residues: 8432
  helix:  0.69 (0.14), residues: 1376
  sheet:  0.26 (0.09), residues: 3616
  loop : -0.94 (0.11), residues: 3440

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  563 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 93
    poor density    : 470
  time to evaluate  : 5.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 93
  outliers final: 41
  residues processed: 542
  average time/residue: 0.6393
  time to fit residues: 595.6302
Evaluate side-chains
  456 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 415
  time to evaluate  : 5.275 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 41
  outliers final: 1
  residues processed: 41
  average time/residue: 0.5318
  time to fit residues: 47.6278
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 682 optimal weight:    3.9990
   chunk 465 optimal weight:    8.9990
   chunk 11 optimal weight:   30.0000
   chunk 610 optimal weight:    4.9990
   chunk 338 optimal weight:    8.9990
   chunk 699 optimal weight:    2.9990
   chunk 566 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 418 optimal weight:    1.9990
   chunk 735 optimal weight:    3.9990
   chunk 206 optimal weight:   20.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 GLN
A 230 GLN
A 490 ASN
B 299 HIS
C  97 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 570 GLN
D 231 ASN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 217 GLN
E 231 ASN
E 490 ASN
F 401 ASN
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 401 ASN
K  32 GLN
** K  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 217 GLN
K 401 ASN
** L  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 186 GLN
L 234 ASN
** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 399 GLN
M  32 GLN
** M  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 234 ASN
** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  93 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 535 ASN
O 233 GLN
O 539 ASN
P  32 GLN
** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 233 GLN
P 276 GLN
P 345 ASN
P 417 HIS
P 560 GLN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1154
moved from start:          0.5925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.182  68624  Z= 0.334
  Angle     :  0.856  16.660  93136  Z= 0.438
  Chirality :  0.053   0.426  10816
  Planarity :  0.007   0.220  11792
  Dihedral  :  5.947  59.471   9216
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.48 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.23 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.09), residues: 8432
  helix: -0.05 (0.14), residues: 1396
  sheet:  0.14 (0.09), residues: 3257
  loop : -1.51 (0.10), residues: 3779

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  643 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 150
    poor density    : 493
  time to evaluate  : 5.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 150
  outliers final: 74
  residues processed: 611
  average time/residue: 0.6856
  time to fit residues: 716.4134
Evaluate side-chains
  504 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 430
  time to evaluate  : 5.278 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 74
  outliers final: 1
  residues processed: 74
  average time/residue: 0.5008
  time to fit residues: 77.1637
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 275 optimal weight:    6.9990
   chunk 738 optimal weight:    7.9990
   chunk 162 optimal weight:   10.0000
   chunk 481 optimal weight:   10.0000
   chunk 202 optimal weight:   50.0000
   chunk 820 optimal weight:    5.9990
   chunk 681 optimal weight:    2.9990
   chunk 379 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 271 optimal weight:   10.0000
   chunk 430 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 GLN
A 186 GLN
A 217 GLN
C 299 HIS
** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 234 ASN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 230 GLN
F  53 ASN
F 220 HIS
G 233 GLN
G 234 ASN
G 417 HIS
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  53 ASN
H 154 ASN
H 293 GLN
I  77 GLN
I 144 GLN
** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 220 HIS
I 259 GLN
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
** J  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 134 GLN
** J 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 490 ASN
** J 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 490 ASN
** K 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 151 GLN
** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 259 GLN
** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 471 ASN
N  69 ASN
N  93 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 383 GLN
N 401 ASN
O 144 GLN
O 560 GLN
** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 311 HIS

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1438
moved from start:          0.7586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.115  68624  Z= 0.388
  Angle     :  0.947  18.416  93136  Z= 0.483
  Chirality :  0.056   0.472  10816
  Planarity :  0.009   0.272  11792
  Dihedral  :  6.766  59.785   9216
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 22.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.94 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.61 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.01 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.45 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.09), residues: 8432
  helix: -0.27 (0.14), residues: 1288
  sheet: -0.15 (0.09), residues: 3140
  loop : -1.87 (0.09), residues: 4004

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  661 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 147
    poor density    : 514
  time to evaluate  : 5.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 147
  outliers final: 69
  residues processed: 626
  average time/residue: 0.6520
  time to fit residues: 704.5438
Evaluate side-chains
  525 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 456
  time to evaluate  : 5.539 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 69
  outliers final: 3
  residues processed: 69
  average time/residue: 0.5828
  time to fit residues: 80.1032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 791 optimal weight:    5.9990
   chunk 92 optimal weight:   50.0000
   chunk 467 optimal weight:    0.0770
   chunk 599 optimal weight:    2.9990
   chunk 464 optimal weight:    4.9990
   chunk 690 optimal weight:    0.9980
   chunk 458 optimal weight:    0.5980
   chunk 817 optimal weight:   50.0000
   chunk 511 optimal weight:    8.9990
   chunk 498 optimal weight:    6.9990
   chunk 377 optimal weight:   10.0000
   overall best weight:    1.9342

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 GLN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 ASN
B 108 GLN
B 186 GLN
B 230 GLN
** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  53 ASN
** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 151 GLN
** H 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 181 GLN
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  53 ASN
J 134 GLN
J 401 ASN
J 486 ASN
J 570 GLN
K  56 ASN
K 259 GLN
L  32 GLN
L 185 ASN
** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 234 ASN
** L 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 421 GLN
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 151 GLN
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 144 GLN
O 204 HIS
** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 234 ASN
** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1364
moved from start:          0.7784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  68624  Z= 0.221
  Angle     :  0.700  15.163  93136  Z= 0.354
  Chirality :  0.048   0.374  10816
  Planarity :  0.006   0.078  11792
  Dihedral  :  5.813  59.625   9216
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.44 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.74 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.22 %
    Twisted General : 0.01 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.09), residues: 8432
  helix:  0.10 (0.14), residues: 1284
  sheet: -0.14 (0.09), residues: 3246
  loop : -1.71 (0.10), residues: 3902

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  546 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 473
  time to evaluate  : 5.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 73
  outliers final: 39
  residues processed: 528
  average time/residue: 0.6492
  time to fit residues: 586.7906
Evaluate side-chains
  480 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 441
  time to evaluate  : 5.311 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 39
  outliers final: 1
  residues processed: 39
  average time/residue: 0.5222
  time to fit residues: 45.5086
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 505 optimal weight:    1.9990
   chunk 326 optimal weight:    6.9990
   chunk 488 optimal weight:    4.9990
   chunk 246 optimal weight:   50.0000
   chunk 160 optimal weight:   10.0000
   chunk 158 optimal weight:    0.7980
   chunk 519 optimal weight:    0.8980
   chunk 556 optimal weight:    0.8980
   chunk 404 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 642 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 HIS
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 HIS
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 570 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 ASN
H 561 HIS
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 154 ASN
L 185 ASN
** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 293 GLN
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  69 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 186 GLN
** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 560 GLN
** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 259 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1311
moved from start:          0.7897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  68624  Z= 0.173
  Angle     :  0.627  15.743  93136  Z= 0.314
  Chirality :  0.046   0.343  10816
  Planarity :  0.005   0.066  11792
  Dihedral  :  5.345  59.514   9216
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.93 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 14.17 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.09), residues: 8432
  helix:  0.24 (0.14), residues: 1297
  sheet: -0.02 (0.09), residues: 3221
  loop : -1.55 (0.10), residues: 3914

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  496 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 456
  time to evaluate  : 5.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 40
  outliers final: 22
  residues processed: 482
  average time/residue: 0.6698
  time to fit residues: 555.9423
Evaluate side-chains
  454 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 432
  time to evaluate  : 5.287 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 22
  outliers final: 1
  residues processed: 22
  average time/residue: 0.5653
  time to fit residues: 30.1252
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 743 optimal weight:    3.9990
   chunk 783 optimal weight:    0.6980
   chunk 714 optimal weight:    1.9990
   chunk 761 optimal weight:    1.9990
   chunk 782 optimal weight:    0.7980
   chunk 458 optimal weight:    0.6980
   chunk 331 optimal weight:    0.1980
   chunk 598 optimal weight:    1.9990
   chunk 233 optimal weight:   20.0000
   chunk 688 optimal weight:    0.9980
   chunk 720 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
C 570 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 217 GLN
I 220 HIS
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  56 ASN
L 144 GLN
** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 234 ASN
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  32 GLN
N  69 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 204 HIS
P 186 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1262
moved from start:          0.7955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.074  68624  Z= 0.152
  Angle     :  0.597  15.217  93136  Z= 0.297
  Chirality :  0.045   0.316  10816
  Planarity :  0.005   0.093  11792
  Dihedral  :  5.043  59.569   9216
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.33 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.58 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.09), residues: 8432
  helix:  0.43 (0.14), residues: 1293
  sheet:  0.07 (0.09), residues: 3222
  loop : -1.43 (0.10), residues: 3917

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  479 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 455
  time to evaluate  : 5.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 11
  residues processed: 472
  average time/residue: 0.6568
  time to fit residues: 535.4068
Evaluate side-chains
  434 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 423
  time to evaluate  : 5.328 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 11
  average time/residue: 0.5855
  time to fit residues: 19.2396
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 758 optimal weight:    0.6980
   chunk 500 optimal weight:    6.9990
   chunk 805 optimal weight:   30.0000
   chunk 491 optimal weight:    0.5980
   chunk 382 optimal weight:   10.0000
   chunk 559 optimal weight:    3.9990
   chunk 844 optimal weight:   20.0000
   chunk 777 optimal weight:    2.9990
   chunk 672 optimal weight:    8.9990
   chunk 69 optimal weight:   40.0000
   chunk 519 optimal weight:    0.0170
   overall best weight:    1.6622

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 GLN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 217 GLN
** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  56 ASN
** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 234 ASN
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  69 ASN
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 186 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1398
moved from start:          0.8395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  68624  Z= 0.202
  Angle     :  0.660  14.855  93136  Z= 0.330
  Chirality :  0.047   0.332  10816
  Planarity :  0.005   0.069  11792
  Dihedral  :  5.309  56.973   9216
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.44 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 14.79 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.01 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.09), residues: 8432
  helix:  0.43 (0.14), residues: 1276
  sheet:  0.06 (0.09), residues: 3356
  loop : -1.45 (0.10), residues: 3800

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

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

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  16864 Ramachandran restraints generated.
    8432 Oldfield, 0 Emsley, 8432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  470 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 452
  time to evaluate  : 5.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 10
  residues processed: 466
  average time/residue: 0.6502
  time to fit residues: 523.1375
Evaluate side-chains
  445 residues out of total 7504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 435
  time to evaluate  : 5.462 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 10
  outliers final: 1
  residues processed: 10
  average time/residue: 0.5592
  time to fit residues: 18.0134
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 848
   random chunks:
   chunk 412 optimal weight:    0.9990
   chunk 534 optimal weight:    3.9990
   chunk 716 optimal weight:    2.9990
   chunk 206 optimal weight:   50.0000
   chunk 620 optimal weight:    0.8980
   chunk 99 optimal weight:   30.0000
   chunk 186 optimal weight:    8.9990
   chunk 673 optimal weight:    0.0870
   chunk 281 optimal weight:   40.0000
   chunk 691 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.7964

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 230 GLN
** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 561 HIS
I 220 HIS
** I 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  97 ASN
** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 311 HIS
** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 401 ASN
** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5591 r_free = 0.5591 target = 0.365876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5563 r_free = 0.5563 target = 0.357909 restraints weight = 110393.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5559 r_free = 0.5559 target = 0.356935 restraints weight = 99569.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5557 r_free = 0.5557 target = 0.356321 restraints weight = 95986.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.5557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1950
moved from start:          0.8969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  68624  Z= 0.208
  Angle     :  0.670  12.640  93136  Z= 0.336
  Chirality :  0.047   0.401  10816
  Planarity :  0.005   0.086  11792
  Dihedral  :  5.422  57.116   9216
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.35 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 14.94 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.01 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.09), residues: 8432
  helix:  0.34 (0.14), residues: 1292
  sheet: -0.02 (0.09), residues: 3195
  loop : -1.54 (0.10), residues: 3945
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11293.59 seconds
wall clock time: 202 minutes 56.01 seconds (12176.01 seconds total)