Starting phenix.real_space_refine
on Sat Jun 29 06:42:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/06_2024/8rt5_19479.pdb"
  }
  resolution = 2.69
  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=   0.021 sd=   0.060
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      64      5.16       5
     C   10928      2.51       5
     N    3232      2.21       5
     O    3232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  139": "OE1" <-> "OE2"
    Residue "A ARG  144": "NH1" <-> "NH2"
    Residue "B TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   71": "OD1" <-> "OD2"
    Residue "B GLU   73": "OE1" <-> "OE2"
    Residue "B GLU   91": "OE1" <-> "OE2"
    Residue "B TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  109": "NH1" <-> "NH2"
    Residue "B ARG  113": "NH1" <-> "NH2"
    Residue "B TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  139": "OE1" <-> "OE2"
    Residue "D ARG  144": "NH1" <-> "NH2"
    Residue "E TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   71": "OD1" <-> "OD2"
    Residue "E GLU   73": "OE1" <-> "OE2"
    Residue "E GLU   91": "OE1" <-> "OE2"
    Residue "E TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  109": "NH1" <-> "NH2"
    Residue "E ARG  113": "NH1" <-> "NH2"
    Residue "E TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  139": "OE1" <-> "OE2"
    Residue "G ARG  144": "NH1" <-> "NH2"
    Residue "H TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   71": "OD1" <-> "OD2"
    Residue "H GLU   73": "OE1" <-> "OE2"
    Residue "H GLU   91": "OE1" <-> "OE2"
    Residue "H TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG  109": "NH1" <-> "NH2"
    Residue "H ARG  113": "NH1" <-> "NH2"
    Residue "H TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J GLU  139": "OE1" <-> "OE2"
    Residue "J ARG  144": "NH1" <-> "NH2"
    Residue "K TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ASP   71": "OD1" <-> "OD2"
    Residue "K GLU   73": "OE1" <-> "OE2"
    Residue "K GLU   91": "OE1" <-> "OE2"
    Residue "K TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ARG  109": "NH1" <-> "NH2"
    Residue "K ARG  113": "NH1" <-> "NH2"
    Residue "K TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  139": "OE1" <-> "OE2"
    Residue "M ARG  144": "NH1" <-> "NH2"
    Residue "N TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ASP   71": "OD1" <-> "OD2"
    Residue "N GLU   73": "OE1" <-> "OE2"
    Residue "N GLU   91": "OE1" <-> "OE2"
    Residue "N TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG  109": "NH1" <-> "NH2"
    Residue "N ARG  113": "NH1" <-> "NH2"
    Residue "N TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P GLU  139": "OE1" <-> "OE2"
    Residue "P ARG  144": "NH1" <-> "NH2"
    Residue "Q TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ASP   71": "OD1" <-> "OD2"
    Residue "Q GLU   73": "OE1" <-> "OE2"
    Residue "Q GLU   91": "OE1" <-> "OE2"
    Residue "Q TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ARG  109": "NH1" <-> "NH2"
    Residue "Q ARG  113": "NH1" <-> "NH2"
    Residue "Q TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S GLU  139": "OE1" <-> "OE2"
    Residue "S ARG  144": "NH1" <-> "NH2"
    Residue "T TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ASP   71": "OD1" <-> "OD2"
    Residue "T GLU   73": "OE1" <-> "OE2"
    Residue "T GLU   91": "OE1" <-> "OE2"
    Residue "T TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ARG  109": "NH1" <-> "NH2"
    Residue "T ARG  113": "NH1" <-> "NH2"
    Residue "T TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "u GLU  139": "OE1" <-> "OE2"
    Residue "u ARG  144": "NH1" <-> "NH2"
    Residue "v TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "v ASP   71": "OD1" <-> "OD2"
    Residue "v GLU   73": "OE1" <-> "OE2"
    Residue "v GLU   91": "OE1" <-> "OE2"
    Residue "v TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "v ARG  109": "NH1" <-> "NH2"
    Residue "v ARG  113": "NH1" <-> "NH2"
    Residue "v TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU  139": "OE1" <-> "OE2"
    Residue "V ARG  144": "NH1" <-> "NH2"
    Residue "W TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W ASP   71": "OD1" <-> "OD2"
    Residue "W GLU   73": "OE1" <-> "OE2"
    Residue "W GLU   91": "OE1" <-> "OE2"
    Residue "W TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W ARG  109": "NH1" <-> "NH2"
    Residue "W ARG  113": "NH1" <-> "NH2"
    Residue "W TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  139": "OE1" <-> "OE2"
    Residue "Y ARG  144": "NH1" <-> "NH2"
    Residue "Z TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z ASP   71": "OD1" <-> "OD2"
    Residue "Z GLU   73": "OE1" <-> "OE2"
    Residue "Z GLU   91": "OE1" <-> "OE2"
    Residue "Z TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z ARG  109": "NH1" <-> "NH2"
    Residue "Z ARG  113": "NH1" <-> "NH2"
    Residue "Z TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "b GLU  139": "OE1" <-> "OE2"
    Residue "b ARG  144": "NH1" <-> "NH2"
    Residue "c TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c ASP   71": "OD1" <-> "OD2"
    Residue "c GLU   73": "OE1" <-> "OE2"
    Residue "c GLU   91": "OE1" <-> "OE2"
    Residue "c TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c ARG  109": "NH1" <-> "NH2"
    Residue "c ARG  113": "NH1" <-> "NH2"
    Residue "c TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "e GLU  139": "OE1" <-> "OE2"
    Residue "e ARG  144": "NH1" <-> "NH2"
    Residue "f TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "f ASP   71": "OD1" <-> "OD2"
    Residue "f GLU   73": "OE1" <-> "OE2"
    Residue "f GLU   91": "OE1" <-> "OE2"
    Residue "f TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "f ARG  109": "NH1" <-> "NH2"
    Residue "f ARG  113": "NH1" <-> "NH2"
    Residue "f TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h GLU  139": "OE1" <-> "OE2"
    Residue "h ARG  144": "NH1" <-> "NH2"
    Residue "i TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "i ASP   71": "OD1" <-> "OD2"
    Residue "i GLU   73": "OE1" <-> "OE2"
    Residue "i GLU   91": "OE1" <-> "OE2"
    Residue "i TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "i ARG  109": "NH1" <-> "NH2"
    Residue "i ARG  113": "NH1" <-> "NH2"
    Residue "i TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "k GLU  139": "OE1" <-> "OE2"
    Residue "k ARG  144": "NH1" <-> "NH2"
    Residue "l TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "l ASP   71": "OD1" <-> "OD2"
    Residue "l GLU   73": "OE1" <-> "OE2"
    Residue "l GLU   91": "OE1" <-> "OE2"
    Residue "l TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "l ARG  109": "NH1" <-> "NH2"
    Residue "l ARG  113": "NH1" <-> "NH2"
    Residue "l TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "n GLU  139": "OE1" <-> "OE2"
    Residue "n ARG  144": "NH1" <-> "NH2"
    Residue "o TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "o ASP   71": "OD1" <-> "OD2"
    Residue "o GLU   73": "OE1" <-> "OE2"
    Residue "o GLU   91": "OE1" <-> "OE2"
    Residue "o TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "o ARG  109": "NH1" <-> "NH2"
    Residue "o ARG  113": "NH1" <-> "NH2"
    Residue "o TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "y GLU  139": "OE1" <-> "OE2"
    Residue "y ARG  144": "NH1" <-> "NH2"
    Residue "z TYR   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "z ASP   71": "OD1" <-> "OD2"
    Residue "z GLU   73": "OE1" <-> "OE2"
    Residue "z GLU   91": "OE1" <-> "OE2"
    Residue "z TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "z ARG  109": "NH1" <-> "NH2"
    Residue "z ARG  113": "NH1" <-> "NH2"
    Residue "z TYR  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib"
  Total number of atoms: 17456
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "B"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "E"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "G"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "H"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "J"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "K"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "M"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "N"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "P"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "Q"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "S"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "T"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "u"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "v"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "V"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "W"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "Y"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "Z"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "b"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "c"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "e"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "f"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "h"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "i"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "k"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "l"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "n"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "o"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "y"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "z"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 942
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
  Time building chain proxies: 9.22, per 1000 atoms: 0.53
  Number of scatterers: 17456
  At special positions: 0
  Unit cell: (167.519, 167.519, 67.221, 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      64     16.00
     O    3232      8.00
     N    3232      7.00
     C   10928      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.16
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4064

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 32 sheets defined
      18.7% alpha, 32.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 136 through 148
    Processing helix  chain 'B' and resid 71 through 73
      No H-bonds generated for 'chain 'B' and resid 71 through 73'
    Processing helix  chain 'B' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN B 131 " --> pdb=" O   TYR B 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 148
    Processing helix  chain 'E' and resid 71 through 73
      No H-bonds generated for 'chain 'E' and resid 71 through 73'
    Processing helix  chain 'E' and resid 127 through 135
      removed outlier: 3.573A  pdb=" N   GLN E 131 " --> pdb=" O   TYR E 127 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 136 through 148
    Processing helix  chain 'H' and resid 71 through 73
      No H-bonds generated for 'chain 'H' and resid 71 through 73'
    Processing helix  chain 'H' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN H 131 " --> pdb=" O   TYR H 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 136 through 148
    Processing helix  chain 'K' and resid 71 through 73
      No H-bonds generated for 'chain 'K' and resid 71 through 73'
    Processing helix  chain 'K' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN K 131 " --> pdb=" O   TYR K 127 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 136 through 148
    Processing helix  chain 'N' and resid 71 through 73
      No H-bonds generated for 'chain 'N' and resid 71 through 73'
    Processing helix  chain 'N' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN N 131 " --> pdb=" O   TYR N 127 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 136 through 148
    Processing helix  chain 'Q' and resid 71 through 73
      No H-bonds generated for 'chain 'Q' and resid 71 through 73'
    Processing helix  chain 'Q' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN Q 131 " --> pdb=" O   TYR Q 127 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 136 through 148
    Processing helix  chain 'T' and resid 71 through 73
      No H-bonds generated for 'chain 'T' and resid 71 through 73'
    Processing helix  chain 'T' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN T 131 " --> pdb=" O   TYR T 127 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 136 through 148
    Processing helix  chain 'v' and resid 71 through 73
      No H-bonds generated for 'chain 'v' and resid 71 through 73'
    Processing helix  chain 'v' and resid 127 through 135
      removed outlier: 3.573A  pdb=" N   GLN v 131 " --> pdb=" O   TYR v 127 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 136 through 148
    Processing helix  chain 'W' and resid 71 through 73
      No H-bonds generated for 'chain 'W' and resid 71 through 73'
    Processing helix  chain 'W' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN W 131 " --> pdb=" O   TYR W 127 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 136 through 148
    Processing helix  chain 'Z' and resid 71 through 73
      No H-bonds generated for 'chain 'Z' and resid 71 through 73'
    Processing helix  chain 'Z' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN Z 131 " --> pdb=" O   TYR Z 127 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 136 through 148
    Processing helix  chain 'c' and resid 71 through 73
      No H-bonds generated for 'chain 'c' and resid 71 through 73'
    Processing helix  chain 'c' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN c 131 " --> pdb=" O   TYR c 127 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 136 through 148
    Processing helix  chain 'f' and resid 71 through 73
      No H-bonds generated for 'chain 'f' and resid 71 through 73'
    Processing helix  chain 'f' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN f 131 " --> pdb=" O   TYR f 127 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 136 through 148
    Processing helix  chain 'i' and resid 71 through 73
      No H-bonds generated for 'chain 'i' and resid 71 through 73'
    Processing helix  chain 'i' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN i 131 " --> pdb=" O   TYR i 127 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 136 through 148
    Processing helix  chain 'l' and resid 71 through 73
      No H-bonds generated for 'chain 'l' and resid 71 through 73'
    Processing helix  chain 'l' and resid 127 through 135
      removed outlier: 3.573A  pdb=" N   GLN l 131 " --> pdb=" O   TYR l 127 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 136 through 148
    Processing helix  chain 'o' and resid 71 through 73
      No H-bonds generated for 'chain 'o' and resid 71 through 73'
    Processing helix  chain 'o' and resid 127 through 135
      removed outlier: 3.572A  pdb=" N   GLN o 131 " --> pdb=" O   TYR o 127 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 136 through 148
    Processing helix  chain 'z' and resid 71 through 73
      No H-bonds generated for 'chain 'z' and resid 71 through 73'
    Processing helix  chain 'z' and resid 127 through 135
      removed outlier: 3.573A  pdb=" N   GLN z 131 " --> pdb=" O   TYR z 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG B  34 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG B 126 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B  36 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS B  55 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   PHE B 125 " --> pdb=" O   HIS B  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET B  57 " --> pdb=" O   PHE B 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 48
    Processing sheet with id=AA3, first strand: chain 'E' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG E  34 " --> pdb=" O   ALA E 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG E 126 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL E  36 " --> pdb=" O   ARG E 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS E  55 " --> pdb=" O   LEU E 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE E 125 " --> pdb=" O   HIS E  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET E  57 " --> pdb=" O   PHE E 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 48
    Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG H  34 " --> pdb=" O   ALA H 124 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG H 126 " --> pdb=" O   ARG H  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL H  36 " --> pdb=" O   ARG H 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS H  55 " --> pdb=" O   LEU H 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE H 125 " --> pdb=" O   HIS H  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET H  57 " --> pdb=" O   PHE H 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 44 through 48
    Processing sheet with id=AA7, first strand: chain 'K' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG K  34 " --> pdb=" O   ALA K 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG K 126 " --> pdb=" O   ARG K  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL K  36 " --> pdb=" O   ARG K 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS K  55 " --> pdb=" O   LEU K 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE K 125 " --> pdb=" O   HIS K  55 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   MET K  57 " --> pdb=" O   PHE K 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 44 through 48
    Processing sheet with id=AA9, first strand: chain 'N' and resid 25 through 26
      removed outlier: 6.794A  pdb=" N   ARG N  34 " --> pdb=" O   ALA N 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG N 126 " --> pdb=" O   ARG N  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL N  36 " --> pdb=" O   ARG N 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS N  55 " --> pdb=" O   LEU N 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE N 125 " --> pdb=" O   HIS N  55 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   MET N  57 " --> pdb=" O   PHE N 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 44 through 48
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG Q  34 " --> pdb=" O   ALA Q 124 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG Q 126 " --> pdb=" O   ARG Q  34 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL Q  36 " --> pdb=" O   ARG Q 126 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   HIS Q  55 " --> pdb=" O   LEU Q 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE Q 125 " --> pdb=" O   HIS Q  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET Q  57 " --> pdb=" O   PHE Q 125 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'Q' and resid 44 through 48
    Processing sheet with id=AB4, first strand: chain 'T' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG T  34 " --> pdb=" O   ALA T 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG T 126 " --> pdb=" O   ARG T  34 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL T  36 " --> pdb=" O   ARG T 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS T  55 " --> pdb=" O   LEU T 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE T 125 " --> pdb=" O   HIS T  55 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   MET T  57 " --> pdb=" O   PHE T 125 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'T' and resid 44 through 48
    Processing sheet with id=AB6, first strand: chain 'v' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG v  34 " --> pdb=" O   ALA v 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG v 126 " --> pdb=" O   ARG v  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL v  36 " --> pdb=" O   ARG v 126 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   HIS v  55 " --> pdb=" O   LEU v 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE v 125 " --> pdb=" O   HIS v  55 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   MET v  57 " --> pdb=" O   PHE v 125 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'v' and resid 44 through 48
    Processing sheet with id=AB8, first strand: chain 'W' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG W  34 " --> pdb=" O   ALA W 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG W 126 " --> pdb=" O   ARG W  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL W  36 " --> pdb=" O   ARG W 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS W  55 " --> pdb=" O   LEU W 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE W 125 " --> pdb=" O   HIS W  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET W  57 " --> pdb=" O   PHE W 125 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'W' and resid 44 through 48
    Processing sheet with id=AC1, first strand: chain 'Z' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG Z  34 " --> pdb=" O   ALA Z 124 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG Z 126 " --> pdb=" O   ARG Z  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL Z  36 " --> pdb=" O   ARG Z 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS Z  55 " --> pdb=" O   LEU Z 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE Z 125 " --> pdb=" O   HIS Z  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET Z  57 " --> pdb=" O   PHE Z 125 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'Z' and resid 44 through 48
    Processing sheet with id=AC3, first strand: chain 'c' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG c  34 " --> pdb=" O   ALA c 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG c 126 " --> pdb=" O   ARG c  34 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL c  36 " --> pdb=" O   ARG c 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS c  55 " --> pdb=" O   LEU c 123 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   PHE c 125 " --> pdb=" O   HIS c  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET c  57 " --> pdb=" O   PHE c 125 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'c' and resid 44 through 48
    Processing sheet with id=AC5, first strand: chain 'f' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG f  34 " --> pdb=" O   ALA f 124 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG f 126 " --> pdb=" O   ARG f  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL f  36 " --> pdb=" O   ARG f 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS f  55 " --> pdb=" O   LEU f 123 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   PHE f 125 " --> pdb=" O   HIS f  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET f  57 " --> pdb=" O   PHE f 125 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'f' and resid 44 through 48
    Processing sheet with id=AC7, first strand: chain 'i' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG i  34 " --> pdb=" O   ALA i 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG i 126 " --> pdb=" O   ARG i  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL i  36 " --> pdb=" O   ARG i 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS i  55 " --> pdb=" O   LEU i 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE i 125 " --> pdb=" O   HIS i  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET i  57 " --> pdb=" O   PHE i 125 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'i' and resid 44 through 48
    Processing sheet with id=AC9, first strand: chain 'l' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG l  34 " --> pdb=" O   ALA l 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG l 126 " --> pdb=" O   ARG l  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL l  36 " --> pdb=" O   ARG l 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS l  55 " --> pdb=" O   LEU l 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE l 125 " --> pdb=" O   HIS l  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET l  57 " --> pdb=" O   PHE l 125 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'l' and resid 44 through 48
    Processing sheet with id=AD2, first strand: chain 'o' and resid 25 through 26
      removed outlier: 6.796A  pdb=" N   ARG o  34 " --> pdb=" O   ALA o 124 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG o 126 " --> pdb=" O   ARG o  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL o  36 " --> pdb=" O   ARG o 126 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   HIS o  55 " --> pdb=" O   LEU o 123 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE o 125 " --> pdb=" O   HIS o  55 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   MET o  57 " --> pdb=" O   PHE o 125 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'o' and resid 44 through 48
    Processing sheet with id=AD4, first strand: chain 'z' and resid 25 through 26
      removed outlier: 6.795A  pdb=" N   ARG z  34 " --> pdb=" O   ALA z 124 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ARG z 126 " --> pdb=" O   ARG z  34 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL z  36 " --> pdb=" O   ARG z 126 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   HIS z  55 " --> pdb=" O   LEU z 123 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   PHE z 125 " --> pdb=" O   HIS z  55 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   MET z  57 " --> pdb=" O   PHE z 125 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'z' and resid 44 through 48

    640 hydrogen bonds defined for protein.
    1680 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: 5.06

  Time building geometry restraints manager: 6.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5962
        1.34 -     1.45: 2802
        1.45 -     1.57: 8884
        1.57 -     1.68: 16
        1.68 -     1.80: 128
  Bond restraints: 17792
  Sorted by residual:
  bond pdb=" CG  PRO M 137 "
       pdb=" CD  PRO M 137 "
    ideal  model  delta    sigma   weight residual
    1.503  1.439  0.064 3.40e-02 8.65e+02 3.49e+00
  bond pdb=" CG  PRO S 137 "
       pdb=" CD  PRO S 137 "
    ideal  model  delta    sigma   weight residual
    1.503  1.440  0.063 3.40e-02 8.65e+02 3.46e+00
  bond pdb=" CG  PRO u 137 "
       pdb=" CD  PRO u 137 "
    ideal  model  delta    sigma   weight residual
    1.503  1.440  0.063 3.40e-02 8.65e+02 3.45e+00
  bond pdb=" CG  PRO Y 137 "
       pdb=" CD  PRO Y 137 "
    ideal  model  delta    sigma   weight residual
    1.503  1.440  0.063 3.40e-02 8.65e+02 3.45e+00
  bond pdb=" CG  PRO V 137 "
       pdb=" CD  PRO V 137 "
    ideal  model  delta    sigma   weight residual
    1.503  1.440  0.063 3.40e-02 8.65e+02 3.45e+00
  ... (remaining 17787 not shown)

  Histogram of bond angle deviations from ideal:
       98.36 -   104.98: 304
      104.98 -   111.59: 7561
      111.59 -   118.20: 5212
      118.20 -   124.82: 10762
      124.82 -   131.43: 177
  Bond angle restraints: 24016
  Sorted by residual:
  angle pdb=" CA  PRO J 137 "
        pdb=" N   PRO J 137 "
        pdb=" CD  PRO J 137 "
      ideal   model   delta    sigma   weight residual
     112.00  105.72    6.28 1.40e+00 5.10e-01 2.01e+01
  angle pdb=" CA  PRO e 137 "
        pdb=" N   PRO e 137 "
        pdb=" CD  PRO e 137 "
      ideal   model   delta    sigma   weight residual
     112.00  105.73    6.27 1.40e+00 5.10e-01 2.00e+01
  angle pdb=" CA  PRO n 137 "
        pdb=" N   PRO n 137 "
        pdb=" CD  PRO n 137 "
      ideal   model   delta    sigma   weight residual
     112.00  105.74    6.26 1.40e+00 5.10e-01 2.00e+01
  angle pdb=" CA  PRO b 137 "
        pdb=" N   PRO b 137 "
        pdb=" CD  PRO b 137 "
      ideal   model   delta    sigma   weight residual
     112.00  105.75    6.25 1.40e+00 5.10e-01 1.99e+01
  angle pdb=" CA  PRO P 137 "
        pdb=" N   PRO P 137 "
        pdb=" CD  PRO P 137 "
      ideal   model   delta    sigma   weight residual
     112.00  105.75    6.25 1.40e+00 5.10e-01 1.99e+01
  ... (remaining 24011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.06: 9744
       15.06 -    30.12: 816
       30.12 -    45.17: 144
       45.17 -    60.23: 64
       60.23 -    75.29: 16
  Dihedral angle restraints: 10784
    sinusoidal: 4464
      harmonic: 6320
  Sorted by residual:
  dihedral pdb=" CG  ARG N  34 "
           pdb=" CD  ARG N  34 "
           pdb=" NE  ARG N  34 "
           pdb=" CZ  ARG N  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.80  -40.80     2      1.50e+01 4.44e-03 9.11e+00
  dihedral pdb=" CG  ARG o  34 "
           pdb=" CD  ARG o  34 "
           pdb=" NE  ARG o  34 "
           pdb=" CZ  ARG o  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.80  -40.80     2      1.50e+01 4.44e-03 9.11e+00
  dihedral pdb=" CG  ARG Z  34 "
           pdb=" CD  ARG Z  34 "
           pdb=" NE  ARG Z  34 "
           pdb=" CZ  ARG Z  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.79  -40.79     2      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 10781 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1383
       0.033 -    0.066: 757
       0.066 -    0.098: 271
       0.098 -    0.131: 165
       0.131 -    0.164: 16
  Chirality restraints: 2592
  Sorted by residual:
  chirality pdb=" CA  PRO e 137 "
            pdb=" N   PRO e 137 "
            pdb=" C   PRO e 137 "
            pdb=" CB  PRO e 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.16 2.00e-01 2.50e+01 6.72e-01
  chirality pdb=" CA  PRO A 137 "
            pdb=" N   PRO A 137 "
            pdb=" C   PRO A 137 "
            pdb=" CB  PRO A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  PRO Y 137 "
            pdb=" N   PRO Y 137 "
            pdb=" C   PRO Y 137 "
            pdb=" CB  PRO Y 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 2589 not shown)

  Planarity restraints: 3152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 136 "   -0.070 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO S 137 "    0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO S 137 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO S 137 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR k 136 "    0.070 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO k 137 "   -0.177 5.00e-02 4.00e+02
        pdb=" CA  PRO k 137 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO k 137 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G 136 "    0.070 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO G 137 "   -0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO G 137 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO G 137 "    0.056 5.00e-02 4.00e+02
  ... (remaining 3149 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 150
        2.57 -     3.15: 13482
        3.15 -     3.74: 27234
        3.74 -     4.32: 40468
        4.32 -     4.90: 67458
  Nonbonded interactions: 148792
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS i  87 "
            pdb=" O   MET k 145 "
     model   vdw
     1.988 2.520
  nonbonded pdb=" NZ  LYS l  87 "
            pdb=" O   MET n 145 "
     model   vdw
     2.112 2.520
  nonbonded pdb=" NZ  LYS T  87 "
            pdb=" O   MET u 145 "
     model   vdw
     2.115 2.520
  nonbonded pdb=" NH1 ARG n 144 "
            pdb=" OD2 ASP o  71 "
     model   vdw
     2.120 2.520
  nonbonded pdb=" NZ  LYS Q  87 "
            pdb=" O   MET S 145 "
     model   vdw
     2.166 2.520
  ... (remaining 148787 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 'D'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'V'
  selection = chain 'Y'
  selection = chain 'b'
  selection = chain 'e'
  selection = chain 'h'
  selection = chain 'k'
  selection = chain 'n'
  selection = chain 'u'
  selection = chain 'y'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'Z'
  selection = chain 'c'
  selection = chain 'f'
  selection = chain 'i'
  selection = chain 'l'
  selection = chain 'o'
  selection = chain 'v'
  selection = chain 'z'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.990
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     44.490
  Find NCS groups from input model:        1.160
  Set up NCS constraints:                  0.200
  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:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
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      :  0.007   0.079  17792  Z= 0.465
  Angle     :  0.789   7.478  24016  Z= 0.466
  Chirality :  0.050   0.164   2592
  Planarity :  0.008   0.102   3152
  Dihedral  : 12.352  75.289   6720
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.17), residues: 2080
  helix:  2.22 (0.26), residues: 320
  sheet:  0.52 (0.16), residues: 880
  loop : -0.75 (0.21), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS Q  83 
 PHE   0.009   0.002   PHE f  77 
 TYR   0.014   0.002   TYR l 127 
 ARG   0.009   0.001   ARG G 142 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  776 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 776
  time to evaluate  : 2.004 
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: A  136 THR cc_start: 0.7681 (t) cc_final: 0.7428 (t)
REVERT: h  136 THR cc_start: 0.7747 (t) cc_final: 0.7356 (t)
REVERT: l  129 ASP cc_start: 0.6701 (p0) cc_final: 0.6495 (p0)
REVERT: n  136 THR cc_start: 0.6566 (t) cc_final: 0.6033 (t)
  outliers start: 0
  outliers final: 3
  residues processed: 776
  average time/residue: 1.1654
  time to fit residues: 1010.2541
Evaluate side-chains
  608 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 605
  time to evaluate  : 2.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 ASN
Chi-restraints excluded: chain W residue  114 ASN
Chi-restraints excluded: chain c residue  114 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    0.7980
   chunk 145 optimal weight:    0.0470
   chunk 80 optimal weight:   10.0000
   chunk 49 optimal weight:    0.1980
   chunk 98 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 150 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 112 optimal weight:    9.9990
   chunk 174 optimal weight:    7.9990
   overall best weight:    1.8082

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

Flipped N/Q/H residues before XYZ refinement:
B  94 ASN
E  89 GLN
E  94 ASN
H  94 ASN
** K  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  94 ASN
N  94 ASN
Q  89 GLN
Q  94 ASN
T  94 ASN
v  94 ASN
W  45 GLN
W  89 GLN
Z  89 GLN
Z  94 ASN
c  94 ASN
** f  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  94 ASN
i  94 ASN
l  45 GLN
l  89 GLN
l  94 ASN
o  94 ASN
** z  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
z  94 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17792  Z= 0.237
  Angle     :  0.648   6.652  24016  Z= 0.335
  Chirality :  0.047   0.173   2592
  Planarity :  0.005   0.043   3152
  Dihedral  :  4.294  18.605   2502
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.54 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.18), residues: 2080
  helix:  2.68 (0.26), residues: 320
  sheet:  0.44 (0.15), residues: 944
  loop : -0.74 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS T  83 
 PHE   0.010   0.001   PHE v  77 
 TYR   0.017   0.001   TYR k 138 
 ARG   0.009   0.001   ARG c  28 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  733 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 660
  time to evaluate  : 1.982 
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: G  136 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7415 (t)
REVERT: J  136 THR cc_start: 0.8178 (t) cc_final: 0.7969 (t)
REVERT: M  135 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7593 (ttpt)
REVERT: h  135 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7352 (mtmm)
  outliers start: 73
  outliers final: 9
  residues processed: 677
  average time/residue: 1.0469
  time to fit residues: 803.8927
Evaluate side-chains
  605 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 595
  time to evaluate  : 2.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   89 GLN
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain H residue  114 ASN
Chi-restraints excluded: chain T residue  114 ASN
Chi-restraints excluded: chain W residue  114 ASN
Chi-restraints excluded: chain Z residue   57 MET
Chi-restraints excluded: chain b residue  143 GLU
Chi-restraints excluded: chain c residue  114 ASN
Chi-restraints excluded: chain e residue  151 THR
Chi-restraints excluded: chain i residue  114 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 145 optimal weight:    4.9990
   chunk 118 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 174 optimal weight:   10.0000
   chunk 188 optimal weight:    6.9990
   chunk 155 optimal weight:    9.9990
   chunk 173 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 140 optimal weight:    2.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  89 GLN
W  45 GLN
W  89 GLN
W  94 ASN
Z  89 GLN
l  45 GLN
l  89 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  17792  Z= 0.487
  Angle     :  0.678   7.104  24016  Z= 0.355
  Chirality :  0.049   0.220   2592
  Planarity :  0.004   0.033   3152
  Dihedral  :  4.328  21.748   2500
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 18.86 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.18), residues: 2080
  helix:  2.72 (0.25), residues: 320
  sheet:  0.74 (0.17), residues: 896
  loop : -0.64 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS v  55 
 PHE   0.015   0.002   PHE f  77 
 TYR   0.014   0.001   TYR o  29 
 ARG   0.005   0.001   ARG J 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  720 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 102
    poor density    : 618
  time to evaluate  : 1.841 
Fit side-chains
REVERT: A  140 LEU cc_start: 0.7963 (mm) cc_final: 0.7527 (mm)
REVERT: S  143 GLU cc_start: 0.6109 (tp30) cc_final: 0.5425 (tp30)
REVERT: b  140 LEU cc_start: 0.7878 (mm) cc_final: 0.6972 (mm)
REVERT: k  135 LYS cc_start: 0.8012 (mttt) cc_final: 0.7222 (ttpt)
  outliers start: 102
  outliers final: 28
  residues processed: 645
  average time/residue: 1.0774
  time to fit residues: 782.7714
Evaluate side-chains
  578 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 550
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain H residue  114 ASN
Chi-restraints excluded: chain J residue  151 THR
Chi-restraints excluded: chain M residue  142 ARG
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain N residue  130 THR
Chi-restraints excluded: chain Q residue   92 LEU
Chi-restraints excluded: chain Q residue   97 LEU
Chi-restraints excluded: chain Q residue  130 THR
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain T residue  114 ASN
Chi-restraints excluded: chain T residue  130 THR
Chi-restraints excluded: chain u residue  142 ARG
Chi-restraints excluded: chain u residue  151 THR
Chi-restraints excluded: chain V residue  151 THR
Chi-restraints excluded: chain W residue  130 THR
Chi-restraints excluded: chain Z residue   92 LEU
Chi-restraints excluded: chain c residue  130 THR
Chi-restraints excluded: chain e residue  151 THR
Chi-restraints excluded: chain h residue  151 THR
Chi-restraints excluded: chain i residue  130 THR
Chi-restraints excluded: chain k residue  142 ARG
Chi-restraints excluded: chain l residue  114 ASN
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain o residue  114 ASN
Chi-restraints excluded: chain y residue  136 THR
Chi-restraints excluded: chain y residue  151 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 172 optimal weight:    4.9990
   chunk 131 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 117 optimal weight:    4.9990
   chunk 175 optimal weight:    2.9990
   chunk 185 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 166 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
E  89 GLN
K  89 GLN
v  89 GLN
v 131 GLN
W  45 GLN
f  89 GLN
o  45 GLN
z  89 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17792  Z= 0.225
  Angle     :  0.627   7.946  24016  Z= 0.328
  Chirality :  0.048   0.200   2592
  Planarity :  0.003   0.045   3152
  Dihedral  :  4.198  15.136   2496
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 21.82 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.18), residues: 2080
  helix:  2.86 (0.26), residues: 320
  sheet:  0.55 (0.16), residues: 944
  loop : -0.71 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS c  55 
 PHE   0.011   0.002   PHE l  77 
 TYR   0.016   0.001   TYR A 138 
 ARG   0.009   0.000   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  712 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 81
    poor density    : 631
  time to evaluate  : 1.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.5855 (tp30) cc_final: 0.5396 (tp30)
REVERT: B   50 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7659 (tp)
REVERT: G  143 GLU cc_start: 0.6032 (tp30) cc_final: 0.5576 (tp30)
REVERT: M  143 GLU cc_start: 0.5773 (tp30) cc_final: 0.5089 (tp30)
  outliers start: 81
  outliers final: 20
  residues processed: 648
  average time/residue: 1.0675
  time to fit residues: 779.9606
Evaluate side-chains
  588 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 567
  time to evaluate  : 1.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain H residue  114 ASN
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain N residue  114 ASN
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain T residue  114 ASN
Chi-restraints excluded: chain u residue  142 ARG
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain c residue  114 ASN
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain e residue  151 THR
Chi-restraints excluded: chain h residue  151 THR
Chi-restraints excluded: chain l residue  114 ASN
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain o residue  114 ASN
Chi-restraints excluded: chain y residue  136 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 154 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 138 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 158 optimal weight:    3.9990
   chunk 128 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 166 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
K  89 GLN
W  89 GLN
f  89 GLN
z  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17792  Z= 0.329
  Angle     :  0.662   8.172  24016  Z= 0.347
  Chirality :  0.049   0.196   2592
  Planarity :  0.003   0.037   3152
  Dihedral  :  4.280  14.393   2496
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.92 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.18), residues: 2080
  helix:  2.56 (0.27), residues: 320
  sheet:  0.78 (0.17), residues: 864
  loop : -0.80 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS f  55 
 PHE   0.011   0.002   PHE z  77 
 TYR   0.021   0.001   TYR S 138 
 ARG   0.006   0.001   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  685 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 87
    poor density    : 598
  time to evaluate  : 2.127 
Fit side-chains
   revert: symmetry clash
  outliers start: 87
  outliers final: 30
  residues processed: 618
  average time/residue: 1.0519
  time to fit residues: 734.7241
Evaluate side-chains
  572 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 542
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 ASN
Chi-restraints excluded: chain E residue  114 ASN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain K residue   47 ASP
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain Q residue  120 MET
Chi-restraints excluded: chain Q residue  130 THR
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain u residue  151 THR
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain h residue  151 THR
Chi-restraints excluded: chain i residue   56 ILE
Chi-restraints excluded: chain i residue  114 ASN
Chi-restraints excluded: chain k residue  142 ARG
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain l residue  120 MET
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain o residue   71 ASP
Chi-restraints excluded: chain o residue  114 ASN
Chi-restraints excluded: chain y residue  136 THR
Chi-restraints excluded: chain z residue   57 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 167 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0370
   chunk 108 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 185 optimal weight:    2.9990
   chunk 154 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0670
   chunk 15 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
H  89 GLN
Q  45 GLN
T  89 GLN
W  89 GLN
f  89 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  17792  Z= 0.215
  Angle     :  0.688   9.340  24016  Z= 0.354
  Chirality :  0.050   0.250   2592
  Planarity :  0.003   0.026   3152
  Dihedral  :  4.294  14.048   2496
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.55 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.18), residues: 2080
  helix:  2.51 (0.28), residues: 320
  sheet:  0.56 (0.16), residues: 944
  loop : -0.75 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS K  55 
 PHE   0.010   0.001   PHE B  77 
 TYR   0.014   0.001   TYR V 138 
 ARG   0.005   0.000   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  650 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 598
  time to evaluate  : 1.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 52
  outliers final: 17
  residues processed: 613
  average time/residue: 1.0449
  time to fit residues: 725.3414
Evaluate side-chains
  552 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 535
  time to evaluate  : 1.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain v residue   47 ASP
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain y residue  136 THR
Chi-restraints excluded: chain y residue  143 GLU
Chi-restraints excluded: chain z residue   57 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 179 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 105 optimal weight:    4.9990
   chunk 135 optimal weight:    8.9990
   chunk 156 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 185 optimal weight:    8.9990
   chunk 115 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
W  45 GLN
** W  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  89 GLN
l  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  17792  Z= 0.375
  Angle     :  0.755  12.197  24016  Z= 0.385
  Chirality :  0.052   0.319   2592
  Planarity :  0.003   0.025   3152
  Dihedral  :  4.439  14.927   2496
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 27.14 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.18), residues: 2080
  helix:  2.12 (0.28), residues: 320
  sheet:  0.80 (0.17), residues: 864
  loop : -0.79 (0.21), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS o  55 
 PHE   0.013   0.002   PHE v  77 
 TYR   0.014   0.002   TYR k 138 
 ARG   0.008   0.001   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  600 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 543
  time to evaluate  : 2.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.6005 (tp30) cc_final: 0.5440 (tp30)
REVERT: B   57 MET cc_start: 0.6840 (mmm) cc_final: 0.6590 (mmm)
REVERT: N   57 MET cc_start: 0.6873 (mmm) cc_final: 0.6537 (mmm)
  outliers start: 57
  outliers final: 30
  residues processed: 561
  average time/residue: 1.0139
  time to fit residues: 646.4608
Evaluate side-chains
  535 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 505
  time to evaluate  : 1.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain E residue  114 ASN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain N residue  130 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain Q residue  114 ASN
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain T residue  130 THR
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain u residue  143 GLU
Chi-restraints excluded: chain u residue  151 THR
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain W residue  130 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain h residue  151 THR
Chi-restraints excluded: chain i residue   71 ASP
Chi-restraints excluded: chain i residue  130 THR
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain l residue   89 GLN
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain y residue  136 THR
Chi-restraints excluded: chain z residue   57 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 110 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 35 optimal weight:    9.9990
   chunk 117 optimal weight:    7.9990
   chunk 126 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 145 optimal weight:    0.3980
   chunk 168 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** W  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  45 GLN
l  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  17792  Z= 0.234
  Angle     :  0.775  13.274  24016  Z= 0.389
  Chirality :  0.052   0.346   2592
  Planarity :  0.003   0.027   3152
  Dihedral  :  4.422  16.097   2496
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 29.33 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.18), residues: 2080
  helix:  2.13 (0.30), residues: 320
  sheet:  0.58 (0.16), residues: 944
  loop : -0.79 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.000   HIS W  55 
 PHE   0.010   0.001   PHE c  77 
 TYR   0.013   0.001   TYR V 138 
 ARG   0.007   0.000   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  609 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 575
  time to evaluate  : 2.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   57 MET cc_start: 0.6792 (mmm) cc_final: 0.6460 (mmm)
  outliers start: 34
  outliers final: 19
  residues processed: 591
  average time/residue: 1.0497
  time to fit residues: 704.3598
Evaluate side-chains
  532 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 513
  time to evaluate  : 1.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain u residue  140 LEU
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain e residue  140 LEU
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain y residue  136 THR
Chi-restraints excluded: chain y residue  140 LEU
Chi-restraints excluded: chain z residue   57 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 177 optimal weight:   10.0000
   chunk 161 optimal weight:    0.0270
   chunk 172 optimal weight:   10.0000
   chunk 103 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 135 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 155 optimal weight:    9.9990
   chunk 163 optimal weight:    0.7980
   chunk 171 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    1.9242

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  17792  Z= 0.270
  Angle     :  0.818  12.457  24016  Z= 0.412
  Chirality :  0.055   0.331   2592
  Planarity :  0.003   0.028   3152
  Dihedral  :  4.482  19.405   2496
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 29.39 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.18), residues: 2080
  helix:  1.97 (0.30), residues: 320
  sheet:  0.58 (0.16), residues: 944
  loop : -0.81 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS W  55 
 PHE   0.010   0.001   PHE K  77 
 TYR   0.011   0.001   TYR H  29 
 ARG   0.007   0.000   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  564 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 530
  time to evaluate  : 2.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   57 MET cc_start: 0.6710 (mmm) cc_final: 0.6417 (mmm)
  outliers start: 34
  outliers final: 21
  residues processed: 539
  average time/residue: 0.9903
  time to fit residues: 607.5224
Evaluate side-chains
  517 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 496
  time to evaluate  : 1.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  151 THR
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain u residue  140 LEU
Chi-restraints excluded: chain u residue  151 THR
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain e residue  140 LEU
Chi-restraints excluded: chain f residue   71 ASP
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain n residue  151 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 182 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 126 optimal weight:   10.0000
   chunk 191 optimal weight:    2.9990
   chunk 176 optimal weight:   10.0000
   chunk 152 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 117 optimal weight:    8.9990
   chunk 93 optimal weight:    8.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    4.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099  17792  Z= 0.415
  Angle     :  0.872  12.850  24016  Z= 0.440
  Chirality :  0.056   0.329   2592
  Planarity :  0.004   0.026   3152
  Dihedral  :  4.698  18.812   2496
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 20.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 30.48 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.18), residues: 2080
  helix:  1.70 (0.31), residues: 320
  sheet:  0.73 (0.17), residues: 864
  loop : -0.79 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS W  55 
 PHE   0.014   0.002   PHE v  77 
 TYR   0.017   0.002   TYR J 138 
 ARG   0.006   0.001   ARG b 147 

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

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

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4160 Ramachandran restraints generated.
    2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  531 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 501
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
REVERT: Q   50 LEU cc_start: 0.7908 (tp) cc_final: 0.7540 (tp)
REVERT: S  142 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6868 (ttm-80)
REVERT: z   71 ASP cc_start: 0.6185 (t0) cc_final: 0.5837 (t0)
  outliers start: 30
  outliers final: 24
  residues processed: 512
  average time/residue: 1.0467
  time to fit residues: 606.8529
Evaluate side-chains
  507 residues out of total 1824 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 482
  time to evaluate  : 1.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain M residue  151 THR
Chi-restraints excluded: chain P residue  136 THR
Chi-restraints excluded: chain P residue  150 LEU
Chi-restraints excluded: chain S residue  142 ARG
Chi-restraints excluded: chain S residue  151 THR
Chi-restraints excluded: chain u residue  136 THR
Chi-restraints excluded: chain u residue  143 GLU
Chi-restraints excluded: chain u residue  151 THR
Chi-restraints excluded: chain V residue  136 THR
Chi-restraints excluded: chain Y residue  136 THR
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue  120 MET
Chi-restraints excluded: chain b residue  136 THR
Chi-restraints excluded: chain e residue  136 THR
Chi-restraints excluded: chain e residue  140 LEU
Chi-restraints excluded: chain h residue  151 THR
Chi-restraints excluded: chain i residue   71 ASP
Chi-restraints excluded: chain k residue  150 LEU
Chi-restraints excluded: chain n residue  151 THR
Chi-restraints excluded: chain y residue  140 LEU
Chi-restraints excluded: chain y residue  151 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 140 optimal weight:    9.9990
   chunk 22 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 152 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 156 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 133 optimal weight:    7.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
l  89 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.043383 restraints weight = 60351.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 3.94
r_work: 0.2550 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  17792  Z= 0.303
  Angle     :  0.873  13.325  24016  Z= 0.439
  Chirality :  0.057   0.343   2592
  Planarity :  0.003   0.029   3152
  Dihedral  :  4.719  18.958   2496
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 30.59 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.18), residues: 2080
  helix:  1.82 (0.31), residues: 320
  sheet:  0.70 (0.17), residues: 864
  loop : -0.82 (0.20), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS W  55 
 PHE   0.011   0.002   PHE v  77 
 TYR   0.013   0.001   TYR H  29 
 ARG   0.006   0.000   ARG b 147 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9828.04 seconds
wall clock time: 171 minutes 7.35 seconds (10267.35 seconds total)