Starting phenix.real_space_refine
on Wed Feb 21 23:50:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1q_12696/02_2024/7o1q_12696.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C   10402      2.51       5
     N    2842      2.21       5
     O    3220      1.98       5
     H   15921      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR  148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR  182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G TYR  191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 32434
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4636
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "B"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "C"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "D"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "E"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "F"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
    Chain: "G"
      Number of atoms: 4633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4633
          Classifications: {'peptide': 293}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 283}
  Time building chain proxies: 13.95, per 1000 atoms: 0.43
  Number of scatterers: 32434
  At special positions: 0
  Unit cell: (112.27, 112.27, 111.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     O    3220      8.00
     N    2842      7.00
     C   10402      6.00
     H   15921      1.00
    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: 26.71
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3822

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 29 sheets defined
      3.8% alpha, 58.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 209
    Processing helix  chain 'B' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 209
    Processing helix  chain 'C' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 209
    Processing helix  chain 'D' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 205 through 209
    Processing helix  chain 'E' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 209
    Processing helix  chain 'F' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER F 221 " --> pdb=" O   SER F 217 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 205 through 209
    Processing helix  chain 'G' and resid 217 through 222
      removed outlier: 4.010A  pdb=" N   SER G 221 " --> pdb=" O   SER G 217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29
      removed outlier: 6.577A  pdb=" N   THR A 233 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE A  98 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY A  77 " --> pdb=" O   TYR A  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU A  70 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS A  75 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER A  82 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY A 166 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY A  77 " --> pdb=" O   TYR A  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU A  70 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS A  75 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS A  75 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   TRP A 260 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY A  77 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU A 258 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ALA A  79 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR A 256 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP A 254 " --> pdb=" O   PRO A  81 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A  83 " --> pdb=" O   VAL A 252 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ASP A 255 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP A 272 " --> pdb=" O   ASP A 255 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLN A 257 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   THR A 270 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   HIS A 259 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR A 268 " --> pdb=" O   HIS A 259 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 127
      removed outlier: 7.798A  pdb=" N   PHE A 109 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   VAL A 149 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY A 143 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE A 136 " --> pdb=" O   PHE G 124 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   PHE G 124 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY A 138 " --> pdb=" O   LEU G 122 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   PHE G 109 " --> pdb=" O   VAL G 149 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   VAL G 149 " --> pdb=" O   PHE G 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY G 143 " --> pdb=" O   TYR G 115 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER G 131 " --> pdb=" O   GLU G 127 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ILE G 136 " --> pdb=" O   PHE F 124 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   PHE F 124 " --> pdb=" O   ILE G 136 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLY G 138 " --> pdb=" O   LEU F 122 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   PHE F 109 " --> pdb=" O   VAL F 149 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   VAL F 149 " --> pdb=" O   PHE F 109 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY F 143 " --> pdb=" O   TYR F 115 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER F 131 " --> pdb=" O   GLU F 127 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE F 136 " --> pdb=" O   PHE E 124 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   PHE E 124 " --> pdb=" O   ILE F 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY F 138 " --> pdb=" O   LEU E 122 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   PHE E 109 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   VAL E 149 " --> pdb=" O   PHE E 109 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY E 143 " --> pdb=" O   TYR E 115 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER E 131 " --> pdb=" O   GLU E 127 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE E 136 " --> pdb=" O   PHE D 124 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   PHE D 124 " --> pdb=" O   ILE E 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY E 138 " --> pdb=" O   LEU D 122 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   PHE D 109 " --> pdb=" O   VAL D 149 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   VAL D 149 " --> pdb=" O   PHE D 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY D 143 " --> pdb=" O   TYR D 115 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE D 136 " --> pdb=" O   PHE C 124 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   PHE C 124 " --> pdb=" O   ILE D 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY D 138 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   PHE C 109 " --> pdb=" O   VAL C 149 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   VAL C 149 " --> pdb=" O   PHE C 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY C 143 " --> pdb=" O   TYR C 115 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER C 131 " --> pdb=" O   GLU C 127 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE C 136 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   PHE B 124 " --> pdb=" O   ILE C 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY C 138 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   PHE B 109 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   VAL B 149 " --> pdb=" O   PHE B 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY B 143 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ILE B 136 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   PHE A 124 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B 138 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 29
      removed outlier: 6.577A  pdb=" N   THR B 233 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE B  98 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY B  77 " --> pdb=" O   TYR B  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU B  70 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS B  75 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER B  82 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY B 166 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY B  77 " --> pdb=" O   TYR B  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU B  70 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS B  75 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS B  75 " --> pdb=" O   TRP B 260 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   TRP B 260 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU B 258 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ALA B  79 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR B 256 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP B 254 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B  83 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ASP B 255 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP B 272 " --> pdb=" O   ASP B 255 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLN B 257 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   THR B 270 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   HIS B 259 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR B 268 " --> pdb=" O   HIS B 259 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 175
    Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 29
      removed outlier: 6.578A  pdb=" N   THR C 233 " --> pdb=" O   ILE C  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE C  98 " --> pdb=" O   THR C 233 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 70
      removed outlier: 6.959A  pdb=" N   GLY C  77 " --> pdb=" O   TYR C  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU C  70 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS C  75 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER C  82 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY C 166 " --> pdb=" O   GLU C 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 70
      removed outlier: 6.959A  pdb=" N   GLY C  77 " --> pdb=" O   TYR C  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU C  70 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS C  75 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS C  75 " --> pdb=" O   TRP C 260 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   TRP C 260 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY C  77 " --> pdb=" O   LEU C 258 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU C 258 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA C  79 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TYR C 256 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP C 254 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA C  83 " --> pdb=" O   VAL C 252 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ASP C 255 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ASP C 272 " --> pdb=" O   ASP C 255 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLN C 257 " --> pdb=" O   THR C 270 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   THR C 270 " --> pdb=" O   GLN C 257 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   HIS C 259 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR C 268 " --> pdb=" O   HIS C 259 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 174 through 175
    Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 29
      removed outlier: 6.578A  pdb=" N   THR D 233 " --> pdb=" O   ILE D  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE D  98 " --> pdb=" O   THR D 233 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY D  77 " --> pdb=" O   TYR D  68 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   GLU D  70 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS D  75 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER D  82 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY D 166 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY D  77 " --> pdb=" O   TYR D  68 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   GLU D  70 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS D  75 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS D  75 " --> pdb=" O   TRP D 260 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   TRP D 260 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY D  77 " --> pdb=" O   LEU D 258 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU D 258 " --> pdb=" O   GLY D  77 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA D  79 " --> pdb=" O   TYR D 256 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   TYR D 256 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ASP D 254 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA D  83 " --> pdb=" O   VAL D 252 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ASP D 255 " --> pdb=" O   ASP D 272 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP D 272 " --> pdb=" O   ASP D 255 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLN D 257 " --> pdb=" O   THR D 270 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   THR D 270 " --> pdb=" O   GLN D 257 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   HIS D 259 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR D 268 " --> pdb=" O   HIS D 259 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 175
    Processing sheet with id=AB9, first strand: chain 'E' and resid 20 through 29
      removed outlier: 6.578A  pdb=" N   THR E 233 " --> pdb=" O   ILE E  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE E  98 " --> pdb=" O   THR E 233 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY E  77 " --> pdb=" O   TYR E  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU E  70 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS E  75 " --> pdb=" O   GLU E  70 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   SER E  82 " --> pdb=" O   PHE E 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY E 166 " --> pdb=" O   GLU E 158 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY E  77 " --> pdb=" O   TYR E  68 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   GLU E  70 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS E  75 " --> pdb=" O   GLU E  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS E  75 " --> pdb=" O   TRP E 260 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   TRP E 260 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY E  77 " --> pdb=" O   LEU E 258 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   LEU E 258 " --> pdb=" O   GLY E  77 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA E  79 " --> pdb=" O   TYR E 256 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR E 256 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP E 254 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA E  83 " --> pdb=" O   VAL E 252 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ASP E 255 " --> pdb=" O   ASP E 272 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP E 272 " --> pdb=" O   ASP E 255 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLN E 257 " --> pdb=" O   THR E 270 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   THR E 270 " --> pdb=" O   GLN E 257 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   HIS E 259 " --> pdb=" O   THR E 268 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   THR E 268 " --> pdb=" O   HIS E 259 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 174 through 175
    Processing sheet with id=AC4, first strand: chain 'F' and resid 20 through 29
      removed outlier: 6.577A  pdb=" N   THR F 233 " --> pdb=" O   ILE F  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE F  98 " --> pdb=" O   THR F 233 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 66 through 70
      removed outlier: 6.959A  pdb=" N   GLY F  77 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU F  70 " --> pdb=" O   LYS F  75 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS F  75 " --> pdb=" O   GLU F  70 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER F  82 " --> pdb=" O   PHE F 171 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY F 166 " --> pdb=" O   GLU F 158 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 66 through 70
      removed outlier: 6.959A  pdb=" N   GLY F  77 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU F  70 " --> pdb=" O   LYS F  75 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS F  75 " --> pdb=" O   GLU F  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS F  75 " --> pdb=" O   TRP F 260 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   TRP F 260 " --> pdb=" O   LYS F  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY F  77 " --> pdb=" O   LEU F 258 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   LEU F 258 " --> pdb=" O   GLY F  77 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ALA F  79 " --> pdb=" O   TYR F 256 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TYR F 256 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP F 254 " --> pdb=" O   PRO F  81 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA F  83 " --> pdb=" O   VAL F 252 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ASP F 255 " --> pdb=" O   ASP F 272 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ASP F 272 " --> pdb=" O   ASP F 255 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLN F 257 " --> pdb=" O   THR F 270 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   THR F 270 " --> pdb=" O   GLN F 257 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   HIS F 259 " --> pdb=" O   THR F 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR F 268 " --> pdb=" O   HIS F 259 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 175
    Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 29
      removed outlier: 6.578A  pdb=" N   THR G 233 " --> pdb=" O   ILE G  98 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ILE G  98 " --> pdb=" O   THR G 233 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY G  77 " --> pdb=" O   TYR G  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU G  70 " --> pdb=" O   LYS G  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS G  75 " --> pdb=" O   GLU G  70 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   SER G  82 " --> pdb=" O   PHE G 171 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLY G 166 " --> pdb=" O   GLU G 158 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 70
      removed outlier: 6.960A  pdb=" N   GLY G  77 " --> pdb=" O   TYR G  68 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLU G  70 " --> pdb=" O   LYS G  75 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS G  75 " --> pdb=" O   GLU G  70 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS G  75 " --> pdb=" O   TRP G 260 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   TRP G 260 " --> pdb=" O   LYS G  75 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   GLY G  77 " --> pdb=" O   LEU G 258 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU G 258 " --> pdb=" O   GLY G  77 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA G  79 " --> pdb=" O   TYR G 256 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   TYR G 256 " --> pdb=" O   ALA G  79 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP G 254 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA G  83 " --> pdb=" O   VAL G 252 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ASP G 255 " --> pdb=" O   ASP G 272 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ASP G 272 " --> pdb=" O   ASP G 255 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLN G 257 " --> pdb=" O   THR G 270 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   THR G 270 " --> pdb=" O   GLN G 257 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   HIS G 259 " --> pdb=" O   THR G 268 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR G 268 " --> pdb=" O   HIS G 259 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'G' and resid 174 through 175

    763 hydrogen bonds defined for protein.
    2121 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: 13.14

  Time building geometry restraints manager: 27.42 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 15921
        1.03 -     1.22: 0
        1.22 -     1.41: 7260
        1.41 -     1.61: 9540
        1.61 -     1.80: 98
  Bond restraints: 32819
  Sorted by residual:
  bond pdb=" CB  PRO F 103 "
       pdb=" CG  PRO F 103 "
    ideal  model  delta    sigma   weight residual
    1.506  1.445  0.061 3.90e-02 6.57e+02 2.43e+00
  bond pdb=" CB  PRO A 103 "
       pdb=" CG  PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.506  1.446  0.060 3.90e-02 6.57e+02 2.40e+00
  bond pdb=" CB  PRO G 103 "
       pdb=" CG  PRO G 103 "
    ideal  model  delta    sigma   weight residual
    1.506  1.446  0.060 3.90e-02 6.57e+02 2.38e+00
  bond pdb=" CB  PRO E 103 "
       pdb=" CG  PRO E 103 "
    ideal  model  delta    sigma   weight residual
    1.506  1.446  0.060 3.90e-02 6.57e+02 2.37e+00
  bond pdb=" CB  PRO B 103 "
       pdb=" CG  PRO B 103 "
    ideal  model  delta    sigma   weight residual
    1.506  1.446  0.060 3.90e-02 6.57e+02 2.36e+00
  ... (remaining 32814 not shown)

  Histogram of bond angle deviations from ideal:
       98.82 -   105.86: 276
      105.86 -   112.90: 37654
      112.90 -   119.94: 8699
      119.94 -   126.98: 12204
      126.98 -   134.02: 239
  Bond angle restraints: 59072
  Sorted by residual:
  angle pdb=" N   SER F 262 "
        pdb=" CA  SER F 262 "
        pdb=" CB  SER F 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.74    3.43 1.14e+00 7.69e-01 9.04e+00
  angle pdb=" N   SER G 262 "
        pdb=" CA  SER G 262 "
        pdb=" CB  SER G 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.74    3.43 1.14e+00 7.69e-01 9.04e+00
  angle pdb=" N   SER B 262 "
        pdb=" CA  SER B 262 "
        pdb=" CB  SER B 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.75    3.42 1.14e+00 7.69e-01 9.00e+00
  angle pdb=" N   SER A 262 "
        pdb=" CA  SER A 262 "
        pdb=" CB  SER A 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.78    3.39 1.14e+00 7.69e-01 8.87e+00
  angle pdb=" N   SER D 262 "
        pdb=" CA  SER D 262 "
        pdb=" CB  SER D 262 "
      ideal   model   delta    sigma   weight residual
     114.17  110.78    3.39 1.14e+00 7.69e-01 8.86e+00
  ... (remaining 59067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 14722
       17.84 -    35.68: 576
       35.68 -    53.53: 136
       53.53 -    71.37: 29
       71.37 -    89.21: 14
  Dihedral angle restraints: 15477
    sinusoidal: 8274
      harmonic: 7203
  Sorted by residual:
  dihedral pdb=" CA  PRO G 226 "
           pdb=" C   PRO G 226 "
           pdb=" N   ASP G 227 "
           pdb=" CA  ASP G 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.99   14.01     0      5.00e+00 4.00e-02 7.85e+00
  dihedral pdb=" CA  PRO C 226 "
           pdb=" C   PRO C 226 "
           pdb=" N   ASP C 227 "
           pdb=" CA  ASP C 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.03   13.97     0      5.00e+00 4.00e-02 7.81e+00
  dihedral pdb=" CA  PRO B 226 "
           pdb=" C   PRO B 226 "
           pdb=" N   ASP B 227 "
           pdb=" CA  ASP B 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.03   13.97     0      5.00e+00 4.00e-02 7.81e+00
  ... (remaining 15474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1188
       0.029 -    0.058: 826
       0.058 -    0.087: 179
       0.087 -    0.116: 166
       0.116 -    0.145: 56
  Chirality restraints: 2415
  Sorted by residual:
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE F 232 "
            pdb=" N   ILE F 232 "
            pdb=" C   ILE F 232 "
            pdb=" CB  ILE F 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 2412 not shown)

  Planarity restraints: 4949
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 159 "    0.019 5.00e-02 4.00e+02   2.83e-02 1.29e+00
        pdb=" N   PRO B 160 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 160 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 160 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F 159 "   -0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO F 160 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO F 160 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO F 160 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 159 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO C 160 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO C 160 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 160 "    0.016 5.00e-02 4.00e+02
  ... (remaining 4946 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 833
        2.11 -     2.73: 58933
        2.73 -     3.35: 88631
        3.35 -     3.98: 123965
        3.98 -     4.60: 194743
  Nonbonded interactions: 467105
  Sorted by model distance:
  nonbonded pdb=" HG1 THR A  60 "
            pdb=" OH  TYR G 101 "
     model   vdw
     1.486 1.850
  nonbonded pdb=" OH  TYR E 101 "
            pdb=" HG1 THR F  60 "
     model   vdw
     1.488 1.850
  nonbonded pdb=" OH  TYR B 101 "
            pdb=" HG1 THR C  60 "
     model   vdw
     1.489 1.850
  nonbonded pdb=" OH  TYR A 101 "
            pdb=" HG1 THR B  60 "
     model   vdw
     1.489 1.850
  nonbonded pdb=" OH  TYR C 101 "
            pdb=" HG1 THR D  60 "
     model   vdw
     1.489 1.850
  ... (remaining 467100 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' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ 
r name HA or name HB1 or name HB2 or name HB3)) or resid 2 through 293))
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.450
  Extract box with map and model:          3.370
  Check model and map are aligned:         0.430
  Set scattering table:                    0.290
  Process input model:                     101.670
  Find NCS groups from input model:        1.500
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  111.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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   0.061  16898  Z= 0.434
  Angle     :  0.550   4.080  22869  Z= 0.322
  Chirality :  0.047   0.145   2415
  Planarity :  0.003   0.028   2968
  Dihedral  :  9.972  89.210   6202
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.33 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.21 (0.18), residues: 2037
  helix: -4.43 (0.08), residues: 42
  sheet:  0.32 (0.16), residues: 1057
  loop : -0.35 (0.20), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 274 
 HIS   0.003   0.001   HIS B  48 
 PHE   0.010   0.001   PHE E 125 
 TYR   0.014   0.002   TYR G  65 
 ARG   0.002   0.000   ARG A  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 370
  time to evaluate  : 2.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.0822 (tpt) cc_final: -0.0917 (ppp)
REVERT: A  170 ILE cc_start: 0.9196 (mm) cc_final: 0.8932 (tp)
REVERT: B  140 MET cc_start: 0.1324 (tpt) cc_final: -0.0810 (ppp)
REVERT: B  170 ILE cc_start: 0.9186 (mm) cc_final: 0.8892 (tp)
REVERT: C  140 MET cc_start: 0.1085 (tpt) cc_final: -0.0644 (ppp)
REVERT: C  162 ASP cc_start: 0.7892 (p0) cc_final: 0.7688 (p0)
REVERT: C  170 ILE cc_start: 0.9209 (mm) cc_final: 0.8910 (tp)
REVERT: D  140 MET cc_start: 0.1541 (tpt) cc_final: -0.0895 (ppp)
REVERT: D  170 ILE cc_start: 0.9166 (mm) cc_final: 0.8896 (tp)
REVERT: E  140 MET cc_start: 0.1484 (tpt) cc_final: -0.0027 (ppp)
REVERT: E  162 ASP cc_start: 0.7893 (p0) cc_final: 0.7688 (p0)
REVERT: E  170 ILE cc_start: 0.9104 (mm) cc_final: 0.8859 (tp)
REVERT: F  140 MET cc_start: 0.1209 (tpt) cc_final: -0.0470 (ppp)
REVERT: F  170 ILE cc_start: 0.9201 (mm) cc_final: 0.8938 (tp)
REVERT: G  140 MET cc_start: 0.0599 (tpt) cc_final: -0.0794 (ppp)
REVERT: G  162 ASP cc_start: 0.7977 (p0) cc_final: 0.7773 (p0)
REVERT: G  170 ILE cc_start: 0.9166 (mm) cc_final: 0.8900 (tp)
  outliers start: 7
  outliers final: 0
  residues processed: 377
  average time/residue: 0.8389
  time to fit residues: 431.6977
Evaluate side-chains
  214 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 2.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 171 optimal weight:    0.5980
   chunk 153 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 159 optimal weight:   50.0000
   chunk 61 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   chunk 184 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C 214 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  16898  Z= 0.150
  Angle     :  0.488   4.401  22869  Z= 0.263
  Chirality :  0.047   0.159   2415
  Planarity :  0.003   0.050   2968
  Dihedral  :  4.588  20.317   2219
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  9.58 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.21 (0.19), residues: 2037
  helix: -4.33 (0.09), residues: 42
  sheet:  0.48 (0.16), residues: 1057
  loop :  0.11 (0.21), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 260 
 HIS   0.004   0.001   HIS G 259 
 PHE   0.007   0.001   PHE G 124 
 TYR   0.012   0.001   TYR C  65 
 ARG   0.006   0.000   ARG D  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 247
  time to evaluate  : 2.470 
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: B  156 ILE cc_start: 0.9175 (mt) cc_final: 0.8915 (mt)
REVERT: C  170 ILE cc_start: 0.9110 (mm) cc_final: 0.8909 (tp)
REVERT: F  170 ILE cc_start: 0.9092 (mm) cc_final: 0.8874 (tp)
  outliers start: 9
  outliers final: 9
  residues processed: 255
  average time/residue: 0.8224
  time to fit residues: 290.0154
Evaluate side-chains
  222 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 213
  time to evaluate  : 3.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain G residue  139 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 153 optimal weight:    3.9990
   chunk 125 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 184 optimal weight:    3.9990
   chunk 199 optimal weight:    7.9990
   chunk 164 optimal weight:    6.9990
   chunk 183 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 148 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 259 HIS
B 105 ASN
B 172 ASN
C 259 HIS
D 259 HIS
E 172 ASN
E 259 HIS
F 201 ASN
F 259 HIS
G 259 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  16898  Z= 0.427
  Angle     :  0.532   4.320  22869  Z= 0.287
  Chirality :  0.047   0.141   2415
  Planarity :  0.003   0.031   2968
  Dihedral  :  4.968  38.180   2219
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.30 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.01 (0.19), residues: 2037
  helix: -2.61 (0.48), residues: 42
  sheet:  0.33 (0.16), residues: 1050
  loop : -0.14 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G 167 
 HIS   0.005   0.001   HIS F 259 
 PHE   0.007   0.001   PHE A 171 
 TYR   0.016   0.002   TYR G  65 
 ARG   0.005   0.000   ARG C  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 204
  time to evaluate  : 2.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  140 MET cc_start: 0.1181 (tpt) cc_final: 0.0934 (tpt)
  outliers start: 30
  outliers final: 28
  residues processed: 224
  average time/residue: 0.9326
  time to fit residues: 291.8633
Evaluate side-chains
  219 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 2.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue    2 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue   24 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue    2 ASP
Chi-restraints excluded: chain E residue   24 ASP
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 182 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 185 optimal weight:   40.0000
   chunk 196 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 175 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 259 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  16898  Z= 0.153
  Angle     :  0.469   4.047  22869  Z= 0.250
  Chirality :  0.046   0.143   2415
  Planarity :  0.003   0.031   2968
  Dihedral  :  4.536  29.904   2219
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.02 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.26 (0.19), residues: 2037
  helix: -3.11 (0.33), residues: 42
  sheet:  0.47 (0.16), residues: 1064
  loop :  0.13 (0.21), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 260 
 HIS   0.003   0.001   HIS F 259 
 PHE   0.008   0.001   PHE C 196 
 TYR   0.009   0.001   TYR G  65 
 ARG   0.004   0.000   ARG C  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 226
  time to evaluate  : 2.611 
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: E  140 MET cc_start: 0.1236 (tpt) cc_final: -0.0543 (ppp)
  outliers start: 16
  outliers final: 14
  residues processed: 239
  average time/residue: 0.8147
  time to fit residues: 268.4143
Evaluate side-chains
  223 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 209
  time to evaluate  : 2.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  178 ASN
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 163 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 146 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 167 optimal weight:    1.9990
   chunk 135 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 100 optimal weight:   40.0000
   chunk 176 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 259 HIS
D 172 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 172 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  16898  Z= 0.411
  Angle     :  0.519   4.219  22869  Z= 0.280
  Chirality :  0.046   0.137   2415
  Planarity :  0.003   0.072   2968
  Dihedral  :  4.839  36.502   2219
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.41 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.09 (0.19), residues: 2037
  helix: -0.86 (0.75), residues: 42
  sheet:  0.41 (0.16), residues: 1050
  loop : -0.17 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 167 
 HIS   0.003   0.001   HIS E  48 
 PHE   0.009   0.001   PHE F 196 
 TYR   0.015   0.002   TYR G  65 
 ARG   0.005   0.000   ARG E  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 2.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 36
  outliers final: 35
  residues processed: 219
  average time/residue: 0.8654
  time to fit residues: 258.3652
Evaluate side-chains
  225 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 2.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue   24 ASP
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain B residue    2 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   24 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain D residue   17 ASN
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  208 ASP
Chi-restraints excluded: chain E residue    2 ASP
Chi-restraints excluded: chain E residue   17 ASN
Chi-restraints excluded: chain E residue   24 ASP
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  178 ASN
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  178 ASN
Chi-restraints excluded: chain G residue  208 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 176 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 196 optimal weight:    1.9990
   chunk 163 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 259 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  16898  Z= 0.188
  Angle     :  0.464   4.034  22869  Z= 0.248
  Chirality :  0.045   0.152   2415
  Planarity :  0.003   0.060   2968
  Dihedral  :  4.496  27.940   2219
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.13 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.19), residues: 2037
  helix: -0.88 (0.64), residues: 42
  sheet:  0.54 (0.16), residues: 1050
  loop : -0.05 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 260 
 HIS   0.002   0.001   HIS E  48 
 PHE   0.010   0.001   PHE B 196 
 TYR   0.010   0.001   TYR F  65 
 ARG   0.005   0.000   ARG G  56 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 3.205 
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: C  234 MET cc_start: 0.7812 (ttm) cc_final: 0.7588 (tpp)
  outliers start: 28
  outliers final: 27
  residues processed: 231
  average time/residue: 0.8193
  time to fit residues: 262.3807
Evaluate side-chains
  226 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 2.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 189 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 143 optimal weight:    6.9990
   chunk 165 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 195 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 259 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  16898  Z= 0.320
  Angle     :  0.486   4.094  22869  Z= 0.261
  Chirality :  0.045   0.143   2415
  Planarity :  0.004   0.077   2968
  Dihedral  :  4.636  30.049   2219
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.46 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.20 (0.19), residues: 2037
  helix:  0.61 (0.85), residues: 42
  sheet:  0.47 (0.16), residues: 1050
  loop : -0.16 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 167 
 HIS   0.003   0.001   HIS E  48 
 PHE   0.008   0.001   PHE D 196 
 TYR   0.012   0.001   TYR G  65 
 ARG   0.005   0.000   ARG E  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 2.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.7830 (ttm) cc_final: 0.7618 (ttm)
  outliers start: 32
  outliers final: 30
  residues processed: 220
  average time/residue: 0.8229
  time to fit residues: 249.0521
Evaluate side-chains
  224 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 194
  time to evaluate  : 2.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue   17 ASN
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  208 ASP
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 116 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 133 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 153 optimal weight:    0.9990
   chunk 177 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  16898  Z= 0.313
  Angle     :  0.484   4.085  22869  Z= 0.261
  Chirality :  0.045   0.143   2415
  Planarity :  0.003   0.066   2968
  Dihedral  :  4.587  27.423   2219
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.46 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.17 (0.19), residues: 2037
  helix:  0.68 (0.81), residues: 42
  sheet:  0.47 (0.16), residues: 1043
  loop : -0.22 (0.20), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 260 
 HIS   0.003   0.001   HIS E  48 
 PHE   0.011   0.001   PHE F 196 
 TYR   0.012   0.001   TYR G  65 
 ARG   0.005   0.000   ARG E  66 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 2.643 
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: A  234 MET cc_start: 0.7926 (ttm) cc_final: 0.7686 (ttm)
  outliers start: 30
  outliers final: 30
  residues processed: 221
  average time/residue: 0.8611
  time to fit residues: 264.5043
Evaluate side-chains
  225 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 2.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   17 ASN
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue   17 ASN
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 187 optimal weight:   50.0000
   chunk 171 optimal weight:   10.0000
   chunk 182 optimal weight:    0.9980
   chunk 109 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 143 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 164 optimal weight:    7.9990
   chunk 172 optimal weight:    6.9990
   chunk 181 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  16898  Z= 0.228
  Angle     :  0.463   4.639  22869  Z= 0.249
  Chirality :  0.045   0.144   2415
  Planarity :  0.003   0.061   2968
  Dihedral  :  4.484  24.113   2219
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.79 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.19), residues: 2037
  helix:  1.35 (0.89), residues: 42
  sheet:  0.47 (0.16), residues: 1050
  loop : -0.13 (0.21), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 260 
 HIS   0.002   0.001   HIS C  48 
 PHE   0.011   0.001   PHE F 196 
 TYR   0.010   0.001   TYR G  65 
 ARG   0.006   0.000   ARG B  56 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 2.776 
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: A  234 MET cc_start: 0.7896 (ttm) cc_final: 0.7675 (ttm)
REVERT: C  234 MET cc_start: 0.7817 (ttm) cc_final: 0.7585 (tpp)
  outliers start: 30
  outliers final: 30
  residues processed: 223
  average time/residue: 0.8284
  time to fit residues: 255.5973
Evaluate side-chains
  229 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 2.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 192 optimal weight:    6.9990
   chunk 117 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 134 optimal weight:    2.9990
   chunk 202 optimal weight:    6.9990
   chunk 186 optimal weight:   30.0000
   chunk 161 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 98 optimal weight:   50.0000
   chunk 127 optimal weight:   40.0000
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  16898  Z= 0.263
  Angle     :  0.472   4.882  22869  Z= 0.254
  Chirality :  0.045   0.142   2415
  Planarity :  0.003   0.057   2968
  Dihedral  :  4.480  24.057   2219
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.85 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.16 (0.19), residues: 2037
  helix:  1.25 (0.86), residues: 42
  sheet:  0.44 (0.16), residues: 1050
  loop : -0.23 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 260 
 HIS   0.003   0.001   HIS E  48 
 PHE   0.013   0.001   PHE D 196 
 TYR   0.011   0.001   TYR G  65 
 ARG   0.005   0.000   ARG B  56 

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 200
  time to evaluate  : 2.791 
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: A  234 MET cc_start: 0.7872 (ttm) cc_final: 0.7632 (ttm)
REVERT: C  234 MET cc_start: 0.7829 (ttm) cc_final: 0.7616 (tpp)
  outliers start: 31
  outliers final: 31
  residues processed: 224
  average time/residue: 0.8578
  time to fit residues: 265.8796
Evaluate side-chains
  226 residues out of total 1806 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 2.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ASN
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain B residue   17 ASN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  272 ASP
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  272 ASP
Chi-restraints excluded: chain D residue   24 ASP
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  272 ASP
Chi-restraints excluded: chain E residue   17 ASN
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  159 SER
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  272 ASP
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  161 THR
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain G residue   24 ASP
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  161 THR
Chi-restraints excluded: chain G residue  272 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 171 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 148 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:    0.2980
   chunk 161 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 165 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 141 optimal weight:    8.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.108030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.069614 restraints weight = 88791.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 3.64
r_work: 0.2658 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16898  Z= 0.187
  Angle     :  0.464   9.311  22869  Z= 0.248
  Chirality :  0.045   0.144   2415
  Planarity :  0.003   0.058   2968
  Dihedral  :  4.353  20.254   2219
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.96 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.27 (0.19), residues: 2037
  helix:  1.43 (0.89), residues: 42
  sheet:  0.50 (0.16), residues: 1050
  loop : -0.14 (0.21), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C 260 
 HIS   0.002   0.001   HIS C  48 
 PHE   0.015   0.001   PHE D 196 
 TYR   0.009   0.001   TYR G  65 
 ARG   0.006   0.000   ARG F  66 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7221.19 seconds
wall clock time: 129 minutes 37.29 seconds (7777.29 seconds total)