Starting phenix.real_space_refine (version: 1.21rc1)
on Mon May 15 13:41:06 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/05_2023/7jy8_22524_trim_updated.pdb"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 46728 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     Mg      9      5.21       5
     S     116      5.16       5
     C   14481      2.51       5
     N    4017      2.21       5
     O    4673      1.98       5
     H   23368      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU    4": "OE1" <-> "OE2"
    Residue "A GLU   31": "OE1" <-> "OE2"
    Residue "A ASP   48": "OD1" <-> "OD2"
    Residue "A PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   94": "OD1" <-> "OD2"
    Residue "A ASP  100": "OD1" <-> "OD2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  120": "OD1" <-> "OD2"
    Residue "A GLU  127": "OE1" <-> "OE2"
    Residue "A ASP  139": "OD1" <-> "OD2"
    Residue "A GLU  154": "OE1" <-> "OE2"
    Residue "A GLU  156": "OE1" <-> "OE2"
    Residue "A GLU  158": "OE1" <-> "OE2"
    Residue "A PHE  203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  233": "OE1" <-> "OE2"
    Residue "A GLU  235": "OE1" <-> "OE2"
    Residue "A GLU  266": "OE1" <-> "OE2"
    Residue "A GLU  273": "OE1" <-> "OE2"
    Residue "A ASP  311": "OD1" <-> "OD2"
    Residue "A GLU  314": "OE1" <-> "OE2"
    Residue "A GLU  325": "OE1" <-> "OE2"
    Residue "B GLU   18": "OE1" <-> "OE2"
    Residue "B GLU   68": "OE1" <-> "OE2"
    Residue "B PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP  100": "OD1" <-> "OD2"
    Residue "B ASP  110": "OD1" <-> "OD2"
    Residue "B GLU  127": "OE1" <-> "OE2"
    Residue "B GLU  154": "OE1" <-> "OE2"
    Residue "B GLU  156": "OE1" <-> "OE2"
    Residue "B ASP  161": "OD1" <-> "OD2"
    Residue "B PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  266": "OE1" <-> "OE2"
    Residue "B GLU  285": "OE1" <-> "OE2"
    Residue "B GLU  296": "OE1" <-> "OE2"
    Residue "B GLU  318": "OE1" <-> "OE2"
    Residue "B GLU  325": "OE1" <-> "OE2"
    Residue "C GLU    4": "OE1" <-> "OE2"
    Residue "C GLU   18": "OE1" <-> "OE2"
    Residue "C PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP  100": "OD1" <-> "OD2"
    Residue "C ASP  110": "OD1" <-> "OD2"
    Residue "C GLU  127": "OE1" <-> "OE2"
    Residue "C GLU  154": "OE1" <-> "OE2"
    Residue "C GLU  156": "OE1" <-> "OE2"
    Residue "C GLU  158": "OE1" <-> "OE2"
    Residue "C TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  233": "OE1" <-> "OE2"
    Residue "C GLU  285": "OE1" <-> "OE2"
    Residue "C ASP  311": "OD1" <-> "OD2"
    Residue "C GLU  318": "OE1" <-> "OE2"
    Residue "C GLU  325": "OE1" <-> "OE2"
    Residue "D GLU    4": "OE1" <-> "OE2"
    Residue "D PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  100": "OD1" <-> "OD2"
    Residue "D GLU  127": "OE1" <-> "OE2"
    Residue "D ASP  139": "OD1" <-> "OD2"
    Residue "D GLU  154": "OE1" <-> "OE2"
    Residue "D GLU  156": "OE1" <-> "OE2"
    Residue "D GLU  158": "OE1" <-> "OE2"
    Residue "D PHE  203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  235": "OE1" <-> "OE2"
    Residue "D GLU  266": "OE1" <-> "OE2"
    Residue "D TYR  291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  311": "OD1" <-> "OD2"
    Residue "D GLU  325": "OE1" <-> "OE2"
    Residue "E GLU   18": "OE1" <-> "OE2"
    Residue "E GLU   31": "OE1" <-> "OE2"
    Residue "E GLU   68": "OE1" <-> "OE2"
    Residue "E PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E ASP  100": "OD1" <-> "OD2"
    Residue "E ASP  110": "OD1" <-> "OD2"
    Residue "E GLU  127": "OE1" <-> "OE2"
    Residue "E ASP  139": "OD1" <-> "OD2"
    Residue "E GLU  154": "OE1" <-> "OE2"
    Residue "E GLU  156": "OE1" <-> "OE2"
    Residue "E GLU  158": "OE1" <-> "OE2"
    Residue "E PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU  233": "OE1" <-> "OE2"
    Residue "E GLU  235": "OE1" <-> "OE2"
    Residue "E ASP  276": "OD1" <-> "OD2"
    Residue "E TYR  291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU  296": "OE1" <-> "OE2"
    Residue "F GLU    4": "OE1" <-> "OE2"
    Residue "F GLU   18": "OE1" <-> "OE2"
    Residue "F TYR   65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F ASP  100": "OD1" <-> "OD2"
    Residue "F ASP  110": "OD1" <-> "OD2"
    Residue "F GLU  127": "OE1" <-> "OE2"
    Residue "F GLU  154": "OE1" <-> "OE2"
    Residue "F GLU  156": "OE1" <-> "OE2"
    Residue "F PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F GLU  233": "OE1" <-> "OE2"
    Residue "F GLU  266": "OE1" <-> "OE2"
    Residue "F GLU  281": "OE1" <-> "OE2"
    Residue "F GLU  285": "OE1" <-> "OE2"
    Residue "F GLU  325": "OE1" <-> "OE2"
    Residue "G ASP    3": "OD1" <-> "OD2"
    Residue "G GLU    4": "OE1" <-> "OE2"
    Residue "G GLU   18": "OE1" <-> "OE2"
    Residue "G PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G ASP  100": "OD1" <-> "OD2"
    Residue "G ASP  110": "OD1" <-> "OD2"
    Residue "G GLU  127": "OE1" <-> "OE2"
    Residue "G GLU  154": "OE1" <-> "OE2"
    Residue "G GLU  156": "OE1" <-> "OE2"
    Residue "G GLU  158": "OE1" <-> "OE2"
    Residue "G TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU  233": "OE1" <-> "OE2"
    Residue "G GLU  241": "OE1" <-> "OE2"
    Residue "G GLU  266": "OE1" <-> "OE2"
    Residue "G TYR  291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP    3": "OD1" <-> "OD2"
    Residue "H GLU    4": "OE1" <-> "OE2"
    Residue "H GLU   18": "OE1" <-> "OE2"
    Residue "H GLU   31": "OE1" <-> "OE2"
    Residue "H PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP  100": "OD1" <-> "OD2"
    Residue "H ASP  110": "OD1" <-> "OD2"
    Residue "H GLU  127": "OE1" <-> "OE2"
    Residue "H GLU  154": "OE1" <-> "OE2"
    Residue "H GLU  156": "OE1" <-> "OE2"
    Residue "H GLU  158": "OE1" <-> "OE2"
    Residue "H PHE  203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU  233": "OE1" <-> "OE2"
    Residue "H GLU  266": "OE1" <-> "OE2"
    Residue "H ASP  276": "OD1" <-> "OD2"
    Residue "H GLU  285": "OE1" <-> "OE2"
    Residue "H TYR  291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP  311": "OD1" <-> "OD2"
    Residue "H GLU  314": "OE1" <-> "OE2"
    Residue "H GLU  325": "OE1" <-> "OE2"
    Residue "I GLU   38": "OE1" <-> "OE2"
    Residue "I GLU   68": "OE1" <-> "OE2"
    Residue "I PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP  100": "OD1" <-> "OD2"
    Residue "I ASP  110": "OD1" <-> "OD2"
    Residue "I GLU  154": "OE1" <-> "OE2"
    Residue "I GLU  156": "OE1" <-> "OE2"
    Residue "I GLU  158": "OE1" <-> "OE2"
    Residue "I PHE  217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I TYR  218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU  233": "OE1" <-> "OE2"
    Residue "I GLU  235": "OE1" <-> "OE2"
    Residue "I GLU  266": "OE1" <-> "OE2"
    Residue "I GLU  285": "OE1" <-> "OE2"
    Residue "I TYR  291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU  296": "OE1" <-> "OE2"
    Residue "I GLU  314": "OE1" <-> "OE2"
    Residue "I GLU  325": "OE1" <-> "OE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib"
  Total number of atoms: 46728
  Number of models: 1
  Model: ""
    Number of chains: 20
    Chain: "A"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "B"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "C"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "D"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "E"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "F"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "G"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "H"
      Number of atoms: 5085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5085
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "I"
      Number of atoms: 4575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 4575
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 9, 'TRANS': 290}
    Chain: "S"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 865
          Classifications: {'DNA': 27}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 26}
    Chain: "T"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 320
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "I"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 14.62, per 1000 atoms: 0.31
  Number of scatterers: 46728
  At special positions: 0
  Unit cell: (132.594, 121.814, 198.352, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S     116     16.00
     P      64     15.00
     Mg      9     11.99
     O    4673      8.00
     N    4017      7.00
     C   14481      6.00
     H   23368      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: 30.18
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5324

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      108 helices and 36 sheets defined
      39.3% alpha, 19.3% beta
      9 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 17.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 21
      removed outlier: 3.654A  pdb=" N   GLN A   7 " --> pdb=" O   ASP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 72 through 86
      removed outlier: 3.630A  pdb=" N   GLU A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 107
    Processing helix  chain 'A' and resid 122 through 135
    Processing helix  chain 'A' and resid 152 through 156
    Processing helix  chain 'A' and resid 166 through 185
      removed outlier: 3.665A  pdb=" N   ARG A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   GLY A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ASN A 181 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 313 through 327
    Processing helix  chain 'B' and resid 2 through 21
      removed outlier: 3.626A  pdb=" N   LYS B   6 " --> pdb=" O   ILE B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 25
      No H-bonds generated for 'chain 'B' and resid 23 through 25'
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 45 through 51
    Processing helix  chain 'B' and resid 72 through 86
      removed outlier: 3.768A  pdb=" N   GLU B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 107
    Processing helix  chain 'B' and resid 122 through 135
    Processing helix  chain 'B' and resid 152 through 156
    Processing helix  chain 'B' and resid 166 through 185
      removed outlier: 3.514A  pdb=" N   ARG B 176 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   GLY B 180 " --> pdb=" O   ARG B 176 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ASN B 181 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 218
    Processing helix  chain 'B' and resid 270 through 280
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 313 through 327
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 3.666A  pdb=" N   GLN C   7 " --> pdb=" O   ASP C   3 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS C   8 " --> pdb=" O   GLU C   4 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 31
      No H-bonds generated for 'chain 'C' and resid 29 through 31'
    Processing helix  chain 'C' and resid 45 through 51
    Processing helix  chain 'C' and resid 72 through 86
      removed outlier: 3.647A  pdb=" N   GLU C  86 " --> pdb=" O   ALA C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 107
    Processing helix  chain 'C' and resid 122 through 135
    Processing helix  chain 'C' and resid 152 through 156
    Processing helix  chain 'C' and resid 166 through 185
      removed outlier: 3.531A  pdb=" N   ARG C 176 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   GLY C 180 " --> pdb=" O   ARG C 176 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ASN C 181 " --> pdb=" O   LYS C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 218
    Processing helix  chain 'C' and resid 270 through 280
    Processing helix  chain 'C' and resid 302 through 311
    Processing helix  chain 'C' and resid 313 through 327
    Processing helix  chain 'D' and resid 2 through 21
      removed outlier: 3.666A  pdb=" N   LYS D   6 " --> pdb=" O   ILE D   2 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN D   7 " --> pdb=" O   ASP D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 31
      No H-bonds generated for 'chain 'D' and resid 29 through 31'
    Processing helix  chain 'D' and resid 45 through 51
    Processing helix  chain 'D' and resid 72 through 86
      removed outlier: 3.619A  pdb=" N   GLU D  86 " --> pdb=" O   ALA D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 107
    Processing helix  chain 'D' and resid 122 through 135
    Processing helix  chain 'D' and resid 152 through 156
    Processing helix  chain 'D' and resid 166 through 185
      removed outlier: 4.900A  pdb=" N   GLY D 180 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ASN D 181 " --> pdb=" O   LYS D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 218
    Processing helix  chain 'D' and resid 270 through 280
      removed outlier: 3.533A  pdb=" N   ASP D 276 " --> pdb=" O   GLY D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 311
    Processing helix  chain 'D' and resid 313 through 327
    Processing helix  chain 'E' and resid 2 through 21
      removed outlier: 3.904A  pdb=" N   LYS E   6 " --> pdb=" O   ILE E   2 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN E   7 " --> pdb=" O   ASP E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'E' and resid 45 through 51
    Processing helix  chain 'E' and resid 72 through 86
      removed outlier: 3.672A  pdb=" N   GLU E  86 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 101 through 107
    Processing helix  chain 'E' and resid 122 through 135
    Processing helix  chain 'E' and resid 152 through 156
    Processing helix  chain 'E' and resid 166 through 185
      removed outlier: 3.528A  pdb=" N   ARG E 176 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   GLY E 180 " --> pdb=" O   ARG E 176 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN E 181 " --> pdb=" O   LYS E 177 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 218
    Processing helix  chain 'E' and resid 270 through 280
    Processing helix  chain 'E' and resid 302 through 311
    Processing helix  chain 'E' and resid 313 through 327
    Processing helix  chain 'F' and resid 2 through 21
      removed outlier: 3.568A  pdb=" N   GLN F   7 " --> pdb=" O   ASP F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 31
      No H-bonds generated for 'chain 'F' and resid 29 through 31'
    Processing helix  chain 'F' and resid 33 through 35
      No H-bonds generated for 'chain 'F' and resid 33 through 35'
    Processing helix  chain 'F' and resid 45 through 50
    Processing helix  chain 'F' and resid 72 through 86
      removed outlier: 3.706A  pdb=" N   GLU F  86 " --> pdb=" O   ALA F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 101 through 107
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 152 through 156
    Processing helix  chain 'F' and resid 166 through 185
      removed outlier: 4.945A  pdb=" N   GLY F 180 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ASN F 181 " --> pdb=" O   LYS F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 214 through 218
    Processing helix  chain 'F' and resid 270 through 280
      removed outlier: 3.544A  pdb=" N   ASP F 276 " --> pdb=" O   GLY F 272 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 311
    Processing helix  chain 'F' and resid 313 through 327
    Processing helix  chain 'G' and resid 3 through 21
    Processing helix  chain 'G' and resid 29 through 31
      No H-bonds generated for 'chain 'G' and resid 29 through 31'
    Processing helix  chain 'G' and resid 33 through 35
      No H-bonds generated for 'chain 'G' and resid 33 through 35'
    Processing helix  chain 'G' and resid 45 through 51
    Processing helix  chain 'G' and resid 72 through 86
      removed outlier: 3.789A  pdb=" N   GLU G  86 " --> pdb=" O   ALA G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 101 through 106
    Processing helix  chain 'G' and resid 122 through 135
    Processing helix  chain 'G' and resid 152 through 156
    Processing helix  chain 'G' and resid 166 through 185
      removed outlier: 3.570A  pdb=" N   ARG G 176 " --> pdb=" O   SER G 172 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   GLY G 180 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ASN G 181 " --> pdb=" O   LYS G 177 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 214 through 218
    Processing helix  chain 'G' and resid 270 through 280
    Processing helix  chain 'G' and resid 302 through 311
    Processing helix  chain 'G' and resid 313 through 327
    Processing helix  chain 'H' and resid 3 through 21
      removed outlier: 3.623A  pdb=" N   LYS H   8 " --> pdb=" O   GLU H   4 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 45 through 51
    Processing helix  chain 'H' and resid 72 through 86
      removed outlier: 3.743A  pdb=" N   GLU H  86 " --> pdb=" O   ALA H  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 107
    Processing helix  chain 'H' and resid 122 through 135
    Processing helix  chain 'H' and resid 152 through 156
    Processing helix  chain 'H' and resid 166 through 185
      removed outlier: 3.650A  pdb=" N   ARG H 176 " --> pdb=" O   SER H 172 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY H 180 " --> pdb=" O   ARG H 176 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASN H 181 " --> pdb=" O   LYS H 177 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 214 through 218
    Processing helix  chain 'H' and resid 270 through 280
    Processing helix  chain 'H' and resid 302 through 311
    Processing helix  chain 'H' and resid 313 through 327
    Processing helix  chain 'I' and resid 45 through 50
    Processing helix  chain 'I' and resid 72 through 86
      removed outlier: 3.725A  pdb=" N   GLU I  86 " --> pdb=" O   ALA I  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 101 through 107
    Processing helix  chain 'I' and resid 122 through 135
    Processing helix  chain 'I' and resid 152 through 156
    Processing helix  chain 'I' and resid 166 through 185
      removed outlier: 3.743A  pdb=" N   ARG I 176 " --> pdb=" O   SER I 172 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLY I 180 " --> pdb=" O   ARG I 176 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASN I 181 " --> pdb=" O   LYS I 177 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 214 through 218
    Processing helix  chain 'I' and resid 270 through 280
    Processing helix  chain 'I' and resid 302 through 311
    Processing helix  chain 'I' and resid 313 through 327
    Processing sheet with id=  A, first strand: chain 'A' and resid 257 through 263
      removed outlier: 6.460A  pdb=" N   ARG A 222 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL A 221 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A 189 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   ILE A  64 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   PHE A 191 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   GLY A  66 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ASN A 193 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 195 through 197
    Processing sheet with id=  C, first strand: chain 'A' and resid 285 through 287
      removed outlier: 6.462A  pdb=" N   TYR A 293 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   LYS A 297 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 229 through 233
      removed outlier: 6.737A  pdb=" N   GLU A 233 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 257 through 263
      removed outlier: 6.282A  pdb=" N   ARG B 222 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL B 221 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU B 189 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE B  64 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   PHE B 191 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   GLY B  66 " --> pdb=" O   PHE B 191 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ASN B 193 " --> pdb=" O   GLY B  66 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU B 115 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 195 through 197
    Processing sheet with id=  G, first strand: chain 'B' and resid 285 through 287
      removed outlier: 6.590A  pdb=" N   TYR B 293 " --> pdb=" O   LYS B 297 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LYS B 297 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 229 through 233
      removed outlier: 6.572A  pdb=" N   GLU B 233 " --> pdb=" O   VAL B 237 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 257 through 263
      removed outlier: 6.329A  pdb=" N   ARG C 222 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   VAL C 221 " --> pdb=" O   ILE C  61 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU C 189 " --> pdb=" O   VAL C  62 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ILE C  64 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   PHE C 191 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   GLY C  66 " --> pdb=" O   PHE C 191 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASN C 193 " --> pdb=" O   GLY C  66 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU C 115 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'C' and resid 195 through 197
    Processing sheet with id=  K, first strand: chain 'C' and resid 285 through 287
      removed outlier: 6.399A  pdb=" N   TYR C 293 " --> pdb=" O   LYS C 297 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LYS C 297 " --> pdb=" O   TYR C 293 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'C' and resid 229 through 233
      removed outlier: 6.542A  pdb=" N   GLU C 233 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL C 237 " --> pdb=" O   GLU C 233 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'D' and resid 257 through 263
      removed outlier: 6.292A  pdb=" N   ARG D 222 " --> pdb=" O   VAL D 247 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL D 221 " --> pdb=" O   ILE D  61 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU D 189 " --> pdb=" O   VAL D  62 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ILE D  64 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   PHE D 191 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   GLY D  66 " --> pdb=" O   PHE D 191 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ASN D 193 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LEU D 115 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'D' and resid 195 through 197
    Processing sheet with id=  O, first strand: chain 'D' and resid 285 through 287
      removed outlier: 6.439A  pdb=" N   TYR D 293 " --> pdb=" O   LYS D 297 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   LYS D 297 " --> pdb=" O   TYR D 293 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'D' and resid 229 through 233
      removed outlier: 6.541A  pdb=" N   GLU D 233 " --> pdb=" O   VAL D 237 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   VAL D 237 " --> pdb=" O   GLU D 233 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'E' and resid 257 through 263
      removed outlier: 6.229A  pdb=" N   ARG E 222 " --> pdb=" O   VAL E 247 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL E 221 " --> pdb=" O   ILE E  61 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU E 189 " --> pdb=" O   VAL E  62 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   ILE E  64 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   PHE E 191 " --> pdb=" O   ILE E  64 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   GLY E  66 " --> pdb=" O   PHE E 191 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ASN E 193 " --> pdb=" O   GLY E  66 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU E 115 " --> pdb=" O   PHE E  92 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'E' and resid 195 through 197
    Processing sheet with id=  S, first strand: chain 'E' and resid 284 through 287
      removed outlier: 6.392A  pdb=" N   TYR E 293 " --> pdb=" O   LYS E 297 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   LYS E 297 " --> pdb=" O   TYR E 293 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'E' and resid 229 through 233
      removed outlier: 6.534A  pdb=" N   GLU E 233 " --> pdb=" O   VAL E 237 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   VAL E 237 " --> pdb=" O   GLU E 233 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'F' and resid 257 through 263
      removed outlier: 6.237A  pdb=" N   ARG F 222 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL F 221 " --> pdb=" O   ILE F  61 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU F 189 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   ILE F  64 " --> pdb=" O   LEU F 189 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   PHE F 191 " --> pdb=" O   ILE F  64 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   GLY F  66 " --> pdb=" O   PHE F 191 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ASN F 193 " --> pdb=" O   GLY F  66 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU F 115 " --> pdb=" O   PHE F  92 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'F' and resid 195 through 197
    Processing sheet with id=  W, first strand: chain 'F' and resid 285 through 287
      removed outlier: 6.461A  pdb=" N   TYR F 293 " --> pdb=" O   LYS F 297 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   LYS F 297 " --> pdb=" O   TYR F 293 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'F' and resid 229 through 233
      removed outlier: 3.524A  pdb=" N   GLY F 229 " --> pdb=" O   GLU F 241 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   GLU F 233 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   VAL F 237 " --> pdb=" O   GLU F 233 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'G' and resid 257 through 263
      removed outlier: 6.262A  pdb=" N   ARG G 222 " --> pdb=" O   VAL G 247 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL G 221 " --> pdb=" O   ILE G  61 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU G 189 " --> pdb=" O   VAL G  62 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   ILE G  64 " --> pdb=" O   LEU G 189 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   PHE G 191 " --> pdb=" O   ILE G  64 " (cutoff:3.500A)
      removed outlier: 8.350A  pdb=" N   GLY G  66 " --> pdb=" O   PHE G 191 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ASN G 193 " --> pdb=" O   GLY G  66 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU G 115 " --> pdb=" O   PHE G  92 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'G' and resid 195 through 197
    Processing sheet with id= AA, first strand: chain 'G' and resid 285 through 287
    Processing sheet with id= AB, first strand: chain 'G' and resid 229 through 233
      removed outlier: 6.436A  pdb=" N   GLU G 233 " --> pdb=" O   VAL G 237 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL G 237 " --> pdb=" O   GLU G 233 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'H' and resid 257 through 263
      removed outlier: 6.382A  pdb=" N   ARG H 222 " --> pdb=" O   VAL H 247 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL H 221 " --> pdb=" O   ILE H  61 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU H 189 " --> pdb=" O   VAL H  62 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   ILE H  64 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE H 191 " --> pdb=" O   ILE H  64 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   GLY H  66 " --> pdb=" O   PHE H 191 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASN H 193 " --> pdb=" O   GLY H  66 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU H 115 " --> pdb=" O   PHE H  92 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'H' and resid 195 through 197
    Processing sheet with id= AE, first strand: chain 'H' and resid 285 through 287
      removed outlier: 6.430A  pdb=" N   TYR H 293 " --> pdb=" O   LYS H 297 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   LYS H 297 " --> pdb=" O   TYR H 293 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'H' and resid 229 through 233
      removed outlier: 6.463A  pdb=" N   GLU H 233 " --> pdb=" O   VAL H 237 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL H 237 " --> pdb=" O   GLU H 233 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'I' and resid 257 through 263
      removed outlier: 6.396A  pdb=" N   ARG I 222 " --> pdb=" O   VAL I 247 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL I 221 " --> pdb=" O   ILE I  61 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU I 189 " --> pdb=" O   VAL I  62 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ILE I  64 " --> pdb=" O   LEU I 189 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   PHE I 191 " --> pdb=" O   ILE I  64 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   GLY I  66 " --> pdb=" O   PHE I 191 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ASN I 193 " --> pdb=" O   GLY I  66 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU I 115 " --> pdb=" O   PHE I  92 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   ASP I  94 " --> pdb=" O   LEU I 115 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   SER I 117 " --> pdb=" O   ASP I  94 " (cutoff:3.500A)
    Processing sheet with id= AH, first strand: chain 'I' and resid 195 through 197
    Processing sheet with id= AI, first strand: chain 'I' and resid 285 through 287
      removed outlier: 6.434A  pdb=" N   TYR I 293 " --> pdb=" O   LYS I 297 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   LYS I 297 " --> pdb=" O   TYR I 293 " (cutoff:3.500A)
    Processing sheet with id= AJ, first strand: chain 'I' and resid 229 through 233
      removed outlier: 6.673A  pdb=" N   GLU I 233 " --> pdb=" O   VAL I 237 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL I 237 " --> pdb=" O   GLU I 233 " (cutoff:3.500A)

    1007 hydrogen bonds defined for protein.
    2946 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      18 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 16.09

  Time building geometry restraints manager: 31.74 seconds

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

  Histogram of bond lengths:
        0.85 -     1.09: 23230
        1.09 -     1.34: 7545
        1.34 -     1.59: 16020
        1.59 -     1.84: 274
        1.84 -     2.08: 10
  Bond restraints: 47079
  Sorted by residual:
  bond pdb=" C4  AGS A 402 "
       pdb=" C5  AGS A 402 "
    ideal  model  delta    sigma   weight residual
    1.386  1.477 -0.091 1.00e-02 1.00e+04 8.23e+01
  bond pdb=" N3   DT S   6 "
       pdb=" H3   DT S   6 "
    ideal  model  delta    sigma   weight residual
    0.860  1.041 -0.181 2.00e-02 2.50e+03 8.16e+01
  bond pdb=" N3   DT S  17 "
       pdb=" H3   DT S  17 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.14e+01
  bond pdb=" N3   DT S  10 "
       pdb=" H3   DT S  10 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.13e+01
  bond pdb=" N3   DT S  23 "
       pdb=" H3   DT S  23 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.13e+01
  ... (remaining 47074 not shown)

  Histogram of bond angle deviations from ideal:
       97.22 -   105.14: 747
      105.14 -   113.06: 55855
      113.06 -   120.98: 20860
      120.98 -   128.90: 7958
      128.90 -   136.82: 116
  Bond angle restraints: 85536
  Sorted by residual:
  angle pdb=" C5  AGS E 402 "
        pdb=" N7  AGS E 402 "
        pdb=" C8  AGS E 402 "
      ideal   model   delta    sigma   weight residual
     103.67  108.41   -4.74 4.26e-01 5.51e+00 1.24e+02
  angle pdb=" C5  AGS E 402 "
        pdb=" C4  AGS E 402 "
        pdb=" N3  AGS E 402 "
      ideal   model   delta    sigma   weight residual
     126.80  118.56    8.24 7.41e-01 1.82e+00 1.24e+02
  angle pdb=" C5  AGS A 402 "
        pdb=" C4  AGS A 402 "
        pdb=" N3  AGS A 402 "
      ideal   model   delta    sigma   weight residual
     126.80  118.56    8.24 7.41e-01 1.82e+00 1.24e+02
  angle pdb=" C5  AGS G 402 "
        pdb=" C4  AGS G 402 "
        pdb=" N3  AGS G 402 "
      ideal   model   delta    sigma   weight residual
     126.80  118.88    7.92 7.41e-01 1.82e+00 1.14e+02
  angle pdb=" C5  AGS G 402 "
        pdb=" N7  AGS G 402 "
        pdb=" C8  AGS G 402 "
      ideal   model   delta    sigma   weight residual
     103.67  108.22   -4.55 4.26e-01 5.51e+00 1.14e+02
  ... (remaining 85531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.33: 17185
       32.33 -    64.66: 927
       64.66 -    96.99: 61
       96.99 -   129.32: 7
      129.32 -   161.65: 9
  Dihedral angle restraints: 18189
    sinusoidal: 9060
      harmonic: 9129
  Sorted by residual:
  dihedral pdb=" CA  SER C 145 "
           pdb=" C   SER C 145 "
           pdb=" N   VAL C 146 "
           pdb=" CA  VAL C 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.16   33.84     0      5.00e+00 4.00e-02 4.58e+01
  dihedral pdb=" CA  SER H 145 "
           pdb=" C   SER H 145 "
           pdb=" N   VAL H 146 "
           pdb=" CA  VAL H 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.76   31.24     0      5.00e+00 4.00e-02 3.90e+01
  dihedral pdb=" CA  SER B 145 "
           pdb=" C   SER B 145 "
           pdb=" N   VAL B 146 "
           pdb=" CA  VAL B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.64   30.36     0      5.00e+00 4.00e-02 3.69e+01
  ... (remaining 18186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 2445
       0.093 -    0.186: 1117
       0.186 -    0.280: 114
       0.280 -    0.373: 13
       0.373 -    0.466: 6
  Chirality restraints: 3695
  Sorted by residual:
  chirality pdb=" CA  SER F 145 "
            pdb=" N   SER F 145 "
            pdb=" C   SER F 145 "
            pdb=" CB  SER F 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.43e+00
  chirality pdb=" CA  SER E 145 "
            pdb=" N   SER E 145 "
            pdb=" C   SER E 145 "
            pdb=" CB  SER E 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.53e+00
  chirality pdb=" CA  SER G 145 "
            pdb=" N   SER G 145 "
            pdb=" C   SER G 145 "
            pdb=" CB  SER G 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.25e+00
  ... (remaining 3692 not shown)

  Planarity restraints: 6881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT S   8 "    0.012 2.00e-02 2.50e+03   2.75e-02 2.27e+01
        pdb=" N1   DT S   8 "   -0.056 2.00e-02 2.50e+03
        pdb=" C2   DT S   8 "   -0.008 2.00e-02 2.50e+03
        pdb=" O2   DT S   8 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DT S   8 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DT S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT S   8 "    0.017 2.00e-02 2.50e+03
        pdb=" C5   DT S   8 "   -0.023 2.00e-02 2.50e+03
        pdb=" C7   DT S   8 "   -0.016 2.00e-02 2.50e+03
        pdb=" C6   DT S   8 "   -0.017 2.00e-02 2.50e+03
        pdb=" H3   DT S   8 "    0.017 2.00e-02 2.50e+03
        pdb=" H6   DT S   8 "    0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  65 "   -0.035 2.00e-02 2.50e+03   2.04e-02 1.25e+01
        pdb=" CG  TYR G  65 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  65 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  65 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  65 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  65 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  65 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR G  65 "   -0.018 2.00e-02 2.50e+03
        pdb=" HD1 TYR G  65 "   -0.024 2.00e-02 2.50e+03
        pdb=" HD2 TYR G  65 "   -0.007 2.00e-02 2.50e+03
        pdb=" HE1 TYR G  65 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR G  65 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP G 144 "   -0.016 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ASP G 144 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ASP G 144 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   SER G 145 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 6878 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 492
        2.00 -     2.65: 56312
        2.65 -     3.30: 136277
        3.30 -     3.95: 177796
        3.95 -     4.60: 271090
  Nonbonded interactions: 641967
  Sorted by model distance:
  nonbonded pdb="HH11 ARG G  60 "
            pdb=" HG  SER G 220 "
     model   vdw
     1.353 2.100
  nonbonded pdb=" HH  TYR D 293 "
            pdb=" HZ3 LYS D 322 "
     model   vdw
     1.354 2.100
  nonbonded pdb="HH11 ARG F  60 "
            pdb=" HG  SER F 220 "
     model   vdw
     1.408 2.100
  nonbonded pdb="HH11 ARG B  60 "
            pdb=" HG  SER B 220 "
     model   vdw
     1.416 2.100
  nonbonded pdb="HH11 ARG D  60 "
            pdb=" HG  SER D 220 "
     model   vdw
     1.422 2.100
  ... (remaining 641962 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 34 through 333 or resid 401 through 402))
  selection = (chain 'B' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'C' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'D' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'E' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'F' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'G' and (resid 34 through 333 or resid 401 through 402))
  selection = (chain 'H' and (resid 34 through 333 or resid 401 through 402))
  selection = chain 'I'
}

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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.420
  Construct map_model_manager:             0.510
  Extract box with map and model:          6.760
  Check model and map are aligned:         0.520
  Set scattering table:                    0.300
  Process input model:                     125.210
  Find NCS groups from input model:        1.820
  Set up NCS constraints:                  0.110
  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:11.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  148.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
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      :  0.015   0.159  23711  Z= 0.942
  Angle     :  1.935  14.577  32133  Z= 1.408
  Chirality :  0.096   0.466   3695
  Planarity :  0.005   0.035   3997
  Dihedral  : 19.580 161.648   8993
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.12 %
    Favored  : 96.71 %
  Rotamer Outliers :  7.58 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.00 (0.13), residues: 2946
  helix: -1.58 (0.11), residues: 1250
  sheet:  0.80 (0.22), residues: 461
  loop : -1.79 (0.15), residues: 1235

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  592 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 177
    poor density    : 415
  time to evaluate  : 2.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 177
  outliers final: 43
  residues processed: 558
  average time/residue: 2.3858
  time to fit residues: 1535.9016
Evaluate side-chains
  283 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 240
  time to evaluate  : 2.656 
Switching outliers to nearest non-outliers
  outliers start: 43
  outliers final: 37
  residues processed: 6
  average time/residue: 1.7007
  time to fit residues: 15.7549
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 250 optimal weight:    0.9990
   chunk 225 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 151 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 232 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 141 optimal weight:    0.9990
   chunk 173 optimal weight:    0.8980
   chunk 269 optimal weight:    5.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 300 GLN
E  20 GLN
F   5 ASN
F 184 GLN
F 236 ASN
G 236 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028  23711  Z= 0.201
  Angle     :  0.610   6.913  32133  Z= 0.334
  Chirality :  0.042   0.157   3695
  Planarity :  0.003   0.027   3997
  Dihedral  : 16.044 176.672   3587
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.39 %
    Favored  : 98.47 %
  Rotamer Outliers :  3.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.14), residues: 2946
  helix:  0.88 (0.14), residues: 1259
  sheet:  1.19 (0.22), residues: 500
  loop : -1.92 (0.15), residues: 1187

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 252
  time to evaluate  : 2.713 
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
  outliers start: 76
  outliers final: 30
  residues processed: 312
  average time/residue: 2.3290
  time to fit residues: 840.6872
Evaluate side-chains
  254 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 2.671 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 30
  outliers final: 27
  residues processed: 4
  average time/residue: 0.8306
  time to fit residues: 8.1133
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 149 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 224 optimal weight:    5.9990
   chunk 183 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 270 optimal weight:   20.0000
   chunk 291 optimal weight:   20.0000
   chunk 240 optimal weight:    7.9990
   chunk 267 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 216 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 257 GLN
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 236 ASN
D  20 GLN
E 124 GLN
F 184 GLN
F 236 ASN
F 312 ASN
I 181 ASN
I 330 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.060  23711  Z= 0.322
  Angle     :  0.667   9.509  32133  Z= 0.355
  Chirality :  0.048   0.231   3695
  Planarity :  0.004   0.048   3997
  Dihedral  : 15.959 177.397   3587
  Min Nonbonded Distance : 1.683

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer Outliers :  2.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.14), residues: 2946
  helix:  1.28 (0.14), residues: 1259
  sheet:  1.11 (0.22), residues: 500
  loop : -1.89 (0.15), residues: 1187

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 237
  time to evaluate  : 2.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 62
  outliers final: 40
  residues processed: 289
  average time/residue: 2.3315
  time to fit residues: 781.5050
Evaluate side-chains
  262 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 222
  time to evaluate  : 2.737 
Switching outliers to nearest non-outliers
  outliers start: 40
  outliers final: 35
  residues processed: 5
  average time/residue: 1.7537
  time to fit residues: 14.2079
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 266 optimal weight:   20.0000
   chunk 203 optimal weight:    0.7980
   chunk 140 optimal weight:    2.9990
   chunk 29 optimal weight:   30.0000
   chunk 128 optimal weight:    7.9990
   chunk 181 optimal weight:    0.7980
   chunk 271 optimal weight:    9.9990
   chunk 287 optimal weight:   30.0000
   chunk 141 optimal weight:    0.8980
   chunk 256 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN
I 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.041  23711  Z= 0.203
  Angle     :  0.550   6.652  32133  Z= 0.297
  Chirality :  0.043   0.157   3695
  Planarity :  0.003   0.035   3997
  Dihedral  : 15.927 179.974   3587
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer Outliers :  2.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.15), residues: 2946
  helix:  1.69 (0.15), residues: 1268
  sheet:  1.16 (0.22), residues: 500
  loop : -1.76 (0.15), residues: 1178

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 232
  time to evaluate  : 2.688 
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
  outliers start: 60
  outliers final: 38
  residues processed: 286
  average time/residue: 2.3782
  time to fit residues: 791.3867
Evaluate side-chains
  257 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 219
  time to evaluate  : 2.667 
Switching outliers to nearest non-outliers
  outliers start: 38
  outliers final: 34
  residues processed: 4
  average time/residue: 1.0897
  time to fit residues: 9.2943
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 239 optimal weight:    4.9990
   chunk 162 optimal weight:   10.0000
   chunk 4 optimal weight:   30.0000
   chunk 213 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 244 optimal weight:    9.9990
   chunk 198 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 146 optimal weight:    2.9990
   chunk 257 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN
H 213 ASN
I 181 ASN
I 300 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.060  23711  Z= 0.316
  Angle     :  0.630   9.849  32133  Z= 0.334
  Chirality :  0.047   0.218   3695
  Planarity :  0.004   0.046   3997
  Dihedral  : 15.856 179.313   3587
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer Outliers :  2.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.15), residues: 2946
  helix:  1.25 (0.14), residues: 1317
  sheet:  1.10 (0.22), residues: 500
  loop : -1.73 (0.15), residues: 1129

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 221
  time to evaluate  : 2.751 
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
  outliers start: 64
  outliers final: 41
  residues processed: 276
  average time/residue: 2.3221
  time to fit residues: 742.9784
Evaluate side-chains
  256 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 215
  time to evaluate  : 2.704 
Switching outliers to nearest non-outliers
  outliers start: 41
  outliers final: 36
  residues processed: 5
  average time/residue: 1.0991
  time to fit residues: 10.7216
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 258 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 168 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 287 optimal weight:    8.9990
   chunk 238 optimal weight:    4.9990
   chunk 133 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 150 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 118 GLN
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN
G 118 GLN
H 257 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.056  23711  Z= 0.271
  Angle     :  0.587   9.558  32133  Z= 0.314
  Chirality :  0.045   0.194   3695
  Planarity :  0.004   0.058   3997
  Dihedral  : 15.840 179.895   3587
  Min Nonbonded Distance : 1.715

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer Outliers :  2.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.15), residues: 2946
  helix:  1.31 (0.14), residues: 1326
  sheet:  1.09 (0.22), residues: 500
  loop : -1.64 (0.15), residues: 1120

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 224
  time to evaluate  : 2.763 
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
  outliers start: 51
  outliers final: 36
  residues processed: 270
  average time/residue: 2.3444
  time to fit residues: 734.8335
Evaluate side-chains
  249 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 213
  time to evaluate  : 2.771 
Switching outliers to nearest non-outliers
  outliers start: 36
  outliers final: 33
  residues processed: 3
  average time/residue: 1.5717
  time to fit residues: 9.3293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 277 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 163 optimal weight:    0.2980
   chunk 209 optimal weight:    0.7980
   chunk 162 optimal weight:    6.9990
   chunk 241 optimal weight:    0.6980
   chunk 160 optimal weight:    8.9990
   chunk 286 optimal weight:   10.0000
   chunk 179 optimal weight:    1.9990
   chunk 174 optimal weight:    0.7980
   chunk 132 optimal weight:   10.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 118 GLN
F 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.028  23711  Z= 0.149
  Angle     :  0.494   5.545  32133  Z= 0.269
  Chirality :  0.042   0.149   3695
  Planarity :  0.003   0.067   3997
  Dihedral  : 15.762 178.445   3587
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer Outliers :  2.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.15), residues: 2946
  helix:  1.76 (0.15), residues: 1325
  sheet:  1.21 (0.22), residues: 500
  loop : -1.50 (0.15), residues: 1121

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

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

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5892 Ramachandran restraints generated.
    2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 226
  time to evaluate  : 2.725 
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
  outliers start: 47
  outliers final: 34
  residues processed: 268
  average time/residue: 2.2817
  time to fit residues: 709.8863
Evaluate side-chains
  251 residues out of total 2334 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 217
  time to evaluate  : 2.669 
Switching outliers to nearest non-outliers
  outliers start: 34
  outliers final: 32
  residues processed: 2
  average time/residue: 1.0029
  time to fit residues: 6.2073
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 297
   random chunks:
   chunk 177 optimal weight:    4.9990
   chunk 114 optimal weight:    0.2980
   chunk 170 optimal weight:    0.0980
   chunk 86 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0470
   chunk 55 optimal weight:    6.9990
   chunk 181 optimal weight:    4.9990
   chunk 195 optimal weight:   10.0000
   chunk 141 optimal weight:    0.7980
   chunk 26 optimal weight:   20.0000
   chunk 225 optimal weight:    6.9990
   overall best weight:    0.3278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: