Starting phenix.real_space_refine
on Wed Dec 13 13:39:24 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgg_11205/12_2023/6zgg_11205.pdb"
  }
  resolution = 3.8
  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=   0.003 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     117      5.16       5
     C   16014      2.51       5
     N    4191      2.21       5
     O    4774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  175": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  275": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  490": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  508": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  543": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  612": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  695": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  800": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  906": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  275": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  490": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  508": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  612": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  643": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  695": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  175": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  204": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  306": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  329": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  369": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  490": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  508": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  515": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  541": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  543": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  612": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  695": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  718": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  906": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.10s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 25096
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1069, 8366
          Classifications: {'peptide': 1069}
          Link IDs: {'PTRANS': 53, 'TRANS': 1015}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 8380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1071, 8380
          Classifications: {'peptide': 1071}
          Link IDs: {'PTRANS': 53, 'TRANS': 1017}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 8350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1067, 8350
          Classifications: {'peptide': 1067}
          Link IDs: {'PTRANS': 53, 'TRANS': 1013}
          Chain breaks: 5
  Time building chain proxies: 13.64, per 1000 atoms: 0.54
  Number of scatterers: 25096
  At special positions: 0
  Unit cell: (156.31, 149.842, 196.196, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     117     16.00
     O    4774      8.00
     N    4191      7.00
     C   16014      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  15 " - pdb=" SG  CYS C 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 9.60
  Conformation dependent library (CDL) restraints added in 4.3 seconds
  

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6006

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 48 sheets defined
      21.7% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.610A  pdb=" N   ASN A 370 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 4.069A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 737 through 742
    Processing helix  chain 'A' and resid 747 through 754
    Processing helix  chain 'A' and resid 756 through 782
      removed outlier: 3.954A  pdb=" N   CYS A 760 " --> pdb=" O   TYR A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 3.553A  pdb=" N   LYS A 825 " --> pdb=" O   LEU A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 855
    Processing helix  chain 'A' and resid 866 through 885
    Processing helix  chain 'A' and resid 897 through 907
    Processing helix  chain 'A' and resid 913 through 919
    Processing helix  chain 'A' and resid 919 through 939
    Processing helix  chain 'A' and resid 945 through 948
    Processing helix  chain 'A' and resid 949 through 965
    Processing helix  chain 'A' and resid 966 through 968
      No H-bonds generated for 'chain 'A' and resid 966 through 968'
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 989 through 1033
    Processing helix  chain 'A' and resid 1140 through 1146
      removed outlier: 3.513A  pdb=" N   GLU A1144 " --> pdb=" O   PRO A1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 304
      removed outlier: 3.526A  pdb=" N   GLU B 298 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.992A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.961A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 737 through 743
      removed outlier: 3.509A  pdb=" N   TYR B 741 " --> pdb=" O   ASP B 737 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 753
    Processing helix  chain 'B' and resid 756 through 782
      removed outlier: 3.575A  pdb=" N   CYS B 760 " --> pdb=" O   TYR B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 824
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 866 through 884
    Processing helix  chain 'B' and resid 886 through 890
      removed outlier: 3.568A  pdb=" N   GLY B 889 " --> pdb=" O   TRP B 886 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 890 " --> pdb=" O   THR B 887 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 886 through 890'
    Processing helix  chain 'B' and resid 897 through 910
      removed outlier: 3.920A  pdb=" N   ILE B 909 " --> pdb=" O   ARG B 905 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY B 910 " --> pdb=" O   PHE B 906 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 913 through 919
    Processing helix  chain 'B' and resid 919 through 938
      removed outlier: 3.543A  pdb=" N   ILE B 923 " --> pdb=" O   ASN B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 949 through 965
    Processing helix  chain 'B' and resid 976 through 984
      removed outlier: 3.544A  pdb=" N   ARG B 983 " --> pdb=" O   ASP B 979 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 985 through 1033
      removed outlier: 6.060A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   GLN B 992 " --> pdb=" O   GLU B 988 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1140 through 1146
      removed outlier: 3.712A  pdb=" N   GLU B1144 " --> pdb=" O   PRO B1140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 304
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 4.169A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'C' and resid 738 through 743
    Processing helix  chain 'C' and resid 747 through 754
    Processing helix  chain 'C' and resid 756 through 782
      removed outlier: 3.602A  pdb=" N   CYS C 760 " --> pdb=" O   TYR C 756 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 816 through 826
      removed outlier: 3.728A  pdb=" N   LYS C 825 " --> pdb=" O   LEU C 821 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL C 826 " --> pdb=" O   LEU C 822 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 852 through 856
      removed outlier: 3.525A  pdb=" N   ASN C 856 " --> pdb=" O   GLN C 853 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 866 through 884
    Processing helix  chain 'C' and resid 897 through 908
    Processing helix  chain 'C' and resid 913 through 919
    Processing helix  chain 'C' and resid 919 through 939
    Processing helix  chain 'C' and resid 949 through 965
    Processing helix  chain 'C' and resid 966 through 968
      No H-bonds generated for 'chain 'C' and resid 966 through 968'
    Processing helix  chain 'C' and resid 976 through 984
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 5.614A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   GLN C 992 " --> pdb=" O   GLU C 988 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1140 through 1146
      removed outlier: 3.746A  pdb=" N   GLU C1144 " --> pdb=" O   PRO C1140 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASP C1146 " --> pdb=" O   GLN C1142 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29
      removed outlier: 3.907A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE A  65 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR A 265 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 3.868A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 277 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU A 276 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55
      removed outlier: 3.821A  pdb=" N   ASP A  53 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG A 273 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 11.181A  pdb=" N   VAL A 126 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 9.921A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 11.409A  pdb=" N   ILE A 128 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   VAL A 130 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ASN A 165 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   CYS A 136 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 10.445A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 9.218A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 10.492A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 8.874A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85
      removed outlier: 9.193A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   ARG A 246 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL A 143 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 314
    Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.651A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   VAL A 395 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   SER A 514 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ALA A 397 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL A 512 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   SER A 399 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL A 510 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   VAL A 401 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TYR A 508 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655
      removed outlier: 5.975A  pdb=" N   GLU A 654 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 8.598A  pdb=" N   THR A 696 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A 693 " --> pdb=" O   SER A 673 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 673 " --> pdb=" O   ILE A 693 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   TYR A 695 " --> pdb=" O   CYS A 671 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   CYS A 671 " --> pdb=" O   TYR A 695 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703
    Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713
      removed outlier: 3.879A  pdb=" N   ILE A 712 " --> pdb=" O   PHE A1075 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A1075 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728
      removed outlier: 3.913A  pdb=" N   ASN A 717 " --> pdb=" O   ALA A1070 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL A1068 " --> pdb=" O   THR A 719 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   THR A 723 " --> pdb=" O   HIS A1064 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU A 725 " --> pdb=" O   PHE A1062 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A1062 " --> pdb=" O   GLU A 725 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 727 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728
      removed outlier: 3.913A  pdb=" N   ASN A 717 " --> pdb=" O   ALA A1070 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL A1068 " --> pdb=" O   THR A 719 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   THR A 723 " --> pdb=" O   HIS A1064 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU A 725 " --> pdb=" O   PHE A1062 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A1062 " --> pdb=" O   GLU A 725 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 727 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A1056 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A1061 " --> pdb=" O   GLN A1054 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735
    Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789
      removed outlier: 6.246A  pdb=" N   ILE A 788 " --> pdb=" O   ASN C 703 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122
      removed outlier: 3.522A  pdb=" N   CYS A1082 " --> pdb=" O   VAL A1133 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097
    Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30
      removed outlier: 3.648A  pdb=" N   ALA B  27 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR B  63 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   VAL B 267 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B  65 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   TYR B 265 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LYS B 187 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 51
      removed outlier: 3.877A  pdb=" N   THR B  51 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   PHE B 275 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85
      removed outlier: 11.165A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 9.778A  pdb=" N   GLU B 169 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 11.267A  pdb=" N   ILE B 128 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   THR B 167 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   VAL B 130 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ASN B 165 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   ALA B 163 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   CYS B 136 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
      removed outlier: 10.804A  pdb=" N   ASP B 138 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
      removed outlier: 9.414A  pdb=" N   PHE B 157 " --> pdb=" O   ASP B 138 " (cutoff:3.500A)
      removed outlier: 10.648A  pdb=" N   PHE B 140 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
      removed outlier: 8.930A  pdb=" N   SER B 155 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   GLY B 142 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   MET B 153 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85
    Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316
      removed outlier: 5.947A  pdb=" N   ILE B 312 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   THR B 599 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   GLN B 314 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL B 597 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER B 316 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL B 610 " --> pdb=" O   ILE B 651 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   CYS B 649 " --> pdb=" O   TYR B 612 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327
      removed outlier: 3.547A  pdb=" N   ASN B 542 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.924A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AD1, first strand: chain 'B' and resid 664 through 665
      removed outlier: 3.737A  pdb=" N   CYS B 671 " --> pdb=" O   TYR B 695 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TYR B 695 " --> pdb=" O   CYS B 671 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER B 673 " --> pdb=" O   ILE B 693 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE B 693 " --> pdb=" O   SER B 673 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B 675 " --> pdb=" O   SER B 691 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702
      removed outlier: 6.737A  pdb=" N   ALA B 701 " --> pdb=" O   ILE C 788 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728
      removed outlier: 3.715A  pdb=" N   VAL B1068 " --> pdb=" O   THR B 719 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER B 721 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR B 723 " --> pdb=" O   HIS B1064 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU B 725 " --> pdb=" O   PHE B1062 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 727 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B1063 " --> pdb=" O   SER B1051 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER B1051 " --> pdb=" O   LEU B1063 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B1065 " --> pdb=" O   LEU B1049 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728
      removed outlier: 3.715A  pdb=" N   VAL B1068 " --> pdb=" O   THR B 719 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER B 721 " --> pdb=" O   THR B1066 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR B 723 " --> pdb=" O   HIS B1064 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU B 725 " --> pdb=" O   PHE B1062 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 727 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA B1056 " --> pdb=" O   GLY B1059 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736
      removed outlier: 4.404A  pdb=" N   LYS B 733 " --> pdb=" O   LEU B 861 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 1076 through 1078
      removed outlier: 3.905A  pdb=" N   THR B1076 " --> pdb=" O   SER B1097 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE B1095 " --> pdb=" O   ALA B1078 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122
      removed outlier: 3.769A  pdb=" N   ILE B1081 " --> pdb=" O   HIS B1088 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   CYS B1082 " --> pdb=" O   VAL B1133 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.745A  pdb=" N   ALA C  27 " --> pdb=" O   TRP C  64 " (cutoff:3.500A)
      removed outlier: 8.546A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR C  63 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL C 267 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE C  65 " --> pdb=" O   TYR C 265 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR C 265 " --> pdb=" O   PHE C  65 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85
      removed outlier: 6.385A  pdb=" N   VAL C 126 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL C 171 " --> pdb=" O   VAL C 126 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE C 128 " --> pdb=" O   GLU C 169 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLU C 169 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL C 130 " --> pdb=" O   THR C 167 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 152 through 160
      removed outlier: 3.696A  pdb=" N   MET C 153 " --> pdb=" O   TYR C 144 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   GLY C 142 " --> pdb=" O   SER C 155 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   PHE C 157 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE C 140 " --> pdb=" O   PHE C 157 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   VAL C 159 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASP C 138 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 275 through 279
      removed outlier: 4.234A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314
    Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.596A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL C 395 " --> pdb=" O   SER C 514 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER C 514 " --> pdb=" O   VAL C 395 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ALA C 397 " --> pdb=" O   VAL C 512 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL C 512 " --> pdb=" O   ALA C 397 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   SER C 399 " --> pdb=" O   VAL C 510 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL C 510 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   VAL C 401 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   TYR C 508 " --> pdb=" O   VAL C 401 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AE6, first strand: chain 'C' and resid 539 through 543
      removed outlier: 5.911A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655
      removed outlier: 6.082A  pdb=" N   GLU C 654 " --> pdb=" O   ALA C 694 " (cutoff:3.500A)
      removed outlier: 8.746A  pdb=" N   THR C 696 " --> pdb=" O   GLU C 654 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN C 675 " --> pdb=" O   SER C 691 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER C 673 " --> pdb=" O   ILE C 693 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR C 695 " --> pdb=" O   CYS C 671 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS C 671 " --> pdb=" O   TYR C 695 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712
      removed outlier: 3.504A  pdb=" N   PHE C1075 " --> pdb=" O   ILE C 712 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR C1076 " --> pdb=" O   SER C1097 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 722
      removed outlier: 3.727A  pdb=" N   THR C 719 " --> pdb=" O   VAL C1068 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   VAL C1068 " --> pdb=" O   THR C 719 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER C 721 " --> pdb=" O   THR C1066 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 722
      removed outlier: 3.727A  pdb=" N   THR C 719 " --> pdb=" O   VAL C1068 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   VAL C1068 " --> pdb=" O   THR C 719 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER C 721 " --> pdb=" O   THR C1066 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA C1056 " --> pdb=" O   GLY C1059 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   MET C1050 " --> pdb=" O   VAL C1065 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   TYR C1067 " --> pdb=" O   HIS C1048 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   HIS C1048 " --> pdb=" O   TYR C1067 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736
    Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122

    909 hydrogen bonds defined for protein.
    2472 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: 12.29

  Time building geometry restraints manager: 10.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 8133
        1.35 -     1.46: 6151
        1.46 -     1.58: 11247
        1.58 -     1.70: 0
        1.70 -     1.82: 147
  Bond restraints: 25678
  Sorted by residual:
  bond pdb=" C   PRO A 986 "
       pdb=" N   PRO A 987 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.68e+00
  bond pdb=" C   MET A 177 "
       pdb=" O   MET A 177 "
    ideal  model  delta    sigma   weight residual
    1.227  1.235 -0.008 7.80e-03 1.64e+04 1.07e+00
  bond pdb=" CA  ASN B 211 "
       pdb=" C   ASN B 211 "
    ideal  model  delta    sigma   weight residual
    1.533  1.523  0.010 9.60e-03 1.09e+04 1.06e+00
  bond pdb=" N   PHE B 329 "
       pdb=" CA  PHE B 329 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.41e-02 5.03e+03 1.02e+00
  bond pdb=" CA  ARG A 102 "
       pdb=" C   ARG A 102 "
    ideal  model  delta    sigma   weight residual
    1.517  1.523 -0.006 6.30e-03 2.52e+04 9.93e-01
  ... (remaining 25673 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   107.31: 823
      107.31 -   113.98: 14249
      113.98 -   120.66: 10053
      120.66 -   127.33: 9594
      127.33 -   134.00: 222
  Bond angle restraints: 34941
  Sorted by residual:
  angle pdb=" CA  ALA C 344 "
        pdb=" C   ALA C 344 "
        pdb=" N   THR C 345 "
      ideal   model   delta    sigma   weight residual
     119.56  116.93    2.63 5.80e-01 2.97e+00 2.06e+01
  angle pdb=" N   ILE A 973 "
        pdb=" CA  ILE A 973 "
        pdb=" C   ILE A 973 "
      ideal   model   delta    sigma   weight residual
     113.53  109.33    4.20 9.80e-01 1.04e+00 1.84e+01
  angle pdb=" C   MET A 177 "
        pdb=" CA  MET A 177 "
        pdb=" CB  MET A 177 "
      ideal   model   delta    sigma   weight residual
     116.54  110.78    5.76 1.46e+00 4.69e-01 1.56e+01
  angle pdb=" C   ASP B 215 "
        pdb=" CA  ASP B 215 "
        pdb=" CB  ASP B 215 "
      ideal   model   delta    sigma   weight residual
     115.89  110.76    5.13 1.32e+00 5.74e-01 1.51e+01
  angle pdb=" C   ASP C 215 "
        pdb=" CA  ASP C 215 "
        pdb=" CB  ASP C 215 "
      ideal   model   delta    sigma   weight residual
     115.89  110.83    5.06 1.32e+00 5.74e-01 1.47e+01
  ... (remaining 34936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 15035
       17.59 -    35.18: 269
       35.18 -    52.77: 15
       52.77 -    70.36: 1
       70.36 -    87.94: 3
  Dihedral angle restraints: 15323
    sinusoidal: 5987
      harmonic: 9336
  Sorted by residual:
  dihedral pdb=" N   PHE B 329 "
           pdb=" C   PHE B 329 "
           pdb=" CA  PHE B 329 "
           pdb=" CB  PHE B 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.21   -9.41     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" C   PHE B 329 "
           pdb=" N   PHE B 329 "
           pdb=" CA  PHE B 329 "
           pdb=" CB  PHE B 329 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.02    8.42     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" SG  CYS C 391 "
           pdb=" CB  CYS C 525 "
           pdb=" SG  CYS C 525 "
           pdb=" CA  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -20.00  -53.00     1      2.00e+01 2.50e-03 9.56e+00
  ... (remaining 15320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 3576
       0.069 -    0.138: 376
       0.138 -    0.207: 0
       0.207 -    0.276: 0
       0.276 -    0.345: 1
  Chirality restraints: 3953
  Sorted by residual:
  chirality pdb=" CA  PHE B 329 "
            pdb=" N   PHE B 329 "
            pdb=" C   PHE B 329 "
            pdb=" CB  PHE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  ILE C 664 "
            pdb=" N   ILE C 664 "
            pdb=" C   ILE C 664 "
            pdb=" CB  ILE C 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  ILE A 664 "
            pdb=" N   ILE A 664 "
            pdb=" C   ILE A 664 "
            pdb=" CB  ILE A 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 3950 not shown)

  Planarity restraints: 4539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 985 "    0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO A 986 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 986 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 986 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 985 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO B 986 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 986 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 986 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 985 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO C 986 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 986 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 986 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 4536 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 3633
        2.76 -     3.30: 22256
        3.30 -     3.83: 39472
        3.83 -     4.37: 43811
        4.37 -     4.90: 79501
  Nonbonded interactions: 188673
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 130 "
            pdb=" OG1 THR A 167 "
     model   vdw
     2.231 2.440
  nonbonded pdb=" OE1 GLU C1031 "
            pdb=" NH1 ARG C1039 "
     model   vdw
     2.297 2.520
  nonbonded pdb=" OG1 THR C1076 "
            pdb=" OG  SER C1097 "
     model   vdw
     2.305 2.440
  nonbonded pdb=" OE2 GLU A1031 "
            pdb=" NH2 ARG C1039 "
     model   vdw
     2.305 2.520
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   LEU C  54 "
     model   vdw
     2.306 2.440
  ... (remaining 188668 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 14 through 827 or resid 851 through 1146))
  selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 851 throu \ 
gh 1146))
  selection = chain 'C'
}

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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.100
  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:             0.020
  Extract box with map and model:          14.280
  Check model and map are aligned:         0.370
  Set scattering table:                    0.230
  Process input model:                     68.330
  Find NCS groups from input model:        1.850
  Set up NCS constraints:                  0.100
  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:             0.000
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   94.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
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      :  0.001   0.030  25678  Z= 0.091
  Angle     :  0.414   8.387  34941  Z= 0.244
  Chirality :  0.039   0.345   3953
  Planarity :  0.003   0.034   4539
  Dihedral  :  5.801  87.945   9191
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 12.36 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  3.07 %
    Favored  : 95.94 %
  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: -2.52 (0.14), residues: 3171
  helix:  1.00 (0.21), residues: 607
  sheet: -0.84 (0.20), residues: 626
  loop : -3.06 (0.12), residues: 1938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.000   TRP A 436 
   HIS   0.001   0.000   HIS B1048 
   PHE   0.006   0.000   PHE A 157 
   TYR   0.009   0.000   TYR B 204 
   ARG   0.002   0.000   ARG A 357 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  502 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 474
  time to evaluate  : 3.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 3
  residues processed: 498
  average time/residue: 0.4122
  time to fit residues: 317.8126
Evaluate side-chains
  238 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 235
  time to evaluate  : 4.238 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.3774
  time to fit residues: 7.0592
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 269 optimal weight:    6.9990
   chunk 241 optimal weight:    0.6980
   chunk 134 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 163 optimal weight:    0.9980
   chunk 129 optimal weight:    8.9990
   chunk 250 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 152 optimal weight:   20.0000
   chunk 186 optimal weight:    5.9990
   chunk 289 optimal weight:    4.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  17 ASN
** A  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 GLN
A 149 ASN
A 173 GLN
A 185 ASN
A 211 ASN
A 321 GLN
A 331 ASN
A 394 ASN
A 414 GLN
A 613 GLN
A 675 GLN
A 690 GLN
A 787 GLN
A 907 ASN
A 920 GLN
A 935 GLN
A1005 GLN
A1036 GLN
A1054 GLN
A1064 HIS
A1098 ASN
A1106 GLN
A1108 ASN
A1125 ASN
A1142 GLN
B  14 GLN
B  52 GLN
B  61 ASN
B  69 HIS
B 115 GLN
B 211 ASN
B 218 GLN
B 239 GLN
B 245 HIS
B 271 GLN
** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
B 414 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 540 ASN
B 613 GLN
B 690 GLN
B 787 GLN
B 920 GLN
B 925 ASN
B 935 GLN
B 954 GLN
B 957 GLN
B1011 GLN
B1064 HIS
B1071 GLN
B1106 GLN
C  14 GLN
C  17 ASN
C  23 GLN
C  52 GLN
C  61 ASN
C 115 GLN
C 146 HIS
C 218 GLN
C 271 GLN
C 314 GLN
C 370 ASN
C 422 ASN
C 519 HIS
C 613 GLN
C 675 GLN
C 764 ASN
C 784 GLN
C 853 GLN
C 907 ASN
C 920 GLN
C 935 GLN
C 954 GLN
C1005 GLN
C1011 GLN
C1054 GLN
** C1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1071 GLN

Total number of N/Q/H flips: 77

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.164  25678  Z= 0.438
  Angle     :  0.752  12.839  34941  Z= 0.389
  Chirality :  0.046   0.271   3953
  Planarity :  0.005   0.050   4539
  Dihedral  :  3.927  24.665   3438
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.40 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  :  9.27 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.14), residues: 3171
  helix:  1.25 (0.21), residues: 636
  sheet: -0.31 (0.20), residues: 698
  loop : -2.64 (0.12), residues: 1837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.034   0.002   TRP C 104 
   HIS   0.011   0.002   HIS C  66 
   PHE   0.033   0.002   PHE C 782 
   TYR   0.037   0.002   TYR C 396 
   ARG   0.009   0.001   ARG A  44 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 89
    poor density    : 193
  time to evaluate  : 2.831 
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
  outliers start: 89
  outliers final: 51
  residues processed: 261
  average time/residue: 0.3638
  time to fit residues: 153.7337
Evaluate side-chains
  183 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 132
  time to evaluate  : 3.029 
Switching outliers to nearest non-outliers
  outliers start: 51
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2689
  time to fit residues: 29.0239
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 160 optimal weight:   20.0000
   chunk 89 optimal weight:    2.9990
   chunk 241 optimal weight:    0.8980
   chunk 197 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 290 optimal weight:    7.9990
   chunk 313 optimal weight:    0.0980
   chunk 258 optimal weight:    9.9990
   chunk 287 optimal weight:    0.4980
   chunk 98 optimal weight:    0.7980
   chunk 232 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 965 GLN
C1064 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.071  25678  Z= 0.147
  Angle     :  0.519  13.198  34941  Z= 0.257
  Chirality :  0.041   0.162   3953
  Planarity :  0.003   0.044   4539
  Dihedral  :  3.214  17.423   3438
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.83 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.73 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.15), residues: 3171
  helix:  2.10 (0.22), residues: 630
  sheet:  0.05 (0.21), residues: 637
  loop : -2.41 (0.12), residues: 1904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP C 436 
   HIS   0.004   0.001   HIS C 207 
   PHE   0.017   0.001   PHE C 338 
   TYR   0.021   0.001   TYR C 396 
   ARG   0.005   0.000   ARG C1014 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 3.023 
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: 32
  outliers final: 16
  residues processed: 185
  average time/residue: 0.3350
  time to fit residues: 104.6593
Evaluate side-chains
  147 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 2.994 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.2307
  time to fit residues: 10.8344
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 286 optimal weight:    3.9990
   chunk 218 optimal weight:    9.9990
   chunk 150 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 138 optimal weight:    5.9990
   chunk 194 optimal weight:    2.9990
   chunk 291 optimal weight:    1.9990
   chunk 308 optimal weight:    3.9990
   chunk 152 optimal weight:   30.0000
   chunk 276 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0040
   overall best weight:    1.9598

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  66 HIS
A 125 ASN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
B  69 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 540 ASN
B 955 ASN
B1083 HIS
C  66 HIS
C 710 ASN
C1058 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.130  25678  Z= 0.304
  Angle     :  0.587  10.812  34941  Z= 0.301
  Chirality :  0.043   0.151   3953
  Planarity :  0.004   0.042   4539
  Dihedral  :  3.645  19.639   3438
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.18 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.52 %
    Favored  : 86.88 %
  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: -1.20 (0.15), residues: 3171
  helix:  1.87 (0.21), residues: 629
  sheet:  0.16 (0.20), residues: 678
  loop : -2.28 (0.13), residues: 1864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP C 436 
   HIS   0.025   0.002   HIS A  49 
   PHE   0.027   0.002   PHE C 782 
   TYR   0.023   0.001   TYR C 396 
   ARG   0.014   0.001   ARG A  44 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 3.284 
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
  outliers start: 45
  outliers final: 25
  residues processed: 168
  average time/residue: 0.3264
  time to fit residues: 94.2381
Evaluate side-chains
  140 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 2.955 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2197
  time to fit residues: 14.4139
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 256 optimal weight:   10.0000
   chunk 175 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 229 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   chunk 263 optimal weight:    0.0980
   chunk 213 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 157 optimal weight:    0.0000
   chunk 276 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.6190

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
A  49 HIS
A 188 ASN
A 207 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 HIS
B  69 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 536 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.5239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  25678  Z= 0.238
  Angle     :  0.527  12.602  34941  Z= 0.268
  Chirality :  0.042   0.156   3953
  Planarity :  0.003   0.039   4539
  Dihedral  :  3.536  18.625   3438
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.08 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.26 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.15), residues: 3171
  helix:  2.04 (0.22), residues: 630
  sheet:  0.17 (0.20), residues: 670
  loop : -2.16 (0.13), residues: 1871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP C 886 
   HIS   0.005   0.001   HIS A1064 
   PHE   0.025   0.001   PHE C 855 
   TYR   0.018   0.001   TYR C 396 
   ARG   0.008   0.000   ARG A 190 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 3.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 32
  outliers final: 15
  residues processed: 149
  average time/residue: 0.3341
  time to fit residues: 86.1927
Evaluate side-chains
  126 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 3.118 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.4656
  time to fit residues: 16.9473
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 277 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 181 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 308 optimal weight:    2.9990
   chunk 256 optimal weight:    9.9990
   chunk 142 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 102 optimal weight:    0.5980
   chunk 162 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN
A 872 GLN
B  69 HIS
B 360 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 580 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.5406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  25678  Z= 0.177
  Angle     :  0.503  12.374  34941  Z= 0.250
  Chirality :  0.041   0.185   3953
  Planarity :  0.003   0.044   4539
  Dihedral  :  3.415  17.347   3438
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.60 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.73 %
    Favored  : 86.35 %
  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: -0.84 (0.15), residues: 3171
  helix:  2.21 (0.22), residues: 630
  sheet:  0.32 (0.20), residues: 663
  loop : -2.01 (0.13), residues: 1878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP C 886 
   HIS   0.003   0.001   HIS A  49 
   PHE   0.017   0.001   PHE C 855 
   TYR   0.017   0.001   TYR B 904 
   ARG   0.006   0.000   ARG B 905 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 3.033 
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
  outliers start: 26
  outliers final: 12
  residues processed: 135
  average time/residue: 0.3570
  time to fit residues: 81.1530
Evaluate side-chains
  118 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 2.965 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.2362
  time to fit residues: 9.2828
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 297 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 175 optimal weight:    3.9990
   chunk 225 optimal weight:    4.9990
   chunk 174 optimal weight:    2.9990
   chunk 259 optimal weight:   20.0000
   chunk 172 optimal weight:    0.5980
   chunk 307 optimal weight:    2.9990
   chunk 192 optimal weight:    4.9990
   chunk 187 optimal weight:    1.9990
   chunk 141 optimal weight:    9.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 872 GLN
B  69 HIS
B 125 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.6096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.117  25678  Z= 0.371
  Angle     :  0.629  12.873  34941  Z= 0.320
  Chirality :  0.043   0.214   3953
  Planarity :  0.004   0.043   4539
  Dihedral  :  3.964  19.307   3438
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.28 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.80 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.15), residues: 3171
  helix:  1.79 (0.21), residues: 626
  sheet:  0.13 (0.19), residues: 733
  loop : -2.07 (0.14), residues: 1812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP A1102 
   HIS   0.009   0.001   HIS A  49 
   PHE   0.019   0.002   PHE C 782 
   TYR   0.019   0.002   TYR C 396 
   ARG   0.007   0.001   ARG A  44 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 2.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 36
  outliers final: 18
  residues processed: 135
  average time/residue: 0.3354
  time to fit residues: 77.1599
Evaluate side-chains
  110 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 2.945 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.2326
  time to fit residues: 11.8638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 190 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   chunk 183 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 195 optimal weight:    0.7980
   chunk 209 optimal weight:    1.9990
   chunk 152 optimal weight:    0.0470
   chunk 28 optimal weight:    0.7980
   chunk 241 optimal weight:    0.7980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 644 GLN
** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  25678  Z= 0.138
  Angle     :  0.506  13.695  34941  Z= 0.250
  Chirality :  0.041   0.153   3953
  Planarity :  0.003   0.041   4539
  Dihedral  :  3.550  18.348   3438
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.10 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 13.73 %
    Favored  : 85.88 %
  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: -0.76 (0.15), residues: 3171
  helix:  2.21 (0.22), residues: 628
  sheet:  0.29 (0.19), residues: 710
  loop : -1.95 (0.14), residues: 1833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP C 886 
   HIS   0.002   0.000   HIS A  49 
   PHE   0.029   0.001   PHE B  55 
   TYR   0.015   0.001   TYR B1067 
   ARG   0.005   0.000   ARG B 355 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 3.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 5
  residues processed: 110
  average time/residue: 0.3528
  time to fit residues: 67.4094
Evaluate side-chains
  102 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 3.276 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.2829
  time to fit residues: 6.6500
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 279 optimal weight:    3.9990
   chunk 294 optimal weight:    0.9980
   chunk 268 optimal weight:    4.9990
   chunk 286 optimal weight:    0.9990
   chunk 172 optimal weight:    0.6980
   chunk 124 optimal weight:    8.9990
   chunk 224 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 258 optimal weight:    2.9990
   chunk 270 optimal weight:    5.9990
   chunk 285 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 GLN
** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.6170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  25678  Z= 0.217
  Angle     :  0.526  12.403  34941  Z= 0.262
  Chirality :  0.042   0.190   3953
  Planarity :  0.003   0.045   4539
  Dihedral  :  3.598  19.349   3438
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.11 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.01 %
    Favored  : 85.67 %
  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: -0.80 (0.15), residues: 3171
  helix:  2.03 (0.21), residues: 640
  sheet:  0.26 (0.19), residues: 692
  loop : -1.91 (0.14), residues: 1839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 152 
   HIS   0.005   0.001   HIS A  49 
   PHE   0.029   0.001   PHE B  55 
   TYR   0.017   0.001   TYR C 421 
   ARG   0.007   0.000   ARG A 273 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 2.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 107
  average time/residue: 0.3473
  time to fit residues: 64.9603
Evaluate side-chains
  96 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 2.983 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.2445
  time to fit residues: 5.7512
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 188 optimal weight:    0.6980
   chunk 302 optimal weight:    3.9990
   chunk 184 optimal weight:    4.9990
   chunk 143 optimal weight:   10.0000
   chunk 210 optimal weight:    4.9990
   chunk 317 optimal weight:    1.9990
   chunk 292 optimal weight:    2.9990
   chunk 253 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 195 optimal weight:    0.1980
   chunk 155 optimal weight:    5.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  69 HIS
B 498 GLN
** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.6301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  25678  Z= 0.197
  Angle     :  0.517  12.773  34941  Z= 0.257
  Chirality :  0.042   0.172   3953
  Planarity :  0.003   0.044   4539
  Dihedral  :  3.602  20.881   3438
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.70 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 14.44 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.15), residues: 3171
  helix:  2.01 (0.21), residues: 647
  sheet:  0.26 (0.20), residues: 681
  loop : -1.83 (0.14), residues: 1843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP B 886 
   HIS   0.005   0.001   HIS A  49 
   PHE   0.030   0.001   PHE B  55 
   TYR   0.027   0.001   TYR B 904 
   ARG   0.007   0.000   ARG A 273 

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

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

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6342 Ramachandran restraints generated.
    3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 2.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 99
  average time/residue: 0.3447
  time to fit residues: 60.5014
Evaluate side-chains
  96 residues out of total 2805 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 3.380 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.2483
  time to fit residues: 4.6831
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 201 optimal weight:    1.9990
   chunk 269 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 233 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 253 optimal weight:    0.7980
   chunk 106 optimal weight:   20.0000
   chunk 260 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 ASN
A 185 ASN
A 245 HIS
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 GLN
** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 644 GLN
C 703 ASN
** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.080898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.052509 restraints weight = 114330.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.054093 restraints weight = 58996.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.055058 restraints weight = 33493.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.6734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.115  25678  Z= 0.341
  Angle     :  0.611  11.341  34941  Z= 0.310
  Chirality :  0.043   0.171   3953
  Planarity :  0.004   0.044   4539
  Dihedral  :  4.031  21.616   3438
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.96 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 14.51 %
    Favored  : 85.20 %
  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: -0.96 (0.15), residues: 3171
  helix:  1.63 (0.21), residues: 643
  sheet:  0.18 (0.19), residues: 717
  loop : -1.95 (0.14), residues: 1811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP A1102 
   HIS   0.009   0.001   HIS A  49 
   PHE   0.028   0.002   PHE B  55 
   TYR   0.031   0.002   TYR B 904 
   ARG   0.006   0.001   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4214.68 seconds
wall clock time: 78 minutes 46.39 seconds (4726.39 seconds total)