Starting phenix.real_space_refine
on Sun Dec 10 19:35:49 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/12_2023/8sh9_40481_updated.pdb"
  }
  resolution = 2.7
  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=   0.004 sd=   0.051
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: 8
    Type Number    sf(0)   Gaussians
     Al     16      5.89       5
     P      32      5.49       5
     Mg     16      5.21       5
     S     415      5.16       5
     C   41982      2.51       5
     N   11685      2.21       5
     O   13003      1.98       5
     F      48      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE    8": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   51": "OD1" <-> "OD2"
    Residue "A ASP  529": "OD1" <-> "OD2"
    Residue "B ASP   77": "OD1" <-> "OD2"
    Residue "B GLU  495": "OE1" <-> "OE2"
    Residue "D ASP   63": "OD1" <-> "OD2"
    Residue "D PHE  251": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  331": "OE1" <-> "OE2"
    Residue "D TYR  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  467": "OE1" <-> "OE2"
    Residue "E GLU   32": "OE1" <-> "OE2"
    Residue "E GLU  212": "OE1" <-> "OE2"
    Residue "E TYR  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  532": "OD1" <-> "OD2"
    Residue "H GLU   11": "OE1" <-> "OE2"
    Residue "H TYR  475": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q GLU   27": "OE1" <-> "OE2"
    Residue "Q ASP  393": "OD1" <-> "OD2"
    Residue "Q TYR  505": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z GLU  415": "OE1" <-> "OE2"
    Residue "a GLU   66": "OE1" <-> "OE2"
    Residue "a GLU   77": "OE1" <-> "OE2"
    Residue "a GLU  207": "OE1" <-> "OE2"
    Residue "a GLU  354": "OE1" <-> "OE2"
    Residue "a GLU  416": "OE1" <-> "OE2"
    Residue "b GLU   19": "OE1" <-> "OE2"
    Residue "b ASP   77": "OD1" <-> "OD2"
    Residue "d ASP   46": "OD1" <-> "OD2"
    Residue "d GLU  101": "OE1" <-> "OE2"
    Residue "d ASP  118": "OD1" <-> "OD2"
    Residue "d TYR  179": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d GLU  279": "OE1" <-> "OE2"
    Residue "d GLU  399": "OE1" <-> "OE2"
    Residue "d GLU  402": "OE1" <-> "OE2"
    Residue "e TYR  420": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g ASP  242": "OD1" <-> "OD2"
    Residue "g TYR  303": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g TYR  506": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h ASP   70": "OD1" <-> "OD2"
    Residue "h GLU  103": "OE1" <-> "OE2"
    Residue "h TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h PHE  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "h ASP  451": "OD1" <-> "OD2"
    Residue "z GLU  112": "OE1" <-> "OE2"
    Residue "z ASP  496": "OD1" <-> "OD2"
    Residue "P TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE  260": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.15s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 67197
  Number of models: 1
  Model: ""
    Number of chains: 50
    Chain: "N"
      Number of atoms: 322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 322
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 4069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4069
          Classifications: {'peptide': 536}
          Link IDs: {'PTRANS': 14, 'TRANS': 521}
    Chain: "B"
      Number of atoms: 3952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 3952
          Classifications: {'peptide': 526}
          Link IDs: {'PTRANS': 10, 'TRANS': 515}
    Chain: "D"
      Number of atoms: 3923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 3923
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 14, 'TRANS': 505}
    Chain: "E"
      Number of atoms: 4132
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 535, 4121
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 18, 'TRANS': 516}
      Conformer: "C"
        Number of residues, atoms: 535, 4121
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 18, 'TRANS': 516}
          bond proxies already assigned to first conformer: 4158
    Chain: "G"
      Number of atoms: 4089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 4089
          Classifications: {'peptide': 526}
          Link IDs: {'PTRANS': 17, 'TRANS': 508}
    Chain: "H"
      Number of atoms: 4054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4054
          Classifications: {'peptide': 528}
          Link IDs: {'PTRANS': 16, 'TRANS': 511}
    Chain: "Q"
      Number of atoms: 4086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4086
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 18, 'TRANS': 519}
    Chain: "Z"
      Number of atoms: 4022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 525, 4022
          Classifications: {'peptide': 525}
          Link IDs: {'PTRANS': 14, 'TRANS': 510}
    Chain: "a"
      Number of atoms: 4041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4041
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 13, 'TRANS': 518}
    Chain: "b"
      Number of atoms: 3943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 525, 3943
          Classifications: {'peptide': 525}
          Link IDs: {'PTRANS': 10, 'TRANS': 514}
    Chain: "d"
      Number of atoms: 3917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 3917
          Classifications: {'peptide': 520}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 505}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "e"
      Number of atoms: 4169
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 540, 4158
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 18, 'TRANS': 521}
      Conformer: "B"
        Number of residues, atoms: 540, 4158
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 18, 'TRANS': 521}
          bond proxies already assigned to first conformer: 4195
    Chain: "g"
      Number of atoms: 4102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4102
          Classifications: {'peptide': 528}
          Link IDs: {'PTRANS': 17, 'TRANS': 510}
    Chain: "h"
      Number of atoms: 4032
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 525, 4032
          Classifications: {'peptide': 525}
          Link IDs: {'PTRANS': 16, 'TRANS': 508}
    Chain: "q"
      Number of atoms: 4053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4053
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 16, 'TRANS': 516}
    Chain: "z"
      Number of atoms: 4033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4033
          Classifications: {'peptide': 527}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 512}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "P"
      Number of atoms: 1727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1727
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 6, 'TRANS': 211}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "H"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "Q"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "Z"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "a"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "b"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "d"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "e"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "g"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "h"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "q"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "z"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "Q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "Z"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "a"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "b"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "d"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "e"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "g"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "h"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "z"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  BPHE E   9 " occ=0.38
      ... (20 atoms not shown)
      pdb=" CZ CPHE E   9 " occ=0.62
    residue:
      pdb=" N  APHE e   9 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE e   9 " occ=0.50
  Time building chain proxies: 28.57, per 1000 atoms: 0.43
  Number of scatterers: 67197
  At special positions: 0
  Unit cell: (180.918, 176.686, 179.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S     415     16.00
     P      32     15.00
     Al     16     13.00
     Mg     16     11.99
     F      48      9.00
     O   13003      8.00
     N   11685      7.00
     C   41982      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM66848  O3A ADP H 601 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM66720  O3A ADP B 601 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM66752  O3A ADP D 601 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM67104  O3A ADP h 601 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM66976  O3A ADP b 601 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM66784  O3A ADP E 601 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 21.81
  Conformation dependent library (CDL) restraints added in 10.0 seconds
  

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  16252

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      323 helices and 111 sheets defined
      50.9% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 10.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 35
      removed outlier: 3.672A  pdb=" N   VAL A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   SER A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   SER A  35 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 70 through 85
    Processing helix  chain 'A' and resid 90 through 110
      removed outlier: 3.710A  pdb=" N   VAL A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLN A 110 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 135
    Processing helix  chain 'A' and resid 140 through 142
      No H-bonds generated for 'chain 'A' and resid 140 through 142'
    Processing helix  chain 'A' and resid 144 through 156
    Processing helix  chain 'A' and resid 163 through 178
      removed outlier: 4.475A  pdb=" N   ASP A 166 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ALA A 169 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 186
      No H-bonds generated for 'chain 'A' and resid 184 through 186'
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 257 through 280
      removed outlier: 4.100A  pdb=" N   ASP A 261 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   ILE A 270 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 313 through 323
    Processing helix  chain 'A' and resid 342 through 344
      No H-bonds generated for 'chain 'A' and resid 342 through 344'
    Processing helix  chain 'A' and resid 382 through 404
    Processing helix  chain 'A' and resid 414 through 429
      removed outlier: 4.477A  pdb=" N   THR A 428 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   SER A 429 " --> pdb=" O   ASN A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 455
      removed outlier: 3.778A  pdb=" N   LEU A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   VAL A 447 " --> pdb=" O   ARG A 443 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   ILE A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 449  - end of helix
    Processing helix  chain 'A' and resid 460 through 476
    Processing helix  chain 'A' and resid 478 through 485
      removed outlier: 3.817A  pdb=" N   LYS A 481 " --> pdb=" O   PRO A 478 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ASN A 482 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
      No H-bonds generated for 'chain 'A' and resid 498 through 501'
    Processing helix  chain 'A' and resid 507 through 525
    Processing helix  chain 'B' and resid 21 through 39
    Processing helix  chain 'B' and resid 67 through 72
    Processing helix  chain 'B' and resid 79 through 94
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.565A  pdb=" N   THR B 103 " --> pdb=" O   THR B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'B' and resid 152 through 169
      removed outlier: 4.511A  pdb=" N   SER B 169 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 190
      removed outlier: 3.623A  pdb=" N   HIS B 174 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS B 176 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ASP B 177 " --> pdb=" O   HIS B 174 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE B 179 " --> pdb=" O   LYS B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 198
      No H-bonds generated for 'chain 'B' and resid 196 through 198'
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 261 through 285
      removed outlier: 3.984A  pdb=" N   HIS B 285 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 307
    Processing helix  chain 'B' and resid 317 through 327
    Processing helix  chain 'B' and resid 338 through 340
      No H-bonds generated for 'chain 'B' and resid 338 through 340'
    Processing helix  chain 'B' and resid 380 through 402
    Processing helix  chain 'B' and resid 412 through 427
      removed outlier: 3.854A  pdb=" N   ARG B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 454
      Proline residue:  B 447  - end of helix
      removed outlier: 3.719A  pdb=" N   ALA B 454 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 471
    Processing helix  chain 'B' and resid 488 through 491
      No H-bonds generated for 'chain 'B' and resid 488 through 491'
    Processing helix  chain 'B' and resid 497 through 515
    Processing helix  chain 'D' and resid 29 through 51
      removed outlier: 4.461A  pdb=" N   THR D  50 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   SER D  51 " --> pdb=" O   ALA D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 80
    Processing helix  chain 'D' and resid 86 through 101
    Processing helix  chain 'D' and resid 106 through 125
      removed outlier: 4.213A  pdb=" N   VAL D 110 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS D 122 " --> pdb=" O   ASP D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 151
    Processing helix  chain 'D' and resid 160 through 172
    Processing helix  chain 'D' and resid 180 through 192
      Proline residue:  D 185  - end of helix
    Processing helix  chain 'D' and resid 205 through 207
      No H-bonds generated for 'chain 'D' and resid 205 through 207'
    Processing helix  chain 'D' and resid 218 through 220
      No H-bonds generated for 'chain 'D' and resid 218 through 220'
    Processing helix  chain 'D' and resid 269 through 293
      removed outlier: 4.107A  pdb=" N   ASP D 273 " --> pdb=" O   TYR D 269 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   THR D 293 " --> pdb=" O   GLN D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 319
    Processing helix  chain 'D' and resid 330 through 340
      removed outlier: 4.450A  pdb=" N   GLU D 334 " --> pdb=" O   GLU D 331 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ILE D 340 " --> pdb=" O   CYS D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 348 through 350
      No H-bonds generated for 'chain 'D' and resid 348 through 350'
    Processing helix  chain 'D' and resid 353 through 355
      No H-bonds generated for 'chain 'D' and resid 353 through 355'
    Processing helix  chain 'D' and resid 395 through 417
    Processing helix  chain 'D' and resid 427 through 441
    Processing helix  chain 'D' and resid 447 through 468
      removed outlier: 3.904A  pdb=" N   VAL D 460 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   ILE D 461 " --> pdb=" O   ALA D 457 " (cutoff:3.500A)
      Proline residue:  D 462  - end of helix
    Processing helix  chain 'D' and resid 473 through 486
    Processing helix  chain 'D' and resid 503 through 506
    Processing helix  chain 'D' and resid 512 through 530
    Processing helix  chain 'E' and resid 22 through 24
      No H-bonds generated for 'chain 'E' and resid 22 through 24'
    Processing helix  chain 'E' and resid 30 through 51
      removed outlier: 3.617A  pdb=" N   LEU E  34 " --> pdb=" O   GLY E  30 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   THR E  50 " --> pdb=" O   ASN E  46 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   SER E  51 " --> pdb=" O   THR E  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 80
    Processing helix  chain 'E' and resid 86 through 101
    Processing helix  chain 'E' and resid 108 through 126
      removed outlier: 3.598A  pdb=" N   GLN E 122 " --> pdb=" O   GLU E 118 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG E 126 " --> pdb=" O   GLN E 122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 130 through 150
    Processing helix  chain 'E' and resid 163 through 175
      removed outlier: 4.674A  pdb=" N   SER E 175 " --> pdb=" O   THR E 171 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 180
      removed outlier: 3.955A  pdb=" N   SER E 180 " --> pdb=" O   VAL E 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 177 through 180'
    Processing helix  chain 'E' and resid 182 through 195
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 219 through 221
      No H-bonds generated for 'chain 'E' and resid 219 through 221'
    Processing helix  chain 'E' and resid 271 through 295
      removed outlier: 3.890A  pdb=" N   THR E 295 " --> pdb=" O   GLN E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 308 through 316
    Processing helix  chain 'E' and resid 327 through 337
    Processing helix  chain 'E' and resid 345 through 347
      No H-bonds generated for 'chain 'E' and resid 345 through 347'
    Processing helix  chain 'E' and resid 392 through 414
    Processing helix  chain 'E' and resid 424 through 437
    Processing helix  chain 'E' and resid 442 through 465
      removed outlier: 3.947A  pdb=" N   TYR E 446 " --> pdb=" O   THR E 442 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA E 447 " --> pdb=" O   LEU E 443 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL E 457 " --> pdb=" O   ASP E 453 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ILE E 458 " --> pdb=" O   ALA E 454 " (cutoff:3.500A)
      Proline residue:  E 459  - end of helix
    Processing helix  chain 'E' and resid 470 through 483
    Processing helix  chain 'E' and resid 501 through 504
      No H-bonds generated for 'chain 'E' and resid 501 through 504'
    Processing helix  chain 'E' and resid 510 through 528
    Processing helix  chain 'G' and resid 20 through 40
      removed outlier: 3.814A  pdb=" N   ILE G  37 " --> pdb=" O   ILE G  33 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   THR G  39 " --> pdb=" O   ASP G  35 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   CYS G  40 " --> pdb=" O   ILE G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 68
    Processing helix  chain 'G' and resid 75 through 90
    Processing helix  chain 'G' and resid 95 through 115
      removed outlier: 3.647A  pdb=" N   ILE G  99 " --> pdb=" O   THR G  95 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE G 100 " --> pdb=" O   THR G  96 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS G 111 " --> pdb=" O   SER G 107 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE G 112 " --> pdb=" O   VAL G 108 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN G 115 " --> pdb=" O   HIS G 111 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 119 through 139
    Processing helix  chain 'G' and resid 149 through 160
    Processing helix  chain 'G' and resid 164 through 183
      removed outlier: 4.185A  pdb=" N   ARG G 167 " --> pdb=" O   ALA G 164 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   SER G 170 " --> pdb=" O   ARG G 167 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 198
      No H-bonds generated for 'chain 'G' and resid 195 through 198'
    Processing helix  chain 'G' and resid 209 through 211
      No H-bonds generated for 'chain 'G' and resid 209 through 211'
    Processing helix  chain 'G' and resid 261 through 285
      removed outlier: 4.101A  pdb=" N   PHE G 264 " --> pdb=" O   GLU G 261 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR G 265 " --> pdb=" O   GLU G 262 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN G 284 " --> pdb=" O   ASP G 281 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 298 through 307
      removed outlier: 3.592A  pdb=" N   ALA G 307 " --> pdb=" O   TYR G 303 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 317 through 327
    Processing helix  chain 'G' and resid 335 through 337
      No H-bonds generated for 'chain 'G' and resid 335 through 337'
    Processing helix  chain 'G' and resid 381 through 403
    Processing helix  chain 'G' and resid 413 through 428
      removed outlier: 4.161A  pdb=" N   ALA G 428 " --> pdb=" O   GLU G 424 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 432 through 455
      removed outlier: 3.617A  pdb=" N   TRP G 435 " --> pdb=" O   VAL G 432 " (cutoff:3.500A)
      Proline residue:  G 436  - end of helix
      removed outlier: 3.885A  pdb=" N   ILE G 447 " --> pdb=" O   LEU G 444 " (cutoff:3.500A)
      Proline residue:  G 448  - end of helix
    Processing helix  chain 'G' and resid 459 through 470
    Processing helix  chain 'G' and resid 490 through 493
      No H-bonds generated for 'chain 'G' and resid 490 through 493'
    Processing helix  chain 'G' and resid 499 through 517
    Processing helix  chain 'H' and resid 19 through 34
    Processing helix  chain 'H' and resid 37 through 39
      No H-bonds generated for 'chain 'H' and resid 37 through 39'
    Processing helix  chain 'H' and resid 62 through 68
    Processing helix  chain 'H' and resid 76 through 89
      removed outlier: 3.597A  pdb=" N   GLU H  89 " --> pdb=" O   GLN H  86 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 113
      removed outlier: 4.169A  pdb=" N   THR H  98 " --> pdb=" O   THR H  94 " (cutoff:3.500A)
      Proline residue:  H 110  - end of helix
    Processing helix  chain 'H' and resid 118 through 139
    Processing helix  chain 'H' and resid 148 through 163
    Processing helix  chain 'H' and resid 169 through 185
      removed outlier: 5.359A  pdb=" N   ALA H 173 " --> pdb=" O   GLN H 170 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL H 183 " --> pdb=" O   VAL H 180 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET H 184 " --> pdb=" O   ASP H 181 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 192 through 194
      No H-bonds generated for 'chain 'H' and resid 192 through 194'
    Processing helix  chain 'H' and resid 205 through 207
      No H-bonds generated for 'chain 'H' and resid 205 through 207'
    Processing helix  chain 'H' and resid 225 through 227
      No H-bonds generated for 'chain 'H' and resid 225 through 227'
    Processing helix  chain 'H' and resid 260 through 284
      removed outlier: 3.509A  pdb=" N   SER H 284 " --> pdb=" O   LYS H 280 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 297 through 305
    Processing helix  chain 'H' and resid 316 through 326
    Processing helix  chain 'H' and resid 339 through 341
      No H-bonds generated for 'chain 'H' and resid 339 through 341'
    Processing helix  chain 'H' and resid 379 through 401
    Processing helix  chain 'H' and resid 411 through 426
      removed outlier: 4.039A  pdb=" N   THR H 426 " --> pdb=" O   ASP H 422 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 430 through 453
      removed outlier: 4.003A  pdb=" N   LEU H 434 " --> pdb=" O   LYS H 430 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU H 443 " --> pdb=" O   ALA H 439 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ILE H 444 " --> pdb=" O   LYS H 440 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ILE H 445 " --> pdb=" O   ALA H 441 " (cutoff:3.500A)
      Proline residue:  H 446  - end of helix
    Processing helix  chain 'H' and resid 457 through 469
    Processing helix  chain 'H' and resid 496 through 515
    Processing helix  chain 'Q' and resid 11 through 14
      No H-bonds generated for 'chain 'Q' and resid 11 through 14'
    Processing helix  chain 'Q' and resid 25 through 46
      removed outlier: 4.317A  pdb=" N   TYR Q  30 " --> pdb=" O   GLU Q  26 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   ARG Q  31 " --> pdb=" O   GLU Q  27 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   THR Q  45 " --> pdb=" O   GLN Q  41 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   ALA Q  46 " --> pdb=" O   THR Q  42 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 69 through 75
    Processing helix  chain 'Q' and resid 81 through 96
    Processing helix  chain 'Q' and resid 101 through 121
    Processing helix  chain 'Q' and resid 125 through 146
      Proline residue:  Q 144  - end of helix
    Processing helix  chain 'Q' and resid 157 through 167
      removed outlier: 4.154A  pdb=" N   THR Q 166 " --> pdb=" O   SER Q 162 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   SER Q 167 " --> pdb=" O   LEU Q 163 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 177 through 189
    Processing helix  chain 'Q' and resid 199 through 201
      No H-bonds generated for 'chain 'Q' and resid 199 through 201'
    Processing helix  chain 'Q' and resid 212 through 214
      No H-bonds generated for 'chain 'Q' and resid 212 through 214'
    Processing helix  chain 'Q' and resid 262 through 286
      removed outlier: 4.709A  pdb=" N   SER Q 269 " --> pdb=" O   LEU Q 265 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   LYS Q 270 " --> pdb=" O   MET Q 266 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR Q 286 " --> pdb=" O   ALA Q 282 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 299 through 307
    Processing helix  chain 'Q' and resid 318 through 328
    Processing helix  chain 'Q' and resid 382 through 404
    Processing helix  chain 'Q' and resid 414 through 428
      removed outlier: 3.519A  pdb=" N   GLU Q 428 " --> pdb=" O   THR Q 424 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 433 through 456
      removed outlier: 3.699A  pdb=" N   TYR Q 436 " --> pdb=" O   LEU Q 433 " (cutoff:3.500A)
      Proline residue:  Q 449  - end of helix
    Processing helix  chain 'Q' and resid 460 through 473
    Processing helix  chain 'Q' and resid 492 through 495
      No H-bonds generated for 'chain 'Q' and resid 492 through 495'
    Processing helix  chain 'Q' and resid 501 through 520
    Processing helix  chain 'Q' and resid 536 through 538
      No H-bonds generated for 'chain 'Q' and resid 536 through 538'
    Processing helix  chain 'Z' and resid 3 through 7
    Processing helix  chain 'Z' and resid 17 through 37
      removed outlier: 4.814A  pdb=" N   THR Z  36 " --> pdb=" O   ASP Z  32 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   ASN Z  37 " --> pdb=" O   VAL Z  33 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 60 through 66
    Processing helix  chain 'Z' and resid 72 through 87
    Processing helix  chain 'Z' and resid 92 through 112
      removed outlier: 3.614A  pdb=" N   TYR Z 109 " --> pdb=" O   GLN Z 105 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLU Z 112 " --> pdb=" O   LEU Z 108 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 116 through 137
    Processing helix  chain 'Z' and resid 145 through 159
      removed outlier: 3.662A  pdb=" N   THR Z 158 " --> pdb=" O   THR Z 154 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 162 through 179
      removed outlier: 3.571A  pdb=" N   GLU Z 170 " --> pdb=" O   ASP Z 166 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 188 through 190
      No H-bonds generated for 'chain 'Z' and resid 188 through 190'
    Processing helix  chain 'Z' and resid 201 through 203
      No H-bonds generated for 'chain 'Z' and resid 201 through 203'
    Processing helix  chain 'Z' and resid 253 through 281
      removed outlier: 4.087A  pdb=" N   ARG Z 264 " --> pdb=" O   VAL Z 260 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LYS Z 265 " --> pdb=" O   LYS Z 261 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   PHE Z 266 " --> pdb=" O   ALA Z 262 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   ILE Z 267 " --> pdb=" O   GLU Z 263 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG Z 270 " --> pdb=" O   PHE Z 266 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 299 through 308
      removed outlier: 3.713A  pdb=" N   GLU Z 308 " --> pdb=" O   ALA Z 304 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 318 through 327
      removed outlier: 4.272A  pdb=" N   GLU Z 322 " --> pdb=" O   ARG Z 318 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 341 through 343
      No H-bonds generated for 'chain 'Z' and resid 341 through 343'
    Processing helix  chain 'Z' and resid 381 through 403
    Processing helix  chain 'Z' and resid 413 through 428
      Proline residue:  Z 427  - end of helix
    Processing helix  chain 'Z' and resid 431 through 455
      removed outlier: 4.146A  pdb=" N   GLN Z 434 " --> pdb=" O   GLY Z 431 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE Z 447 " --> pdb=" O   LEU Z 444 " (cutoff:3.500A)
      Proline residue:  Z 448  - end of helix
    Processing helix  chain 'Z' and resid 459 through 473
    Processing helix  chain 'Z' and resid 489 through 492
      No H-bonds generated for 'chain 'Z' and resid 489 through 492'
    Processing helix  chain 'Z' and resid 498 through 516
    Processing helix  chain 'a' and resid 15 through 35
      removed outlier: 3.719A  pdb=" N   VAL a  32 " --> pdb=" O   ILE a  28 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   SER a  34 " --> pdb=" O   ASN a  30 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   SER a  35 " --> pdb=" O   ILE a  31 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 58 through 64
    Processing helix  chain 'a' and resid 70 through 85
    Processing helix  chain 'a' and resid 90 through 110
      removed outlier: 3.664A  pdb=" N   VAL a  94 " --> pdb=" O   THR a  90 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN a 110 " --> pdb=" O   GLU a 106 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 114 through 135
    Processing helix  chain 'a' and resid 140 through 142
      No H-bonds generated for 'chain 'a' and resid 140 through 142'
    Processing helix  chain 'a' and resid 144 through 156
    Processing helix  chain 'a' and resid 163 through 179
      removed outlier: 4.410A  pdb=" N   ASP a 166 " --> pdb=" O   ILE a 163 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ALA a 169 " --> pdb=" O   ASP a 166 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 184 through 186
      No H-bonds generated for 'chain 'a' and resid 184 through 186'
    Processing helix  chain 'a' and resid 205 through 207
      No H-bonds generated for 'chain 'a' and resid 205 through 207'
    Processing helix  chain 'a' and resid 257 through 280
      removed outlier: 4.443A  pdb=" N   ASP a 261 " --> pdb=" O   GLU a 258 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ILE a 270 " --> pdb=" O   GLU a 267 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 294 through 302
    Processing helix  chain 'a' and resid 313 through 323
    Processing helix  chain 'a' and resid 342 through 344
      No H-bonds generated for 'chain 'a' and resid 342 through 344'
    Processing helix  chain 'a' and resid 382 through 404
    Processing helix  chain 'a' and resid 414 through 429
      removed outlier: 4.386A  pdb=" N   THR a 428 " --> pdb=" O   GLU a 424 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   SER a 429 " --> pdb=" O   ASN a 425 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 434 through 455
      removed outlier: 3.861A  pdb=" N   LEU a 446 " --> pdb=" O   ALA a 442 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   VAL a 447 " --> pdb=" O   ARG a 443 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   ILE a 448 " --> pdb=" O   SER a 444 " (cutoff:3.500A)
      Proline residue:  a 449  - end of helix
    Processing helix  chain 'a' and resid 460 through 476
    Processing helix  chain 'a' and resid 481 through 485
      removed outlier: 3.800A  pdb=" N   TRP a 485 " --> pdb=" O   ASN a 482 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 498 through 501
      No H-bonds generated for 'chain 'a' and resid 498 through 501'
    Processing helix  chain 'a' and resid 507 through 525
    Processing helix  chain 'b' and resid 21 through 39
    Processing helix  chain 'b' and resid 67 through 72
    Processing helix  chain 'b' and resid 79 through 94
    Processing helix  chain 'b' and resid 99 through 119
    Processing helix  chain 'b' and resid 123 through 144
    Processing helix  chain 'b' and resid 152 through 169
      removed outlier: 4.494A  pdb=" N   SER b 169 " --> pdb=" O   THR b 165 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 171 through 190
      removed outlier: 3.558A  pdb=" N   HIS b 174 " --> pdb=" O   LEU b 171 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS b 176 " --> pdb=" O   THR b 173 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   ASP b 177 " --> pdb=" O   HIS b 174 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 209 through 211
      No H-bonds generated for 'chain 'b' and resid 209 through 211'
    Processing helix  chain 'b' and resid 261 through 285
      removed outlier: 3.933A  pdb=" N   HIS b 285 " --> pdb=" O   ARG b 281 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 298 through 306
    Processing helix  chain 'b' and resid 317 through 327
    Processing helix  chain 'b' and resid 338 through 340
      No H-bonds generated for 'chain 'b' and resid 338 through 340'
    Processing helix  chain 'b' and resid 380 through 402
    Processing helix  chain 'b' and resid 412 through 426
    Processing helix  chain 'b' and resid 431 through 454
      Proline residue:  b 447  - end of helix
      removed outlier: 3.660A  pdb=" N   ALA b 454 " --> pdb=" O   ILE b 450 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 458 through 470
    Processing helix  chain 'b' and resid 488 through 491
      No H-bonds generated for 'chain 'b' and resid 488 through 491'
    Processing helix  chain 'b' and resid 497 through 515
    Processing helix  chain 'd' and resid 29 through 49
    Processing helix  chain 'd' and resid 74 through 80
    Processing helix  chain 'd' and resid 86 through 101
    Processing helix  chain 'd' and resid 106 through 125
      removed outlier: 3.644A  pdb=" N   VAL d 110 " --> pdb=" O   THR d 106 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LYS d 122 " --> pdb=" O   ASP d 118 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 132 through 150
    Processing helix  chain 'd' and resid 160 through 173
      removed outlier: 4.523A  pdb=" N   SER d 173 " --> pdb=" O   THR d 169 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 175 through 177
      No H-bonds generated for 'chain 'd' and resid 175 through 177'
    Processing helix  chain 'd' and resid 180 through 192
      Proline residue:  d 185  - end of helix
    Processing helix  chain 'd' and resid 205 through 207
      No H-bonds generated for 'chain 'd' and resid 205 through 207'
    Processing helix  chain 'd' and resid 218 through 220
      No H-bonds generated for 'chain 'd' and resid 218 through 220'
    Processing helix  chain 'd' and resid 269 through 293
      removed outlier: 4.080A  pdb=" N   LEU d 276 " --> pdb=" O   MET d 272 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR d 293 " --> pdb=" O   GLN d 289 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 311 through 319
    Processing helix  chain 'd' and resid 330 through 340
      removed outlier: 4.520A  pdb=" N   GLU d 334 " --> pdb=" O   GLU d 331 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE d 340 " --> pdb=" O   CYS d 337 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 348 through 350
      No H-bonds generated for 'chain 'd' and resid 348 through 350'
    Processing helix  chain 'd' and resid 353 through 355
      No H-bonds generated for 'chain 'd' and resid 353 through 355'
    Processing helix  chain 'd' and resid 395 through 416
    Processing helix  chain 'd' and resid 427 through 442
      removed outlier: 3.565A  pdb=" N   THR d 442 " --> pdb=" O   GLU d 438 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 446 through 466
      removed outlier: 3.804A  pdb=" N   VAL d 460 " --> pdb=" O   ASP d 456 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ILE d 461 " --> pdb=" O   ALA d 457 " (cutoff:3.500A)
      Proline residue:  d 462  - end of helix
    Processing helix  chain 'd' and resid 473 through 485
    Processing helix  chain 'd' and resid 512 through 530
      removed outlier: 4.923A  pdb=" N   SER d 517 " --> pdb=" O   LEU d 513 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 30 through 51
      removed outlier: 3.659A  pdb=" N   ARG e  49 " --> pdb=" O   ASN e  46 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   THR e  50 " --> pdb=" O   THR e  47 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 74 through 80
    Processing helix  chain 'e' and resid 86 through 101
    Processing helix  chain 'e' and resid 108 through 126
      removed outlier: 3.598A  pdb=" N   GLN e 122 " --> pdb=" O   GLU e 118 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG e 126 " --> pdb=" O   GLN e 122 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 130 through 150
    Processing helix  chain 'e' and resid 163 through 175
      removed outlier: 4.693A  pdb=" N   SER e 175 " --> pdb=" O   THR e 171 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 177 through 195
      removed outlier: 3.978A  pdb=" N   SER e 180 " --> pdb=" O   VAL e 177 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ARG e 183 " --> pdb=" O   SER e 180 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 206 through 208
      No H-bonds generated for 'chain 'e' and resid 206 through 208'
    Processing helix  chain 'e' and resid 219 through 221
      No H-bonds generated for 'chain 'e' and resid 219 through 221'
    Processing helix  chain 'e' and resid 271 through 295
      removed outlier: 3.829A  pdb=" N   THR e 295 " --> pdb=" O   GLN e 291 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 308 through 316
    Processing helix  chain 'e' and resid 327 through 337
    Processing helix  chain 'e' and resid 345 through 347
      No H-bonds generated for 'chain 'e' and resid 345 through 347'
    Processing helix  chain 'e' and resid 350 through 352
      No H-bonds generated for 'chain 'e' and resid 350 through 352'
    Processing helix  chain 'e' and resid 392 through 414
    Processing helix  chain 'e' and resid 424 through 438
    Processing helix  chain 'e' and resid 442 through 465
      removed outlier: 3.954A  pdb=" N   TYR e 446 " --> pdb=" O   THR e 442 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA e 447 " --> pdb=" O   LEU e 443 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL e 457 " --> pdb=" O   ASP e 453 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ILE e 458 " --> pdb=" O   ALA e 454 " (cutoff:3.500A)
      Proline residue:  e 459  - end of helix
    Processing helix  chain 'e' and resid 470 through 483
    Processing helix  chain 'e' and resid 510 through 528
    Processing helix  chain 'g' and resid 20 through 40
      removed outlier: 3.834A  pdb=" N   ILE g  37 " --> pdb=" O   ILE g  33 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   THR g  39 " --> pdb=" O   ASP g  35 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   CYS g  40 " --> pdb=" O   ILE g  36 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 63 through 68
    Processing helix  chain 'g' and resid 75 through 90
    Processing helix  chain 'g' and resid 95 through 114
      removed outlier: 3.795A  pdb=" N   ILE g  99 " --> pdb=" O   THR g  95 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE g 112 " --> pdb=" O   VAL g 108 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 119 through 140
    Processing helix  chain 'g' and resid 149 through 160
    Processing helix  chain 'g' and resid 164 through 183
      removed outlier: 3.943A  pdb=" N   ARG g 167 " --> pdb=" O   ALA g 164 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   SER g 170 " --> pdb=" O   ARG g 167 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU g 171 " --> pdb=" O   TRP g 168 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL g 183 " --> pdb=" O   VAL g 180 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 209 through 211
      No H-bonds generated for 'chain 'g' and resid 209 through 211'
    Processing helix  chain 'g' and resid 263 through 285
      removed outlier: 4.315A  pdb=" N   LEU g 285 " --> pdb=" O   ASP g 281 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 298 through 307
      removed outlier: 3.718A  pdb=" N   ALA g 307 " --> pdb=" O   TYR g 303 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 317 through 327
    Processing helix  chain 'g' and resid 335 through 337
      No H-bonds generated for 'chain 'g' and resid 335 through 337'
    Processing helix  chain 'g' and resid 340 through 342
      No H-bonds generated for 'chain 'g' and resid 340 through 342'
    Processing helix  chain 'g' and resid 381 through 403
    Processing helix  chain 'g' and resid 413 through 428
      removed outlier: 3.674A  pdb=" N   LYS g 427 " --> pdb=" O   THR g 423 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ALA g 428 " --> pdb=" O   GLU g 424 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 434 through 455
      removed outlier: 3.963A  pdb=" N   LEU g 444 " --> pdb=" O   VAL g 440 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLU g 445 " --> pdb=" O   ALA g 441 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   VAL g 446 " --> pdb=" O   GLN g 442 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   ILE g 447 " --> pdb=" O   ALA g 443 " (cutoff:3.500A)
      Proline residue:  g 448  - end of helix
    Processing helix  chain 'g' and resid 459 through 470
    Processing helix  chain 'g' and resid 490 through 493
      No H-bonds generated for 'chain 'g' and resid 490 through 493'
    Processing helix  chain 'g' and resid 499 through 518
    Processing helix  chain 'h' and resid 19 through 36
      removed outlier: 3.794A  pdb=" N   VAL h  36 " --> pdb=" O   ILE h  32 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 62 through 68
    Processing helix  chain 'h' and resid 76 through 89
      removed outlier: 3.587A  pdb=" N   GLU h  89 " --> pdb=" O   GLN h  86 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 94 through 113
      removed outlier: 4.155A  pdb=" N   THR h  98 " --> pdb=" O   THR h  94 " (cutoff:3.500A)
      Proline residue:  h 110  - end of helix
    Processing helix  chain 'h' and resid 118 through 139
    Processing helix  chain 'h' and resid 148 through 163
    Processing helix  chain 'h' and resid 172 through 185
      removed outlier: 3.593A  pdb=" N   MET h 185 " --> pdb=" O   ASP h 181 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 192 through 194
      No H-bonds generated for 'chain 'h' and resid 192 through 194'
    Processing helix  chain 'h' and resid 205 through 207
      No H-bonds generated for 'chain 'h' and resid 205 through 207'
    Processing helix  chain 'h' and resid 225 through 227
      No H-bonds generated for 'chain 'h' and resid 225 through 227'
    Processing helix  chain 'h' and resid 260 through 284
      removed outlier: 3.605A  pdb=" N   SER h 284 " --> pdb=" O   LYS h 280 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 297 through 305
    Processing helix  chain 'h' and resid 316 through 326
    Processing helix  chain 'h' and resid 339 through 341
      No H-bonds generated for 'chain 'h' and resid 339 through 341'
    Processing helix  chain 'h' and resid 379 through 401
    Processing helix  chain 'h' and resid 411 through 426
      removed outlier: 4.155A  pdb=" N   THR h 426 " --> pdb=" O   ASP h 422 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 430 through 453
      removed outlier: 4.082A  pdb=" N   LEU h 434 " --> pdb=" O   LYS h 430 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU h 443 " --> pdb=" O   ALA h 439 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE h 444 " --> pdb=" O   LYS h 440 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   ILE h 445 " --> pdb=" O   ALA h 441 " (cutoff:3.500A)
      Proline residue:  h 446  - end of helix
    Processing helix  chain 'h' and resid 457 through 470
    Processing helix  chain 'h' and resid 496 through 514
    Processing helix  chain 'q' and resid 11 through 14
      No H-bonds generated for 'chain 'q' and resid 11 through 14'
    Processing helix  chain 'q' and resid 25 through 46
      removed outlier: 4.294A  pdb=" N   TYR q  30 " --> pdb=" O   GLU q  26 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   ARG q  31 " --> pdb=" O   GLU q  27 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   THR q  45 " --> pdb=" O   GLN q  41 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   ALA q  46 " --> pdb=" O   THR q  42 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 69 through 75
    Processing helix  chain 'q' and resid 81 through 96
    Processing helix  chain 'q' and resid 101 through 121
    Processing helix  chain 'q' and resid 125 through 146
      Proline residue:  q 144  - end of helix
    Processing helix  chain 'q' and resid 157 through 167
      removed outlier: 4.230A  pdb=" N   THR q 166 " --> pdb=" O   SER q 162 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   SER q 167 " --> pdb=" O   LEU q 163 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 177 through 189
    Processing helix  chain 'q' and resid 212 through 214
      No H-bonds generated for 'chain 'q' and resid 212 through 214'
    Processing helix  chain 'q' and resid 262 through 286
      removed outlier: 4.851A  pdb=" N   SER q 269 " --> pdb=" O   LEU q 265 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   LYS q 270 " --> pdb=" O   MET q 266 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   THR q 286 " --> pdb=" O   ALA q 282 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 299 through 307
    Processing helix  chain 'q' and resid 318 through 328
    Processing helix  chain 'q' and resid 382 through 404
    Processing helix  chain 'q' and resid 414 through 429
      removed outlier: 3.725A  pdb=" N   THR q 429 " --> pdb=" O   SER q 425 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 434 through 456
      removed outlier: 3.753A  pdb=" N   PHE q 445 " --> pdb=" O   PHE q 441 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU q 446 " --> pdb=" O   ALA q 442 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ALA q 447 " --> pdb=" O   GLU q 443 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   ILE q 448 " --> pdb=" O   ALA q 444 " (cutoff:3.500A)
      Proline residue:  q 449  - end of helix
    Processing helix  chain 'q' and resid 460 through 473
    Processing helix  chain 'q' and resid 492 through 495
      No H-bonds generated for 'chain 'q' and resid 492 through 495'
    Processing helix  chain 'q' and resid 501 through 520
    Processing helix  chain 'z' and resid 3 through 7
      removed outlier: 3.561A  pdb=" N   LEU z   7 " --> pdb=" O   ALA z   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'z' and resid 3 through 7'
    Processing helix  chain 'z' and resid 17 through 37
      removed outlier: 4.865A  pdb=" N   THR z  36 " --> pdb=" O   ASP z  32 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   ASN z  37 " --> pdb=" O   VAL z  33 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 60 through 66
    Processing helix  chain 'z' and resid 72 through 87
    Processing helix  chain 'z' and resid 92 through 112
      removed outlier: 3.681A  pdb=" N   TYR z 109 " --> pdb=" O   GLN z 105 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLU z 112 " --> pdb=" O   LEU z 108 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 116 through 137
    Processing helix  chain 'z' and resid 145 through 159
      removed outlier: 4.139A  pdb=" N   THR z 158 " --> pdb=" O   THR z 154 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 162 through 179
      removed outlier: 3.617A  pdb=" N   GLU z 170 " --> pdb=" O   ASP z 166 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 188 through 190
      No H-bonds generated for 'chain 'z' and resid 188 through 190'
    Processing helix  chain 'z' and resid 201 through 203
      No H-bonds generated for 'chain 'z' and resid 201 through 203'
    Processing helix  chain 'z' and resid 253 through 281
      removed outlier: 4.238A  pdb=" N   ARG z 264 " --> pdb=" O   VAL z 260 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LYS z 265 " --> pdb=" O   LYS z 261 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   PHE z 266 " --> pdb=" O   ALA z 262 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   ILE z 267 " --> pdb=" O   GLU z 263 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG z 270 " --> pdb=" O   PHE z 266 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 299 through 308
      removed outlier: 3.764A  pdb=" N   GLU z 308 " --> pdb=" O   ALA z 304 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 318 through 327
      removed outlier: 4.297A  pdb=" N   GLU z 322 " --> pdb=" O   ARG z 318 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 341 through 343
      No H-bonds generated for 'chain 'z' and resid 341 through 343'
    Processing helix  chain 'z' and resid 381 through 403
    Processing helix  chain 'z' and resid 413 through 428
      Proline residue:  z 427  - end of helix
    Processing helix  chain 'z' and resid 432 through 455
      removed outlier: 3.711A  pdb=" N   ILE z 447 " --> pdb=" O   LEU z 444 " (cutoff:3.500A)
      Proline residue:  z 448  - end of helix
    Processing helix  chain 'z' and resid 459 through 473
    Processing helix  chain 'z' and resid 489 through 492
      No H-bonds generated for 'chain 'z' and resid 489 through 492'
    Processing helix  chain 'z' and resid 498 through 516
    Processing helix  chain 'P' and resid 58 through 84
      removed outlier: 4.892A  pdb=" N   ASN P  64 " --> pdb=" O   LYS P  60 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   ASP P  65 " --> pdb=" O   GLY P  61 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   LEU P  72 " --> pdb=" O   ARG P  68 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 137 through 139
      No H-bonds generated for 'chain 'P' and resid 137 through 139'
    Processing helix  chain 'P' and resid 141 through 151
    Processing helix  chain 'P' and resid 167 through 175
    Processing helix  chain 'P' and resid 195 through 208
    Processing helix  chain 'P' and resid 219 through 222
      No H-bonds generated for 'chain 'P' and resid 219 through 222'
    Processing helix  chain 'P' and resid 226 through 231
    Processing helix  chain 'P' and resid 251 through 255
    Processing helix  chain 'P' and resid 261 through 271
      removed outlier: 3.925A  pdb=" N   PHE P 271 " --> pdb=" O   PHE P 267 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'N' and resid 242 through 244
      removed outlier: 3.693A  pdb=" N   CYS N 242 " --> pdb=" O   GLY N 257 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN N 275 " --> pdb=" O   VAL N 265 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ASP N 267 " --> pdb=" O   CYS N 273 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   CYS N 273 " --> pdb=" O   ASP N 267 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'N' and resid 221 through 223
      removed outlier: 3.689A  pdb=" N   GLN N 231 " --> pdb=" O   LEU N 221 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP N 223 " --> pdb=" O   LEU N 229 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LEU N 229 " --> pdb=" O   ASP N 223 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 9 through 13
    Processing sheet with id=  D, first strand: chain 'A' and resid 43 through 46
    Processing sheet with id=  E, first strand: chain 'A' and resid 137 through 139
    Processing sheet with id=  F, first strand: chain 'A' and resid 196 through 199
    Processing sheet with id=  G, first strand: chain 'A' and resid 213 through 216
    Processing sheet with id=  H, first strand: chain 'A' and resid 346 through 348
      removed outlier: 6.535A  pdb=" N   VAL A 285 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   LEU A 237 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU A 287 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   MET A 306 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   THR A 288 " --> pdb=" O   MET A 306 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL A 308 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'A' and resid 486 through 489
    Processing sheet with id=  J, first strand: chain 'B' and resid 17 through 19
    Processing sheet with id=  K, first strand: chain 'B' and resid 50 through 53
    Processing sheet with id=  L, first strand: chain 'B' and resid 199 through 205
      removed outlier: 6.373A  pdb=" N   CYS B 371 " --> pdb=" O   HIS B 200 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   ILE B 202 " --> pdb=" O   CYS B 371 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ILE B 373 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   LYS B 204 " --> pdb=" O   ILE B 373 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   LEU B 375 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  L
    Processing sheet with id=  M, first strand: chain 'B' and resid 218 through 220
    Processing sheet with id=  N, first strand: chain 'B' and resid 344 through 346
      removed outlier: 3.504A  pdb=" N   CYS B 346 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   CYS B 289 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ALA B 240 " --> pdb=" O   CYS B 289 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE B 291 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   MET B 310 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ASN B 292 " --> pdb=" O   MET B 310 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE B 312 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'B' and resid 406 through 408
    Processing sheet with id=  P, first strand: chain 'B' and resid 476 through 479
    Processing sheet with id=  Q, first strand: chain 'D' and resid 59 through 62
    Processing sheet with id=  R, first strand: chain 'D' and resid 208 through 214
      removed outlier: 6.778A  pdb=" N   VAL D 386 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   VAL D 211 " --> pdb=" O   VAL D 386 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ILE D 388 " --> pdb=" O   VAL D 211 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   LYS D 213 " --> pdb=" O   ILE D 388 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL D 390 " --> pdb=" O   LYS D 213 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'D' and resid 227 through 229
    Processing sheet with id=  T, first strand: chain 'D' and resid 357 through 359
      removed outlier: 6.883A  pdb=" N   VAL D 297 " --> pdb=" O   GLY D 247 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE D 249 " --> pdb=" O   VAL D 297 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU D 299 " --> pdb=" O   ILE D 249 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   MET D 323 " --> pdb=" O   LEU D 298 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   ILE D 300 " --> pdb=" O   MET D 323 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE D 325 " --> pdb=" O   ILE D 300 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'D' and resid 421 through 423
    Processing sheet with id=  V, first strand: chain 'D' and resid 491 through 494
      removed outlier: 3.616A  pdb=" N   SER D 501 " --> pdb=" O   GLY D 492 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'E' and resid 59 through 62
    Processing sheet with id=  X, first strand: chain 'E' and resid 209 through 215
      removed outlier: 7.193A  pdb=" N   VAL E 383 " --> pdb=" O   LYS E 210 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLU E 212 " --> pdb=" O   VAL E 383 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   ILE E 385 " --> pdb=" O   GLU E 212 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   LYS E 214 " --> pdb=" O   ILE E 385 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ILE E 387 " --> pdb=" O   LYS E 214 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'E' and resid 228 through 230
    Processing sheet with id=  Z, first strand: chain 'E' and resid 354 through 356
      removed outlier: 6.987A  pdb=" N   LEU E 299 " --> pdb=" O   ALA E 249 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'E' and resid 418 through 420
    Processing sheet with id= AB, first strand: chain 'G' and resid 15 through 17
    Processing sheet with id= AC, first strand: chain 'G' and resid 48 through 51
    Processing sheet with id= AD, first strand: chain 'G' and resid 185 through 187
    Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205
      removed outlier: 6.640A  pdb=" N   CYS G 372 " --> pdb=" O   ARG G 200 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLU G 202 " --> pdb=" O   CYS G 372 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   ILE G 374 " --> pdb=" O   GLU G 202 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ILE G 204 " --> pdb=" O   ILE G 374 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   LEU G 376 " --> pdb=" O   ILE G 204 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR G 373 " --> pdb=" O   LEU G 215 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241
      removed outlier: 6.487A  pdb=" N   VAL G 289 " --> pdb=" O   VAL G 239 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   LEU G 241 " --> pdb=" O   VAL G 289 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE G 291 " --> pdb=" O   LEU G 241 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   THR G 310 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   THR G 292 " --> pdb=" O   THR G 310 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ILE G 312 " --> pdb=" O   THR G 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AF
    Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355
    Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409
    Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 481
      removed outlier: 3.718A  pdb=" N   THR G 486 " --> pdb=" O   ASN G 481 " (cutoff:3.500A)
    Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17
    Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50
    Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201
      removed outlier: 6.403A  pdb=" N   CYS H 370 " --> pdb=" O   GLY H 196 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LYS H 198 " --> pdb=" O   CYS H 370 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   PHE H 372 " --> pdb=" O   LYS H 198 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   VAL H 200 " --> pdb=" O   PHE H 372 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   LEU H 374 " --> pdb=" O   VAL H 200 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR H 371 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217
    Processing sheet with id= AN, first strand: chain 'H' and resid 342 through 344
      removed outlier: 6.839A  pdb=" N   VAL H 288 " --> pdb=" O   ALA H 238 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   LEU H 240 " --> pdb=" O   VAL H 288 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU H 290 " --> pdb=" O   LEU H 240 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   PHE H 309 " --> pdb=" O   VAL H 289 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   SER H 291 " --> pdb=" O   PHE H 309 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ALA H 311 " --> pdb=" O   SER H 291 " (cutoff:3.500A)
    Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407
    Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478
    Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23
    Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57
    Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 208
      removed outlier: 6.660A  pdb=" N   SER Q 373 " --> pdb=" O   ARG Q 203 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   CYS Q 205 " --> pdb=" O   SER Q 373 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE Q 375 " --> pdb=" O   CYS Q 205 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   ILE Q 207 " --> pdb=" O   ILE Q 375 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LEU Q 377 " --> pdb=" O   ILE Q 207 " (cutoff:3.500A)
    Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223
    Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242
      removed outlier: 6.085A  pdb=" N   MET Q 311 " --> pdb=" O   VAL Q 291 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   THR Q 293 " --> pdb=" O   MET Q 311 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL Q 313 " --> pdb=" O   THR Q 293 " (cutoff:3.500A)
    Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500
      removed outlier: 3.935A  pdb=" N   CYS Q 149 " --> pdb=" O   LEU Q 408 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   VAL Q 147 " --> pdb=" O   PRO Q 410 " (cutoff:3.500A)
    Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480
    Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15
    Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48
    Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196
      removed outlier: 6.724A  pdb=" N   VAL Z 372 " --> pdb=" O   GLU Z 192 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   MET Z 194 " --> pdb=" O   VAL Z 372 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LEU Z 374 " --> pdb=" O   MET Z 194 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   MET Z 196 " --> pdb=" O   LEU Z 374 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   ILE Z 376 " --> pdb=" O   MET Z 196 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER Z 205 " --> pdb=" O   LEU Z 375 " (cutoff:3.500A)
    Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212
    Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347
    Processing sheet with id= BC, first strand: chain 'Z' and resid 477 through 479
    Processing sheet with id= BD, first strand: chain 'a' and resid 9 through 13
    Processing sheet with id= BE, first strand: chain 'a' and resid 43 through 46
    Processing sheet with id= BF, first strand: chain 'a' and resid 137 through 139
    Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182
    Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201
      removed outlier: 3.547A  pdb=" N   GLY a 379 " --> pdb=" O   ALA a 200 " (cutoff:3.500A)
    Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216
    Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348
      removed outlier: 6.544A  pdb=" N   VAL a 285 " --> pdb=" O   ALA a 235 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   LEU a 237 " --> pdb=" O   VAL a 285 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU a 287 " --> pdb=" O   LEU a 237 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   MET a 306 " --> pdb=" O   ILE a 286 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   THR a 288 " --> pdb=" O   MET a 306 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL a 308 " --> pdb=" O   THR a 288 " (cutoff:3.500A)
    Processing sheet with id= BK, first strand: chain 'a' and resid 486 through 489
    Processing sheet with id= BL, first strand: chain 'b' and resid 17 through 19
    Processing sheet with id= BM, first strand: chain 'b' and resid 50 through 53
    Processing sheet with id= BN, first strand: chain 'b' and resid 199 through 205
      removed outlier: 6.260A  pdb=" N   CYS b 371 " --> pdb=" O   HIS b 200 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   ILE b 202 " --> pdb=" O   CYS b 371 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ILE b 373 " --> pdb=" O   ILE b 202 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   LYS b 204 " --> pdb=" O   ILE b 373 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   LEU b 375 " --> pdb=" O   LYS b 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= BN
    Processing sheet with id= BO, first strand: chain 'b' and resid 218 through 220
    Processing sheet with id= BP, first strand: chain 'b' and resid 344 through 346
      removed outlier: 3.542A  pdb=" N   CYS b 346 " --> pdb=" O   ALA b 235 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   CYS b 289 " --> pdb=" O   LEU b 238 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ALA b 240 " --> pdb=" O   CYS b 289 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE b 291 " --> pdb=" O   ALA b 240 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   MET b 310 " --> pdb=" O   PHE b 290 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ASN b 292 " --> pdb=" O   MET b 310 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ILE b 312 " --> pdb=" O   ASN b 292 " (cutoff:3.500A)
    Processing sheet with id= BQ, first strand: chain 'b' and resid 406 through 408
    Processing sheet with id= BR, first strand: chain 'b' and resid 476 through 479
    Processing sheet with id= BS, first strand: chain 'd' and resid 59 through 62
    Processing sheet with id= BT, first strand: chain 'd' and resid 208 through 214
      removed outlier: 6.707A  pdb=" N   VAL d 386 " --> pdb=" O   LYS d 209 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   VAL d 211 " --> pdb=" O   VAL d 386 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ILE d 388 " --> pdb=" O   VAL d 211 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   LYS d 213 " --> pdb=" O   ILE d 388 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL d 390 " --> pdb=" O   LYS d 213 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= BT
    Processing sheet with id= BU, first strand: chain 'd' and resid 227 through 229
    Processing sheet with id= BV, first strand: chain 'd' and resid 357 through 359
      removed outlier: 6.585A  pdb=" N   VAL d 297 " --> pdb=" O   GLY d 247 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   ILE d 249 " --> pdb=" O   VAL d 297 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU d 299 " --> pdb=" O   ILE d 249 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   MET d 323 " --> pdb=" O   LEU d 298 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   ILE d 300 " --> pdb=" O   MET d 323 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE d 325 " --> pdb=" O   ILE d 300 " (cutoff:3.500A)
    Processing sheet with id= BW, first strand: chain 'd' and resid 421 through 423
    Processing sheet with id= BX, first strand: chain 'd' and resid 491 through 494
    Processing sheet with id= BY, first strand: chain 'e' and resid 26 through 29
    Processing sheet with id= BZ, first strand: chain 'e' and resid 59 through 62
    Processing sheet with id= CA, first strand: chain 'e' and resid 209 through 215
      removed outlier: 6.987A  pdb=" N   VAL e 383 " --> pdb=" O   LYS e 210 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   GLU e 212 " --> pdb=" O   VAL e 383 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ILE e 385 " --> pdb=" O   GLU e 212 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   LYS e 214 " --> pdb=" O   ILE e 385 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ILE e 387 " --> pdb=" O   LYS e 214 " (cutoff:3.500A)
    Processing sheet with id= CB, first strand: chain 'e' and resid 228 through 230
    Processing sheet with id= CC, first strand: chain 'e' and resid 354 through 356
      removed outlier: 7.077A  pdb=" N   LEU e 299 " --> pdb=" O   ALA e 249 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   LEU e 251 " --> pdb=" O   LEU e 299 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ILE e 301 " --> pdb=" O   LEU e 251 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   CYS e 302 " --> pdb=" O   PRO e 320 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL e 322 " --> pdb=" O   CYS e 302 " (cutoff:3.500A)
    Processing sheet with id= CD, first strand: chain 'e' and resid 418 through 420
    Processing sheet with id= CE, first strand: chain 'g' and resid 15 through 18
    Processing sheet with id= CF, first strand: chain 'g' and resid 48 through 51
    Processing sheet with id= CG, first strand: chain 'g' and resid 185 through 187
    Processing sheet with id= CH, first strand: chain 'g' and resid 200 through 205
      removed outlier: 3.968A  pdb=" N   GLY g 378 " --> pdb=" O   ILE g 204 " (cutoff:3.500A)
    Processing sheet with id= CI, first strand: chain 'g' and resid 218 through 220
    Processing sheet with id= CJ, first strand: chain 'g' and resid 238 through 241
      removed outlier: 6.506A  pdb=" N   VAL g 289 " --> pdb=" O   VAL g 239 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   LEU g 241 " --> pdb=" O   VAL g 289 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE g 291 " --> pdb=" O   LEU g 241 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR g 310 " --> pdb=" O   VAL g 290 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   THR g 292 " --> pdb=" O   THR g 310 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ILE g 312 " --> pdb=" O   THR g 292 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= CJ
    Processing sheet with id= CK, first strand: chain 'g' and resid 407 through 409
    Processing sheet with id= CL, first strand: chain 'g' and resid 478 through 481
      removed outlier: 3.713A  pdb=" N   THR g 486 " --> pdb=" O   ASN g 481 " (cutoff:3.500A)
    Processing sheet with id= CM, first strand: chain 'h' and resid 14 through 17
    Processing sheet with id= CN, first strand: chain 'h' and resid 47 through 50
    Processing sheet with id= CO, first strand: chain 'h' and resid 195 through 201
      removed outlier: 6.615A  pdb=" N   CYS h 370 " --> pdb=" O   GLY h 196 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   LYS h 198 " --> pdb=" O   CYS h 370 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   PHE h 372 " --> pdb=" O   LYS h 198 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   VAL h 200 " --> pdb=" O   PHE h 372 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   LEU h 374 " --> pdb=" O   VAL h 200 " (cutoff:3.500A)
    Processing sheet with id= CP, first strand: chain 'h' and resid 214 through 217
    Processing sheet with id= CQ, first strand: chain 'h' and resid 237 through 240
      removed outlier: 6.992A  pdb=" N   VAL h 288 " --> pdb=" O   ALA h 238 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU h 240 " --> pdb=" O   VAL h 288 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   LEU h 290 " --> pdb=" O   LEU h 240 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   PHE h 309 " --> pdb=" O   VAL h 289 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   SER h 291 " --> pdb=" O   PHE h 309 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ALA h 311 " --> pdb=" O   SER h 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= CQ
    Processing sheet with id= CR, first strand: chain 'h' and resid 405 through 407
    Processing sheet with id= CS, first strand: chain 'h' and resid 475 through 478
    Processing sheet with id= CT, first strand: chain 'q' and resid 20 through 23
    Processing sheet with id= CU, first strand: chain 'q' and resid 54 through 57
    Processing sheet with id= CV, first strand: chain 'q' and resid 202 through 208
      removed outlier: 6.557A  pdb=" N   SER q 373 " --> pdb=" O   ARG q 203 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   CYS q 205 " --> pdb=" O   SER q 373 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE q 375 " --> pdb=" O   CYS q 205 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   ILE q 207 " --> pdb=" O   ILE q 375 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   LEU q 377 " --> pdb=" O   ILE q 207 " (cutoff:3.500A)
    Processing sheet with id= CW, first strand: chain 'q' and resid 220 through 223
    Processing sheet with id= CX, first strand: chain 'q' and resid 240 through 242
      removed outlier: 6.070A  pdb=" N   MET q 311 " --> pdb=" O   VAL q 291 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   THR q 293 " --> pdb=" O   MET q 311 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL q 313 " --> pdb=" O   THR q 293 " (cutoff:3.500A)
    Processing sheet with id= CY, first strand: chain 'q' and resid 498 through 500
      removed outlier: 3.812A  pdb=" N   CYS q 149 " --> pdb=" O   LEU q 408 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   VAL q 147 " --> pdb=" O   PRO q 410 " (cutoff:3.500A)
    Processing sheet with id= CZ, first strand: chain 'q' and resid 478 through 480
    Processing sheet with id= DA, first strand: chain 'z' and resid 12 through 15
    Processing sheet with id= DB, first strand: chain 'z' and resid 45 through 48
    Processing sheet with id= DC, first strand: chain 'z' and resid 191 through 196
      removed outlier: 6.872A  pdb=" N   VAL z 372 " --> pdb=" O   GLU z 192 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   MET z 194 " --> pdb=" O   VAL z 372 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU z 374 " --> pdb=" O   MET z 194 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   MET z 196 " --> pdb=" O   LEU z 374 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   ILE z 376 " --> pdb=" O   MET z 196 " (cutoff:3.500A)
    Processing sheet with id= DD, first strand: chain 'z' and resid 210 through 212
    Processing sheet with id= DE, first strand: chain 'z' and resid 345 through 347
    Processing sheet with id= DF, first strand: chain 'z' and resid 477 through 479
    Processing sheet with id= DG, first strand: chain 'P' and resid 162 through 164
      removed outlier: 4.611A  pdb=" N   LYS P 218 " --> pdb=" O   ILE P 164 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA P 235 " --> pdb=" O   ILE P 187 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LYS P 240 " --> pdb=" O   LEU P 244 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU P 244 " --> pdb=" O   LYS P 240 " (cutoff:3.500A)

    3480 hydrogen bonds defined for protein.
    9180 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: 30.26

  Time building geometry restraints manager: 23.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 22621
        1.34 -     1.46: 11837
        1.46 -     1.58: 32719
        1.58 -     1.70: 48
        1.70 -     1.81: 735
  Bond restraints: 67960
  Sorted by residual:
  bond pdb=" F2  AF3 z 603 "
       pdb="AL   AF3 z 603 "
    ideal  model  delta    sigma   weight residual
    1.637  1.799 -0.162 2.00e-02 2.50e+03 6.54e+01
  bond pdb=" F2  AF3 Z 603 "
       pdb="AL   AF3 Z 603 "
    ideal  model  delta    sigma   weight residual
    1.637  1.797 -0.160 2.00e-02 2.50e+03 6.42e+01
  bond pdb=" F2  AF3 D 603 "
       pdb="AL   AF3 D 603 "
    ideal  model  delta    sigma   weight residual
    1.637  1.797 -0.160 2.00e-02 2.50e+03 6.39e+01
  bond pdb=" F2  AF3 d 603 "
       pdb="AL   AF3 d 603 "
    ideal  model  delta    sigma   weight residual
    1.637  1.797 -0.160 2.00e-02 2.50e+03 6.39e+01
  bond pdb=" F2  AF3 g 603 "
       pdb="AL   AF3 g 603 "
    ideal  model  delta    sigma   weight residual
    1.637  1.797 -0.160 2.00e-02 2.50e+03 6.38e+01
  ... (remaining 67955 not shown)

  Histogram of bond angle deviations from ideal:
       98.26 -   105.89: 1222
      105.89 -   113.51: 39718
      113.51 -   121.14: 33495
      121.14 -   128.76: 17025
      128.76 -   136.39: 295
  Bond angle restraints: 91755
  Sorted by residual:
  angle pdb=" CA  ARG P 149 "
        pdb=" CB  ARG P 149 "
        pdb=" CG  ARG P 149 "
      ideal   model   delta    sigma   weight residual
     114.10  123.76   -9.66 2.00e+00 2.50e-01 2.33e+01
  angle pdb=" C   MET P 148 "
        pdb=" N   ARG P 149 "
        pdb=" CA  ARG P 149 "
      ideal   model   delta    sigma   weight residual
     121.14  115.09    6.05 1.75e+00 3.27e-01 1.20e+01
  angle pdb=" N   GLY Q 209 "
        pdb=" CA  GLY Q 209 "
        pdb=" C   GLY Q 209 "
      ideal   model   delta    sigma   weight residual
     113.18  120.95   -7.77 2.37e+00 1.78e-01 1.07e+01
  angle pdb=" N   GLY q 209 "
        pdb=" CA  GLY q 209 "
        pdb=" C   GLY q 209 "
      ideal   model   delta    sigma   weight residual
     113.18  120.80   -7.62 2.37e+00 1.78e-01 1.03e+01
  angle pdb=" C   CYS E 181 "
        pdb=" N   HIS E 182 "
        pdb=" CA  HIS E 182 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.02e+00
  ... (remaining 91750 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.66: 41312
       35.66 -    71.32: 624
       71.32 -   106.98: 63
      106.98 -   142.63: 11
      142.63 -   178.29: 8
  Dihedral angle restraints: 42018
    sinusoidal: 16924
      harmonic: 25094
  Sorted by residual:
  dihedral pdb=" O2A ADP G 601 "
           pdb=" O3A ADP G 601 "
           pdb=" PA  ADP G 601 "
           pdb=" PB  ADP G 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  118.29 -178.29     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" O2A ADP Q 601 "
           pdb=" O3A ADP Q 601 "
           pdb=" PA  ADP Q 601 "
           pdb=" PB  ADP Q 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  123.46  176.54     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" O2A ADP Z 601 "
           pdb=" O3A ADP Z 601 "
           pdb=" PA  ADP Z 601 "
           pdb=" PB  ADP Z 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  127.50  172.50     1      2.00e+01 2.50e-03 4.78e+01
  ... (remaining 42015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 8475
       0.045 -    0.090: 1758
       0.090 -    0.135: 679
       0.135 -    0.179: 10
       0.179 -    0.224: 1
  Chirality restraints: 10923
  Sorted by residual:
  chirality pdb=" CA  ARG P 149 "
            pdb=" N   ARG P 149 "
            pdb=" C   ARG P 149 "
            pdb=" CB  ARG P 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE g 363 "
            pdb=" N   ILE g 363 "
            pdb=" C   ILE g 363 "
            pdb=" CB  ILE g 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE G 460 "
            pdb=" CA  ILE G 460 "
            pdb=" CG1 ILE G 460 "
            pdb=" CG2 ILE G 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.47e-01
  ... (remaining 10920 not shown)

  Planarity restraints: 11716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS e 440 "    0.033 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO e 441 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO e 441 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO e 441 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET H   2 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO H   3 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO H   3 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H   3 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU P 274 "    0.024 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO P 275 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO P 275 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO P 275 "    0.021 5.00e-02 4.00e+02
  ... (remaining 11713 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 567
        2.54 -     3.13: 52285
        3.13 -     3.72: 106746
        3.72 -     4.31: 151359
        4.31 -     4.90: 256039
  Nonbonded interactions: 566996
  Sorted by model distance:
  nonbonded pdb="MG    MG D 602 "
            pdb=" F2  AF3 D 603 "
     model   vdw
     1.955 2.120
  nonbonded pdb="MG    MG H 602 "
            pdb=" F2  AF3 H 603 "
     model   vdw
     1.957 2.120
  nonbonded pdb="MG    MG E 602 "
            pdb=" F1  AF3 E 603 "
     model   vdw
     1.971 2.120
  nonbonded pdb="MG    MG d 602 "
            pdb=" F1  AF3 d 603 "
     model   vdw
     1.971 2.120
  nonbonded pdb="MG    MG e 602 "
            pdb=" F1  AF3 e 603 "
     model   vdw
     1.987 2.120
  ... (remaining 566991 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 4 through 535 or resid 601 through 603))
  selection = chain 'a'
}
ncs_group {
  reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603))
  selection = chain 'b'
}
ncs_group {
  reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 20 through 538 or resid 601 through 603))
  selection = chain 'd'
}
ncs_group {
  reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 
03))
  selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 
03))
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'g' and (resid 3 through 528 or resid 601 through 603))
}
ncs_group {
  reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603))
  selection = chain 'h'
}
ncs_group {
  reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603))
  selection = chain 'q'
}
ncs_group {
  reference = chain 'Z'
  selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:             0.090
  Extract box with map and model:          8.350
  Check model and map are aligned:         0.750
  Set scattering table:                    0.470
  Process input model:                     150.740
  Find NCS groups from input model:        6.670
  Set up NCS constraints:                  0.650
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:  180.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
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      :  0.004   0.162  67960  Z= 0.276
  Angle     :  0.521   9.658  91755  Z= 0.254
  Chirality :  0.041   0.224  10923
  Planarity :  0.003   0.051  11716
  Dihedral  : 14.495 178.292  25766
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  1.77 (0.09), residues: 8685
  helix:  2.33 (0.08), residues: 4481
  sheet:  0.55 (0.16), residues: 1109
  loop : -0.28 (0.11), residues: 3095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP g 168 
   HIS   0.007   0.001   HIS z 161 
   PHE   0.019   0.001   PHE e 386 
   TYR   0.015   0.001   TYR b 297 
   ARG   0.007   0.000   ARG e  24 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  606 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 606
  time to evaluate  : 5.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 606
  average time/residue: 1.7069
  time to fit residues: 1318.9802
Evaluate side-chains
  492 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 492
  time to evaluate  : 5.892 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 7.8484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 729 optimal weight:   10.0000
   chunk 654 optimal weight:    0.4980
   chunk 363 optimal weight:    0.0970
   chunk 223 optimal weight:    6.9990
   chunk 441 optimal weight:    8.9990
   chunk 349 optimal weight:    9.9990
   chunk 677 optimal weight:    2.9990
   chunk 262 optimal weight:    2.9990
   chunk 411 optimal weight:    1.9990
   chunk 504 optimal weight:    0.8980
   chunk 784 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
N 231 GLN
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 366 ASN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  34 GLN
d 394 ASN
** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 199 ASN
P 227 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.0558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  67960  Z= 0.158
  Angle     :  0.521   8.668  91755  Z= 0.259
  Chirality :  0.040   0.165  10923
  Planarity :  0.004   0.060  11716
  Dihedral  :  7.760 178.731   9433
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  5.92 %
    Favored  : 93.42 %
  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:  1.60 (0.09), residues: 8685
  helix:  2.14 (0.08), residues: 4484
  sheet:  0.54 (0.16), residues: 1080
  loop : -0.30 (0.11), residues: 3121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP P  66 
   HIS   0.008   0.001   HIS z 161 
   PHE   0.021   0.001   PHE P  69 
   TYR   0.026   0.001   TYR A 181 
   ARG   0.009   0.000   ARG P 250 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  572 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 524
  time to evaluate  : 6.007 
Fit side-chains
  outliers start: 48
  outliers final: 11
  residues processed: 543
  average time/residue: 1.6887
  time to fit residues: 1182.2447
Evaluate side-chains
  498 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 487
  time to evaluate  : 5.862 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 5
  residues processed: 6
  average time/residue: 0.8398
  time to fit residues: 15.7839
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 436 optimal weight:    0.1980
   chunk 243 optimal weight:    5.9990
   chunk 653 optimal weight:    0.2980
   chunk 534 optimal weight:    0.7980
   chunk 216 optimal weight:   10.0000
   chunk 786 optimal weight:    3.9990
   chunk 849 optimal weight:    5.9990
   chunk 700 optimal weight:    8.9990
   chunk 779 optimal weight:   10.0000
   chunk 267 optimal weight:    3.9990
   chunk 630 optimal weight:    8.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 HIS
D 366 ASN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 501 ASN
Z  84 GLN
Z 161 HIS
e 515 GLN
h 402 ASN
z  84 GLN
z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 199 ASN
P 227 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.0672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  67960  Z= 0.205
  Angle     :  0.523   9.612  91755  Z= 0.257
  Chirality :  0.041   0.167  10923
  Planarity :  0.004   0.052  11716
  Dihedral  :  7.543 178.956   9433
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.57 %
    Favored  : 91.67 %
  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:  1.50 (0.09), residues: 8685
  helix:  2.04 (0.08), residues: 4479
  sheet:  0.45 (0.16), residues: 1090
  loop : -0.30 (0.11), residues: 3116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP q 319 
   HIS   0.009   0.001   HIS z 161 
   PHE   0.015   0.001   PHE A 167 
   TYR   0.027   0.001   TYR A 181 
   ARG   0.010   0.000   ARG e  24 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  568 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 513
  time to evaluate  : 6.006 
Fit side-chains
   revert: symmetry clash
  outliers start: 55
  outliers final: 18
  residues processed: 537
  average time/residue: 1.6695
  time to fit residues: 1160.2638
Evaluate side-chains
  510 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 492
  time to evaluate  : 5.932 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 8
  residues processed: 10
  average time/residue: 0.9158
  time to fit residues: 21.9648
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 776 optimal weight:    7.9990
   chunk 590 optimal weight:    6.9990
   chunk 407 optimal weight:    9.9990
   chunk 87 optimal weight:    0.8980
   chunk 375 optimal weight:   10.0000
   chunk 527 optimal weight:    0.6980
   chunk 788 optimal weight:    8.9990
   chunk 835 optimal weight:    0.0030
   chunk 412 optimal weight:    3.9990
   chunk 747 optimal weight:    3.9990
   chunk 225 optimal weight:    0.1980
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 366 ASN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 501 ASN
Z 161 HIS
z  84 GLN
z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 199 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.0806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  67960  Z= 0.154
  Angle     :  0.506  10.129  91755  Z= 0.248
  Chirality :  0.040   0.168  10923
  Planarity :  0.003   0.052  11716
  Dihedral  :  7.311 179.985   9433
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.56 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.09), residues: 8685
  helix:  2.05 (0.08), residues: 4481
  sheet:  0.40 (0.16), residues: 1092
  loop : -0.29 (0.11), residues: 3112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP g 168 
   HIS   0.012   0.001   HIS Z 161 
   PHE   0.012   0.001   PHE P  69 
   TYR   0.011   0.001   TYR z 351 
   ARG   0.008   0.000   ARG P  77 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  584 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 527
  time to evaluate  : 5.970 
Fit side-chains
   revert: symmetry clash
  outliers start: 57
  outliers final: 20
  residues processed: 556
  average time/residue: 1.6637
  time to fit residues: 1202.3295
Evaluate side-chains
  515 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 495
  time to evaluate  : 8.112 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 12
  residues processed: 8
  average time/residue: 0.8876
  time to fit residues: 18.7718
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 695 optimal weight:    2.9990
   chunk 474 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 621 optimal weight:    7.9990
   chunk 344 optimal weight:   10.0000
   chunk 712 optimal weight:    1.9990
   chunk 577 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 426 optimal weight:   10.0000
   chunk 749 optimal weight:    4.9990
   chunk 210 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 534 HIS
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 390 ASN
H 501 ASN
Z 161 HIS
** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 390 ASN
h 201 GLN
z  84 GLN
z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 199 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  67960  Z= 0.326
  Angle     :  0.571  10.346  91755  Z= 0.282
  Chirality :  0.043   0.166  10923
  Planarity :  0.004   0.059  11716
  Dihedral  :  7.363 179.571   9433
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.32 %
    Favored  : 89.71 %
  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:  1.33 (0.09), residues: 8685
  helix:  1.88 (0.08), residues: 4509
  sheet:  0.35 (0.16), residues: 1107
  loop : -0.36 (0.11), residues: 3069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP g 168 
   HIS   0.015   0.001   HIS Z 161 
   PHE   0.017   0.002   PHE H 220 
   TYR   0.031   0.001   TYR A 181 
   ARG   0.009   0.000   ARG e  24 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  565 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 494
  time to evaluate  : 6.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 71
  outliers final: 28
  residues processed: 537
  average time/residue: 1.7136
  time to fit residues: 1192.3233
Evaluate side-chains
  509 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 481
  time to evaluate  : 5.902 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 20
  residues processed: 10
  average time/residue: 1.1643
  time to fit residues: 24.3348
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 280 optimal weight:    8.9990
   chunk 752 optimal weight:    2.9990
   chunk 165 optimal weight:    2.9990
   chunk 490 optimal weight:    2.9990
   chunk 206 optimal weight:    6.9990
   chunk 835 optimal weight:    8.9990
   chunk 693 optimal weight:    0.9990
   chunk 387 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 276 optimal weight:    0.8980
   chunk 438 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 ASN
B 302 GLN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 161 HIS
g 390 ASN
z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 153 HIS
P 199 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  67960  Z= 0.225
  Angle     :  0.538  11.092  91755  Z= 0.264
  Chirality :  0.041   0.171  10923
  Planarity :  0.003   0.054  11716
  Dihedral  :  7.171 174.215   9433
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.81 %
    Favored  : 89.30 %
  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:  1.36 (0.09), residues: 8685
  helix:  1.92 (0.08), residues: 4495
  sheet:  0.34 (0.16), residues: 1095
  loop : -0.36 (0.11), residues: 3095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP g 168 
   HIS   0.013   0.001   HIS Z 161 
   PHE   0.014   0.001   PHE P  69 
   TYR   0.031   0.001   TYR A 181 
   ARG   0.009   0.000   ARG e  24 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  566 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 501
  time to evaluate  : 6.076 
Fit side-chains
   revert: symmetry clash
  outliers start: 65
  outliers final: 33
  residues processed: 538
  average time/residue: 1.6684
  time to fit residues: 1170.5663
Evaluate side-chains
  513 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 480
  time to evaluate  : 5.892 
Switching outliers to nearest non-outliers
  outliers start: 33
  outliers final: 22
  residues processed: 11
  average time/residue: 0.9889
  time to fit residues: 24.3282
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 805 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 476 optimal weight:    7.9990
   chunk 610 optimal weight:    9.9990
   chunk 472 optimal weight:    0.3980
   chunk 703 optimal weight:    6.9990
   chunk 466 optimal weight:   10.0000
   chunk 832 optimal weight:    6.9990
   chunk 521 optimal weight:    9.9990
   chunk 507 optimal weight:    7.9990
   chunk 384 optimal weight:    0.9990
   overall best weight:    4.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 HIS
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 161 HIS
** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g 390 ASN
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  67960  Z= 0.430
  Angle     :  0.613  11.267  91755  Z= 0.303
  Chirality :  0.044   0.175  10923
  Planarity :  0.004   0.054  11716
  Dihedral  :  7.325 172.643   9433
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 10.37 %
    Favored  : 88.71 %
  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:  1.18 (0.09), residues: 8685
  helix:  1.75 (0.08), residues: 4509
  sheet:  0.26 (0.16), residues: 1125
  loop : -0.43 (0.11), residues: 3051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP g 168 
   HIS   0.014   0.001   HIS Z 161 
   PHE   0.022   0.002   PHE H 220 
   TYR   0.018   0.002   TYR Z 353 
   ARG   0.011   0.000   ARG P  77 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  554 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 487
  time to evaluate  : 5.959 
Fit side-chains
   revert: symmetry clash
  outliers start: 67
  outliers final: 34
  residues processed: 532
  average time/residue: 1.6411
  time to fit residues: 1141.6106
Evaluate side-chains
  509 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 475
  time to evaluate  : 5.899 
Switching outliers to nearest non-outliers
  outliers start: 34
  outliers final: 22
  residues processed: 13
  average time/residue: 1.0773
  time to fit residues: 28.2391
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 515 optimal weight:    0.8980
   chunk 332 optimal weight:    0.7980
   chunk 497 optimal weight:    0.8980
   chunk 250 optimal weight:    0.8980
   chunk 163 optimal weight:    6.9990
   chunk 161 optimal weight:    0.9980
   chunk 529 optimal weight:    0.8980
   chunk 567 optimal weight:    0.8980
   chunk 411 optimal weight:    0.0980
   chunk 77 optimal weight:    0.9990
   chunk 654 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 501 ASN
Z 161 HIS
b 227 ASN
g 390 ASN
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  67960  Z= 0.144
  Angle     :  0.531  10.981  91755  Z= 0.261
  Chirality :  0.040   0.174  10923
  Planarity :  0.003   0.050  11716
  Dihedral  :  6.925 163.660   9433
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.80 %
    Favored  : 88.50 %
  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:  1.40 (0.09), residues: 8685
  helix:  1.98 (0.08), residues: 4477
  sheet:  0.26 (0.16), residues: 1105
  loop : -0.35 (0.11), residues: 3103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP g 168 
   HIS   0.017   0.001   HIS Z 161 
   PHE   0.013   0.001   PHE P  69 
   TYR   0.011   0.001   TYR q 505 
   ARG   0.013   0.000   ARG P  77 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  554 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 503
  time to evaluate  : 5.988 
Fit side-chains
   revert: symmetry clash
  outliers start: 51
  outliers final: 24
  residues processed: 538
  average time/residue: 1.6428
  time to fit residues: 1153.1239
Evaluate side-chains
  502 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 478
  time to evaluate  : 5.945 
Switching outliers to nearest non-outliers
  outliers start: 24
  outliers final: 19
  residues processed: 5
  average time/residue: 0.7352
  time to fit residues: 14.1523
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 757 optimal weight:    4.9990
   chunk 797 optimal weight:    0.9980
   chunk 727 optimal weight:    0.9990
   chunk 776 optimal weight:    3.9990
   chunk 467 optimal weight:    3.9990
   chunk 338 optimal weight:    8.9990
   chunk 609 optimal weight:    8.9990
   chunk 238 optimal weight:    6.9990
   chunk 701 optimal weight:    7.9990
   chunk 733 optimal weight:    9.9990
   chunk 773 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 501 ASN
Z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  67960  Z= 0.294
  Angle     :  0.564  11.125  91755  Z= 0.276
  Chirality :  0.042   0.168  10923
  Planarity :  0.004   0.052  11716
  Dihedral  :  6.933 164.402   9433
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.12 %
    Favored  : 88.33 %
  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:  1.31 (0.09), residues: 8685
  helix:  1.88 (0.08), residues: 4498
  sheet:  0.26 (0.16), residues: 1117
  loop : -0.36 (0.11), residues: 3070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP g 168 
   HIS   0.017   0.001   HIS Z 161 
   PHE   0.014   0.001   PHE A 167 
   TYR   0.031   0.001   TYR A 181 
   ARG   0.013   0.000   ARG z 523 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  525 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 485
  time to evaluate  : 5.982 
Fit side-chains
  outliers start: 40
  outliers final: 29
  residues processed: 512
  average time/residue: 1.6914
  time to fit residues: 1137.8930
Evaluate side-chains
  502 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 473
  time to evaluate  : 5.845 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 21
  residues processed: 8
  average time/residue: 1.0008
  time to fit residues: 20.0611
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 509 optimal weight:    0.7980
   chunk 820 optimal weight:    5.9990
   chunk 500 optimal weight:    6.9990
   chunk 389 optimal weight:    6.9990
   chunk 570 optimal weight:    9.9990
   chunk 860 optimal weight:   10.0000
   chunk 792 optimal weight:    3.9990
   chunk 685 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   chunk 529 optimal weight:    0.9990
   chunk 420 optimal weight:   10.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 HIS
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  67960  Z= 0.256
  Angle     :  0.565  12.725  91755  Z= 0.276
  Chirality :  0.042   0.191  10923
  Planarity :  0.004   0.053  11716
  Dihedral  :  6.905 162.771   9433
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 11.28 %
    Favored  : 88.27 %
  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:  1.32 (0.09), residues: 8685
  helix:  1.90 (0.08), residues: 4483
  sheet:  0.25 (0.16), residues: 1105
  loop : -0.37 (0.11), residues: 3097

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP q 319 
   HIS   0.018   0.001   HIS Z 161 
   PHE   0.014   0.001   PHE A 167 
   TYR   0.014   0.001   TYR B 439 
   ARG   0.013   0.000   ARG P  77 

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

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

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  17370 Ramachandran restraints generated.
    8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  516 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 483
  time to evaluate  : 6.025 
Fit side-chains
  outliers start: 33
  outliers final: 25
  residues processed: 509
  average time/residue: 1.7142
  time to fit residues: 1143.1814
Evaluate side-chains
  499 residues out of total 7276 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 474
  time to evaluate  : 5.878 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 20
  residues processed: 5
  average time/residue: 1.1843
  time to fit residues: 16.2668
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 864
   random chunks:
   chunk 544 optimal weight:    3.9990
   chunk 730 optimal weight:    1.9990
   chunk 209 optimal weight:    0.9980
   chunk 632 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 190 optimal weight:    8.9990
   chunk 686 optimal weight:    8.9990
   chunk 287 optimal weight:    3.9990
   chunk 704 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9990
   chunk 126 optimal weight:    5.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 534 HIS
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 501 ASN
Q  80 HIS
Z 161 HIS
** P  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.072804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.058831 restraints weight = 181224.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 3.02
r_work: 0.2560 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  67960  Z= 0.169
  Angle     :  0.535  10.758  91755  Z= 0.261
  Chirality :  0.041   0.168  10923
  Planarity :  0.003   0.052  11716
  Dihedral  :  6.710 158.738   9433
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 11.43 %
    Favored  : 88.14 %
  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:  1.41 (0.09), residues: 8685
  helix:  1.98 (0.08), residues: 4474
  sheet:  0.30 (0.16), residues: 1090
  loop : -0.31 (0.11), residues: 3121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.001   TRP q 319 
   HIS   0.018   0.001   HIS Z 161 
   PHE   0.013   0.001   PHE P  69 
   TYR   0.028   0.001   TYR A 181 
   ARG   0.014   0.000   ARG P  77 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17929.94 seconds
wall clock time: 315 minutes 1.06 seconds (18901.06 seconds total)