Starting phenix.real_space_refine
on Sun Mar 17 19:52:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/03_2024/6wqq_21873_updated.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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: 6
    Type Number    sf(0)   Gaussians
     P    2803      5.49       5
     S      56      5.16       5
     C   39961      2.51       5
     N   15060      2.21       5
     O   23253      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   23": "NH1" <-> "NH2"
    Residue "A ARG   29": "NH1" <-> "NH2"
    Residue "A ARG   41": "NH1" <-> "NH2"
    Residue "A ARG   53": "NH1" <-> "NH2"
    Residue "A ARG   64": "NH1" <-> "NH2"
    Residue "A GLU   73": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A GLU   87": "OE1" <-> "OE2"
    Residue "A ARG   91": "NH1" <-> "NH2"
    Residue "A ARG  103": "NH1" <-> "NH2"
    Residue "A ARG  111": "NH1" <-> "NH2"
    Residue "B GLU   23": "OE1" <-> "OE2"
    Residue "B GLU  117": "OE1" <-> "OE2"
    Residue "B GLU  145": "OE1" <-> "OE2"
    Residue "B ARG  261": "NH1" <-> "NH2"
    Residue "C ARG    3": "NH1" <-> "NH2"
    Residue "C ARG   13": "NH1" <-> "NH2"
    Residue "C ARG   48": "NH1" <-> "NH2"
    Residue "C ARG   70": "NH1" <-> "NH2"
    Residue "C GLU   73": "OE1" <-> "OE2"
    Residue "D GLU   54": "OE1" <-> "OE2"
    Residue "D ARG   67": "NH1" <-> "NH2"
    Residue "D ARG   78": "NH1" <-> "NH2"
    Residue "D ARG   84": "NH1" <-> "NH2"
    Residue "E GLU   68": "OE1" <-> "OE2"
    Residue "E GLU   78": "OE1" <-> "OE2"
    Residue "E ARG   84": "NH1" <-> "NH2"
    Residue "E ARG   88": "NH1" <-> "NH2"
    Residue "F GLU   18": "OE1" <-> "OE2"
    Residue "F ARG   32": "NH1" <-> "NH2"
    Residue "F GLU   44": "OE1" <-> "OE2"
    Residue "F ARG   76": "NH1" <-> "NH2"
    Residue "G GLU   36": "OE1" <-> "OE2"
    Residue "G GLU   99": "OE1" <-> "OE2"
    Residue "H GLU   45": "OE1" <-> "OE2"
    Residue "H GLU   47": "OE1" <-> "OE2"
    Residue "H TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG   18": "NH1" <-> "NH2"
    Residue "J ARG   37": "NH1" <-> "NH2"
    Residue "K ARG    7": "NH1" <-> "NH2"
    Residue "K GLU   13": "OE1" <-> "OE2"
    Residue "K GLU   23": "OE1" <-> "OE2"
    Residue "K ARG   29": "NH1" <-> "NH2"
    Residue "K ARG   47": "NH1" <-> "NH2"
    Residue "K ARG   52": "NH1" <-> "NH2"
    Residue "K ARG   60": "NH1" <-> "NH2"
    Residue "L GLU   18": "OE1" <-> "OE2"
    Residue "L GLU   32": "OE1" <-> "OE2"
    Residue "L GLU   42": "OE1" <-> "OE2"
    Residue "L GLU   54": "OE1" <-> "OE2"
    Residue "L GLU   74": "OE1" <-> "OE2"
    Residue "L ARG   86": "NH1" <-> "NH2"
    Residue "L ARG   92": "NH1" <-> "NH2"
    Residue "L ARG  138": "NH1" <-> "NH2"
    Residue "L GLU  191": "OE1" <-> "OE2"
    Residue "L GLU  210": "OE1" <-> "OE2"
    Residue "M ARG   10": "NH1" <-> "NH2"
    Residue "M GLU   24": "OE1" <-> "OE2"
    Residue "M GLU   38": "OE1" <-> "OE2"
    Residue "M ARG   44": "NH1" <-> "NH2"
    Residue "N ARG    6": "NH1" <-> "NH2"
    Residue "N ARG    7": "NH1" <-> "NH2"
    Residue "N GLU   29": "OE1" <-> "OE2"
    Residue "O GLU   28": "OE1" <-> "OE2"
    Residue "P ARG    4": "NH1" <-> "NH2"
    Residue "P ARG   20": "NH1" <-> "NH2"
    Residue "P ARG   22": "NH1" <-> "NH2"
    Residue "P ARG   34": "NH1" <-> "NH2"
    Residue "Q ARG   13": "NH1" <-> "NH2"
    Residue "Q ARG   42": "NH1" <-> "NH2"
    Residue "Q ARG   57": "NH1" <-> "NH2"
    Residue "S GLU   35": "OE1" <-> "OE2"
    Residue "S ARG   54": "NH1" <-> "NH2"
    Residue "S ARG   62": "NH1" <-> "NH2"
    Residue "S ARG  107": "NH1" <-> "NH2"
    Residue "S GLU  120": "OE1" <-> "OE2"
    Residue "S GLU  157": "OE1" <-> "OE2"
    Residue "S ARG  168": "NH1" <-> "NH2"
    Residue "S GLU  204": "OE1" <-> "OE2"
    Residue "V ARG    2": "NH1" <-> "NH2"
    Residue "V ARG   14": "NH1" <-> "NH2"
    Residue "V GLU   22": "OE1" <-> "OE2"
    Residue "V ARG   38": "NH1" <-> "NH2"
    Residue "V GLU   70": "OE1" <-> "OE2"
    Residue "V GLU  103": "OE1" <-> "OE2"
    Residue "V GLU  139": "OE1" <-> "OE2"
    Residue "V ARG  144": "NH1" <-> "NH2"
    Residue "W GLU   18": "OE1" <-> "OE2"
    Residue "W GLU   81": "OE1" <-> "OE2"
    Residue "W GLU  105": "OE1" <-> "OE2"
    Residue "X GLU    5": "OE1" <-> "OE2"
    Residue "X GLU   90": "OE1" <-> "OE2"
    Residue "X GLU   98": "OE1" <-> "OE2"
    Residue "Y ARG   10": "NH1" <-> "NH2"
    Residue "Y GLU   31": "OE1" <-> "OE2"
    Residue "Y ARG   45": "NH1" <-> "NH2"
    Residue "Y ARG   51": "NH1" <-> "NH2"
    Residue "Y ARG   56": "NH1" <-> "NH2"
    Residue "Y ARG   60": "NH1" <-> "NH2"
    Residue "Y GLU   80": "OE1" <-> "OE2"
    Residue "Y GLU   91": "OE1" <-> "OE2"
    Residue "Y GLU  112": "OE1" <-> "OE2"
    Residue "Y ARG  115": "NH1" <-> "NH2"
    Residue "Y GLU  135": "OE1" <-> "OE2"
    Residue "Z ARG   67": "NH1" <-> "NH2"
    Residue "Z GLU   70": "OE1" <-> "OE2"
    Residue "Z GLU   76": "OE1" <-> "OE2"
    Residue "Z GLU   88": "OE1" <-> "OE2"
    Residue "Z GLU   95": "OE1" <-> "OE2"
    Residue "Z GLU  115": "OE1" <-> "OE2"
    Residue "a GLU  118": "OE1" <-> "OE2"
    Residue "I ARG   22": "NH1" <-> "NH2"
    Residue "I GLU   25": "OE1" <-> "OE2"
    Residue "I ARG   28": "NH1" <-> "NH2"
    Residue "I ARG   49": "NH1" <-> "NH2"
    Residue "I ARG   79": "NH1" <-> "NH2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 81134
  Number of models: 1
  Model: ""
    Number of chains: 28
    Chain: "A"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 915
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 4, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 2094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2094
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 17, 'TRANS': 256}
    Chain: "C"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 943
          Classifications: {'peptide': 116}
          Link IDs: {'TRANS': 115}
    Chain: "D"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 785
          Classifications: {'peptide': 100}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97}
    Chain: "E"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 853
          Classifications: {'peptide': 111}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 711
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 2, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 770
          Classifications: {'peptide': 100}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 727
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "J"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 463
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 1, 'TRANS': 57}
    Chain: "K"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 495
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "L"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1628
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 8, 'TRANS': 206}
    Chain: "M"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 432
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 397
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 3, 'TRANS': 46}
    Chain: "O"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 390
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "P"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 372
          Classifications: {'peptide': 44}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
    Chain: "Q"
      Number of atoms: 521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 521
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "R"
      Number of atoms: 296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 296
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
    Chain: "S"
      Number of atoms: 1472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1472
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 9, 'TRANS': 182}
    Chain: "V"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1138
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 6, 'TRANS': 136}
    Chain: "W"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 911
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "X"
      Number of atoms: 1082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1082
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 5, 'TRANS': 138}
    Chain: "Y"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1089
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "Z"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 955
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 1, 'TRANS': 119}
    Chain: "a"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 857
          Classifications: {'peptide': 110}
          Link IDs: {'PCIS': 1, 'TRANS': 108}
          Chain breaks: 1
    Chain: "1"
      Number of atoms: 57851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2698, 57851
          Inner-chain residues flagged as termini: ['pdbres="  A 1 318 "', 'pdbres="  A 11459 "', 'pdbres="  U 11540 "', 'pdbres="  G 11556 "']
          Classifications: {'RNA': 2698}
          Modifications used: {'5*END': 5, 'rna2p_pur': 272, 'rna2p_pyr': 136, 'rna3p_pur': 1281, 'rna3p_pyr': 1009}
          Link IDs: {'rna2p': 408, 'rna3p': 2289}
          Chain breaks: 6
    Chain: "2"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 2358
          Classifications: {'RNA': 111}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 49}
          Link IDs: {'rna2p': 12, 'rna3p': 98}
    Chain: "I"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 597
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "1"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'RD8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 31.28, per 1000 atoms: 0.39
  Number of scatterers: 81134
  At special positions: 0
  Unit cell: (212.04, 234.84, 188.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      56     16.00
     P    2803     15.00
     F       1      9.00
     O   23253      8.00
     N   15060      7.00
     C   39961      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  33 " - pdb=" SG  CYS N  43 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  14 " - pdb=" SG  CYS R  27 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 28.29
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4856

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      66 helices and 39 sheets defined
      21.2% alpha, 16.8% beta
      540 base pairs and 1570 stacking pairs defined.
    Time for finding SS restraints: 34.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 13
      removed outlier: 3.541A  pdb=" N   ALA A   9 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   SER A  13 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 102
      No H-bonds generated for 'chain 'A' and resid 100 through 102'
    Processing helix  chain 'A' and resid 107 through 109
      No H-bonds generated for 'chain 'A' and resid 107 through 109'
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 198 through 200
      No H-bonds generated for 'chain 'B' and resid 198 through 200'
    Processing helix  chain 'B' and resid 208 through 214
      removed outlier: 3.637A  pdb=" N   TRP B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS B 214 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'B' and resid 266 through 268
      No H-bonds generated for 'chain 'B' and resid 266 through 268'
    Processing helix  chain 'C' and resid 10 through 20
      removed outlier: 3.562A  pdb=" N   LYS C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR C  17 " --> pdb=" O   ARG C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 29
    Processing helix  chain 'C' and resid 32 through 72
      removed outlier: 3.905A  pdb=" N   GLN C  37 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLN C  38 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG C  51 " --> pdb=" O   PHE C  47 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LYS C  54 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG C  55 " --> pdb=" O   ARG C  51 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE C  57 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG C  58 " --> pdb=" O   LYS C  54 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU C  60 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG C  64 " --> pdb=" O   LEU C  60 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLN C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   HIS C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 85
      removed outlier: 3.662A  pdb=" N   ASN C  81 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY C  82 " --> pdb=" O   ARG C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 101
      removed outlier: 3.601A  pdb=" N   GLU C  97 " --> pdb=" O   LYS C  93 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C  99 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE C 100 " --> pdb=" O   SER C  96 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER C 101 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 115
      removed outlier: 3.820A  pdb=" N   ALA C 107 " --> pdb=" O   GLU C 103 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN C 108 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 14 through 24
      removed outlier: 4.220A  pdb=" N   LEU E  19 " --> pdb=" O   ARG E  15 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   VAL E  20 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LEU E  23 " --> pdb=" O   LEU E  19 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE E  24 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 37
      removed outlier: 3.755A  pdb=" N   ILE E  33 " --> pdb=" O   ALA E  29 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA E  34 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 60
      removed outlier: 3.515A  pdb=" N   LEU E  55 " --> pdb=" O   LEU E  51 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 68
      No H-bonds generated for 'chain 'E' and resid 66 through 68'
    Processing helix  chain 'E' and resid 89 through 91
      No H-bonds generated for 'chain 'E' and resid 89 through 91'
    Processing helix  chain 'F' and resid 35 through 46
      removed outlier: 3.549A  pdb=" N   MET F  40 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU F  43 " --> pdb=" O   LYS F  39 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 65 through 67
      No H-bonds generated for 'chain 'G' and resid 65 through 67'
    Processing helix  chain 'H' and resid 15 through 24
    Processing helix  chain 'H' and resid 46 through 55
      removed outlier: 3.598A  pdb=" N   LYS H  50 " --> pdb=" O   VAL H  46 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL H  51 " --> pdb=" O   GLU H  47 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG H  53 " --> pdb=" O   ILE H  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU H  54 " --> pdb=" O   LYS H  50 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 51 through 54
      No H-bonds generated for 'chain 'J' and resid 51 through 54'
    Processing helix  chain 'K' and resid 13 through 21
      removed outlier: 3.521A  pdb=" N   SER K  21 " --> pdb=" O   GLN K  17 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 25 through 34
      removed outlier: 3.613A  pdb=" N   ARG K  29 " --> pdb=" O   LEU K  25 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE K  30 " --> pdb=" O   PHE K  26 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 40 through 60
      removed outlier: 3.702A  pdb=" N   ARG K  44 " --> pdb=" O   ALA K  41 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR K  45 " --> pdb=" O   ARG K  42 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG K  47 " --> pdb=" O   ARG K  44 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE K  50 " --> pdb=" O   ARG K  47 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG K  52 " --> pdb=" O   THR K  49 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR K  55 " --> pdb=" O   ARG K  52 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL K  56 " --> pdb=" O   LEU K  53 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG K  58 " --> pdb=" O   THR K  55 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 71 through 74
      No H-bonds generated for 'chain 'L' and resid 71 through 74'
    Processing helix  chain 'L' and resid 107 through 110
    Processing helix  chain 'L' and resid 130 through 134
    Processing helix  chain 'M' and resid 17 through 24
      removed outlier: 3.764A  pdb=" N   THR M  22 " --> pdb=" O   THR M  18 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL M  23 " --> pdb=" O   GLN M  19 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 41 through 47
      removed outlier: 3.707A  pdb=" N   GLN M  46 " --> pdb=" O   ALA M  42 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE M  47 " --> pdb=" O   ILE M  43 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 10 through 18
      removed outlier: 3.620A  pdb=" N   ARG N  17 " --> pdb=" O   LYS N  13 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   THR N  18 " --> pdb=" O   ASN N  14 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 10 through 14
    Processing helix  chain 'P' and resid 19 through 22
      No H-bonds generated for 'chain 'P' and resid 19 through 22'
    Processing helix  chain 'P' and resid 26 through 38
      removed outlier: 3.629A  pdb=" N   VAL P  31 " --> pdb=" O   ASN P  27 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU P  32 " --> pdb=" O   GLY P  28 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA P  33 " --> pdb=" O   ARG P  29 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 8 through 11
      No H-bonds generated for 'chain 'Q' and resid 8 through 11'
    Processing helix  chain 'Q' and resid 38 through 44
    Processing helix  chain 'Q' and resid 52 through 57
      removed outlier: 3.686A  pdb=" N   LYS Q  56 " --> pdb=" O   LYS Q  52 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG Q  57 " --> pdb=" O   SER Q  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 52 through 57'
    Processing helix  chain 'S' and resid 30 through 43
      removed outlier: 3.616A  pdb=" N   GLU S  35 " --> pdb=" O   SER S  31 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE S  37 " --> pdb=" O   LEU S  33 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN S  40 " --> pdb=" O   ALA S  36 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 103 through 119
      removed outlier: 3.996A  pdb=" N   LEU S 108 " --> pdb=" O   LYS S 104 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LYS S 117 " --> pdb=" O   ALA S 113 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL S 118 " --> pdb=" O   LEU S 114 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 136 through 145
      removed outlier: 3.890A  pdb=" N   ASN S 141 " --> pdb=" O   LYS S 137 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL S 142 " --> pdb=" O   GLU S 138 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU S 143 " --> pdb=" O   PHE S 139 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 183 through 188
      removed outlier: 3.521A  pdb=" N   ASN S 188 " --> pdb=" O   LEU S 184 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 196 through 205
      removed outlier: 3.831A  pdb=" N   GLU S 204 " --> pdb=" O   LYS S 200 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 26 through 38
      removed outlier: 3.551A  pdb=" N   SER V  31 " --> pdb=" O   GLY V  27 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU V  32 " --> pdb=" O   ARG V  28 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 69 through 72
      No H-bonds generated for 'chain 'V' and resid 69 through 72'
    Processing helix  chain 'V' and resid 90 through 96
      removed outlier: 3.631A  pdb=" N   ARG V  95 " --> pdb=" O   GLY V  91 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 98 through 107
      removed outlier: 3.652A  pdb=" N   ILE V 102 " --> pdb=" O   PRO V  98 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER V 105 " --> pdb=" O   LEU V 101 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 114 through 118
      removed outlier: 3.592A  pdb=" N   LYS V 118 " --> pdb=" O   ARG V 114 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'V' and resid 114 through 118'
    Processing helix  chain 'V' and resid 120 through 122
      No H-bonds generated for 'chain 'V' and resid 120 through 122'
    Processing helix  chain 'W' and resid 112 through 117
    Processing helix  chain 'X' and resid 38 through 40
      No H-bonds generated for 'chain 'X' and resid 38 through 40'
    Processing helix  chain 'X' and resid 57 through 59
      No H-bonds generated for 'chain 'X' and resid 57 through 59'
    Processing helix  chain 'X' and resid 79 through 84
      removed outlier: 3.744A  pdb=" N   ASN X  83 " --> pdb=" O   LEU X  79 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   LYS X  84 " --> pdb=" O   ASP X  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 79 through 84'
    Processing helix  chain 'X' and resid 93 through 99
      removed outlier: 3.760A  pdb=" N   VAL X  97 " --> pdb=" O   PRO X  93 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU X  98 " --> pdb=" O   ALA X  94 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 134 through 138
    Processing helix  chain 'Y' and resid 44 through 55
    Processing helix  chain 'Y' and resid 111 through 120
      removed outlier: 3.592A  pdb=" N   ARG Y 115 " --> pdb=" O   GLU Y 111 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLU Y 116 " --> pdb=" O   GLU Y 112 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 10 through 26
      removed outlier: 3.528A  pdb=" N   ASP Z  19 " --> pdb=" O   ALA Z  15 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE Z  26 " --> pdb=" O   THR Z  22 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 34 through 53
      removed outlier: 3.845A  pdb=" N   GLU Z  39 " --> pdb=" O   ALA Z  35 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER Z  42 " --> pdb=" O   LYS Z  38 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL Z  43 " --> pdb=" O   GLU Z  39 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU Z  45 " --> pdb=" O   ARG Z  41 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU Z  47 " --> pdb=" O   VAL Z  43 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR Z  49 " --> pdb=" O   GLU Z  45 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU Z  50 " --> pdb=" O   LYS Z  46 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS Z  53 " --> pdb=" O   THR Z  49 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 56 through 61
    Processing helix  chain 'Z' and resid 81 through 84
      No H-bonds generated for 'chain 'Z' and resid 81 through 84'
    Processing helix  chain 'Z' and resid 88 through 92
    Processing helix  chain 'a' and resid 9 through 22
      removed outlier: 3.946A  pdb=" N   LYS a  13 " --> pdb=" O   LYS a   9 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG a  14 " --> pdb=" O   VAL a  10 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG a  17 " --> pdb=" O   LYS a  13 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL a  18 " --> pdb=" O   ARG a  14 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR a  20 " --> pdb=" O   ALA a  16 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ASN a  21 " --> pdb=" O   ARG a  17 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU a  22 " --> pdb=" O   VAL a  18 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 71 through 86
      removed outlier: 3.792A  pdb=" N   GLY a  77 " --> pdb=" O   ALA a  73 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU a  78 " --> pdb=" O   THR a  74 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 104 through 114
      removed outlier: 3.613A  pdb=" N   ALA a 112 " --> pdb=" O   LEU a 108 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 85 through 90
      removed outlier: 3.813A  pdb=" N   LYS A  85 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   THR A  27 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   GLU A  46 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   ILE A  66 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   THR A  62 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   ARG A  52 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   THR A  60 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 3 through 5
    Processing sheet with id=  C, first strand: chain 'B' and resid 114 through 116
      removed outlier: 4.261A  pdb=" N   ILE B  74 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU B  93 " --> pdb=" O   ASP B  79 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ILE B  81 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 129 through 131
    Processing sheet with id=  E, first strand: chain 'B' and resid 171 through 175
    Processing sheet with id=  F, first strand: chain 'D' and resid 11 through 14
      removed outlier: 3.608A  pdb=" N   PHE D  40 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   GLU D   6 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL D  38 " --> pdb=" O   GLU D   6 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'D' and resid 19 through 22
      removed outlier: 3.745A  pdb=" N   LYS D  64 " --> pdb=" O   LYS D  94 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'D' and resid 32 through 35
      removed outlier: 3.514A  pdb=" N   LYS D  99 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   THR D  61 " --> pdb=" O   ILE D  97 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   ILE D  97 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'D' and resid 71 through 77
      removed outlier: 4.800A  pdb=" N   SER D  82 " --> pdb=" O   LYS D  77 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'E' and resid 2 through 7
      removed outlier: 6.629A  pdb=" N   SER E 108 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   VAL E  71 " --> pdb=" O   SER E 108 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 82 through 87
    Processing sheet with id=  L, first strand: chain 'F' and resid 52 through 58
      removed outlier: 3.720A  pdb=" N   SER F  52 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ARG F  75 " --> pdb=" O   TYR F  58 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ARG F  76 " --> pdb=" O   VAL F  29 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'G' and resid 8 through 10
    Processing sheet with id=  N, first strand: chain 'G' and resid 40 through 44
      removed outlier: 3.787A  pdb=" N   THR G  59 " --> pdb=" O   MET G  41 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'G' and resid 23 through 27
      removed outlier: 6.899A  pdb=" N   VAL G  34 " --> pdb=" O   ILE G  24 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   THR G  26 " --> pdb=" O   ARG G  32 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ARG G  32 " --> pdb=" O   THR G  26 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'H' and resid 39 through 44
      removed outlier: 3.548A  pdb=" N   MET H  73 " --> pdb=" O   LEU H  92 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'H' and resid 77 through 80
      removed outlier: 3.953A  pdb=" N   HIS H  88 " --> pdb=" O   GLN H  78 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   ASP H  80 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE H  86 " --> pdb=" O   ASP H  80 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'J' and resid 13 through 16
      removed outlier: 3.519A  pdb=" N   ARG J  27 " --> pdb=" O   GLY J  15 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'J' and resid 33 through 38
      removed outlier: 3.587A  pdb=" N   VAL J  36 " --> pdb=" O   VAL J  47 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'L' and resid 179 through 183
      removed outlier: 6.103A  pdb=" N   ILE L 116 " --> pdb=" O   ASN L 182 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU L 210 " --> pdb=" O   THR L 119 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL L  27 " --> pdb=" O   ILE L  10 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   MET L  12 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL L  25 " --> pdb=" O   MET L  12 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   GLN L  14 " --> pdb=" O   ILE L  23 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ILE L  23 " --> pdb=" O   GLN L  14 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL L 194 " --> pdb=" O   ASP L 189 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN L 187 " --> pdb=" O   LEU L 196 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LYS L 198 " --> pdb=" O   VAL L 185 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL L 185 " --> pdb=" O   LYS L 198 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'L' and resid 89 through 91
      removed outlier: 3.944A  pdb=" N   GLN L  37 " --> pdb=" O   GLN L  50 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLY L  52 " --> pdb=" O   VAL L  35 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL L  35 " --> pdb=" O   GLY L  52 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'M' and resid 34 through 37
      removed outlier: 4.286A  pdb=" N   GLN M   5 " --> pdb=" O   GLU M  57 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'N' and resid 27 through 29
    Processing sheet with id=  X, first strand: chain 'O' and resid 2 through 7
      removed outlier: 3.531A  pdb=" N   LYS O  21 " --> pdb=" O   VAL O   3 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR O  19 " --> pdb=" O   VAL O   5 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'O' and resid 32 through 36
      removed outlier: 3.562A  pdb=" N   LYS O  41 " --> pdb=" O   CYS O  36 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'Q' and resid 14 through 16
    Processing sheet with id= AA, first strand: chain 'R' and resid 15 through 18
    Processing sheet with id= AB, first strand: chain 'S' and resid 123 through 126
      removed outlier: 6.398A  pdb=" N   LEU S 192 " --> pdb=" O   THR S 124 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL S 126 " --> pdb=" O   LEU S 192 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ILE S 194 " --> pdb=" O   VAL S 126 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR S 195 " --> pdb=" O   VAL S 155 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'V' and resid 16 through 20
      removed outlier: 6.704A  pdb=" N   TYR V  54 " --> pdb=" O   TYR V  17 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   ILE V  19 " --> pdb=" O   TYR V  54 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE V  56 " --> pdb=" O   ILE V  19 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'V' and resid 74 through 78
    Processing sheet with id= AE, first strand: chain 'W' and resid 7 through 9
      removed outlier: 6.663A  pdb=" N   VAL W  40 " --> pdb=" O   ILE W  22 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   VAL W  24 " --> pdb=" O   VAL W  38 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   VAL W  38 " --> pdb=" O   VAL W  24 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA W  83 " --> pdb=" O   VAL W  63 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'X' and resid 75 through 77
    Processing sheet with id= AG, first strand: chain 'X' and resid 122 through 124
      removed outlier: 6.806A  pdb=" N   ALA X 142 " --> pdb=" O   VAL X 123 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AG
    Processing sheet with id= AH, first strand: chain 'Y' and resid 33 through 36
    Processing sheet with id= AI, first strand: chain 'Y' and resid 40 through 43
      removed outlier: 3.690A  pdb=" N   ILE Y  42 " --> pdb=" O   ALA Y  95 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA Y  89 " --> pdb=" O   LYS Y  76 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   TYR Y  74 " --> pdb=" O   GLU Y  91 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   TRP Y  93 " --> pdb=" O   THR Y  72 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   THR Y  72 " --> pdb=" O   TRP Y  93 " (cutoff:3.500A)
    Processing sheet with id= AJ, first strand: chain 'Y' and resid 63 through 66
    Processing sheet with id= AK, first strand: chain 'Z' and resid 29 through 33
      removed outlier: 3.612A  pdb=" N   GLY Z 107 " --> pdb=" O   SER Z 116 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE Z 118 " --> pdb=" O   LYS Z 105 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   LYS Z 105 " --> pdb=" O   ILE Z 118 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU Z 120 " --> pdb=" O   ILE Z 103 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   ILE Z 103 " --> pdb=" O   GLU Z 120 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'a' and resid 30 through 34
      removed outlier: 3.886A  pdb=" N   ALA a  54 " --> pdb=" O   ILE a  44 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'I' and resid 74 through 79

    442 hydrogen bonds defined for protein.
    1221 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1264 hydrogen bonds
      2012 hydrogen bond angles
      0 basepair planarities
      540 basepair parallelities
      1570 stacking parallelities
  Total time for adding SS restraints: 108.24

  Time building geometry restraints manager: 31.11 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 7648
        1.31 -     1.44: 40190
        1.44 -     1.57: 35081
        1.57 -     1.70: 5600
        1.70 -     1.83: 98
  Bond restraints: 88617
  Sorted by residual:
  bond pdb=" C30 RD8 13001 "
       pdb=" O29 RD8 13001 "
    ideal  model  delta    sigma   weight residual
    1.334  1.446 -0.112 2.00e-02 2.50e+03 3.15e+01
  bond pdb=" C26 RD8 13001 "
       pdb=" N25 RD8 13001 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.81e+01
  bond pdb=" C30 RD8 13001 "
       pdb=" N21 RD8 13001 "
    ideal  model  delta    sigma   weight residual
    1.368  1.465 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" N16 RD8 13001 "
       pdb=" N17 RD8 13001 "
    ideal  model  delta    sigma   weight residual
    1.289  1.368 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" CG  ASN K   8 "
       pdb=" ND2 ASN K   8 "
    ideal  model  delta    sigma   weight residual
    1.328  1.249  0.079 2.10e-02 2.27e+03 1.41e+01
  ... (remaining 88612 not shown)

  Histogram of bond angle deviations from ideal:
       97.63 -   104.97: 12643
      104.97 -   112.31: 51546
      112.31 -   119.65: 29937
      119.65 -   127.00: 32403
      127.00 -   134.34: 6951
  Bond angle restraints: 133480
  Sorted by residual:
  angle pdb=" O3'   G 12094 "
        pdb=" C3'   G 12094 "
        pdb=" C2'   G 12094 "
      ideal   model   delta    sigma   weight residual
     109.50   97.85   11.65 1.50e+00 4.44e-01 6.03e+01
  angle pdb=" C4'   A 11866 "
        pdb=" C3'   A 11866 "
        pdb=" O3'   A 11866 "
      ideal   model   delta    sigma   weight residual
     113.00  123.90  -10.90 1.50e+00 4.44e-01 5.28e+01
  angle pdb=" O2'   A 1 849 "
        pdb=" C2'   A 1 849 "
        pdb=" C1'   A 1 849 "
      ideal   model   delta    sigma   weight residual
     108.40   97.63   10.77 1.50e+00 4.44e-01 5.15e+01
  angle pdb=" C4'   G 12657 "
        pdb=" C3'   G 12657 "
        pdb=" O3'   G 12657 "
      ideal   model   delta    sigma   weight residual
     113.00  123.50  -10.50 1.50e+00 4.44e-01 4.90e+01
  angle pdb=" N   THR Z  77 "
        pdb=" CA  THR Z  77 "
        pdb=" C   THR Z  77 "
      ideal   model   delta    sigma   weight residual
     112.24  120.60   -8.36 1.28e+00 6.10e-01 4.27e+01
  ... (remaining 133475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 50125
       35.97 -    71.95: 5777
       71.95 -   107.92: 697
      107.92 -   143.89: 14
      143.89 -   179.87: 23
  Dihedral angle restraints: 56636
    sinusoidal: 49077
      harmonic: 7559
  Sorted by residual:
  dihedral pdb=" O4'   C 2  79 "
           pdb=" C1'   C 2  79 "
           pdb=" N1    C 2  79 "
           pdb=" C2    C 2  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   20.13  179.87     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U 12607 "
           pdb=" C1'   U 12607 "
           pdb=" N1    U 12607 "
           pdb=" C2    U 12607 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   21.21  178.79     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   C 12639 "
           pdb=" C1'   C 12639 "
           pdb=" N1    C 12639 "
           pdb=" C2    C 12639 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   12.53 -172.53     1      1.50e+01 4.44e-03 8.50e+01
  ... (remaining 56633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 17071
       0.113 -    0.227: 108
       0.227 -    0.340: 17
       0.340 -    0.453: 4
       0.453 -    0.567: 2
  Chirality restraints: 17202
  Sorted by residual:
  chirality pdb=" CA  THR Z  77 "
            pdb=" N   THR Z  77 "
            pdb=" C   THR Z  77 "
            pdb=" CB  THR Z  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.96    0.57 2.00e-01 2.50e+01 8.03e+00
  chirality pdb=" CA  HIS L 143 "
            pdb=" N   HIS L 143 "
            pdb=" C   HIS L 143 "
            pdb=" CB  HIS L 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.16e+00
  chirality pdb=" C3'   G 12096 "
            pdb=" C4'   G 12096 "
            pdb=" O3'   G 12096 "
            pdb=" C2'   G 12096 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.04   -0.44 2.00e-01 2.50e+01 4.77e+00
  ... (remaining 17199 not shown)

  Planarity restraints: 6446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 1 721 "   -0.059 2.00e-02 2.50e+03   2.92e-02 2.35e+01
        pdb=" N9    A 1 721 "    0.074 2.00e-02 2.50e+03
        pdb=" C8    A 1 721 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A 1 721 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    A 1 721 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A 1 721 "   -0.012 2.00e-02 2.50e+03
        pdb=" N6    A 1 721 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A 1 721 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    A 1 721 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    A 1 721 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    A 1 721 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 11866 "   -0.045 2.00e-02 2.50e+03   2.46e-02 1.66e+01
        pdb=" N9    A 11866 "    0.067 2.00e-02 2.50e+03
        pdb=" C8    A 11866 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A 11866 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    A 11866 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    A 11866 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A 11866 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A 11866 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A 11866 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A 11866 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A 11866 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET L 141 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   MET L 141 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   MET L 141 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER L 142 "    0.021 2.00e-02 2.50e+03
  ... (remaining 6443 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 9777
        2.74 -     3.28: 65360
        3.28 -     3.82: 149207
        3.82 -     4.36: 207141
        4.36 -     4.90: 272934
  Nonbonded interactions: 704419
  Sorted by model distance:
  nonbonded pdb=" O2'   G 1 904 "
            pdb=" O6    G 1 961 "
     model   vdw
     2.203 2.440
  nonbonded pdb=" OG  SER a  36 "
            pdb=" O   HIS a  39 "
     model   vdw
     2.209 2.440
  nonbonded pdb=" OP2   U 11806 "
            pdb=" N6    A 11811 "
     model   vdw
     2.213 2.520
  nonbonded pdb=" O2'   U 12370 "
            pdb=" O2'   U 12400 "
     model   vdw
     2.217 2.440
  nonbonded pdb=" O2'   A 12060 "
            pdb=" OP2   G 12062 "
     model   vdw
     2.219 2.440
  ... (remaining 704414 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.080
  Extract box with map and model:          14.970
  Check model and map are aligned:         0.880
  Set scattering table:                    0.550
  Process input model:                     252.880
  Find NCS groups from input model:        1.310
  Set up NCS constraints:                  0.220
  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:             0.020
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  276.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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      :  0.002   0.112  88617  Z= 0.128
  Angle     :  0.450  11.648 133480  Z= 0.279
  Chirality :  0.029   0.567  17202
  Planarity :  0.003   0.036   6446
  Dihedral  : 22.726 179.866  51774
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.44 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -4.07 (0.12), residues: 2619
  helix: -4.26 (0.10), residues: 572
  sheet: -1.50 (0.21), residues: 511
  loop : -2.56 (0.12), residues: 1536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 213 
 HIS   0.003   0.001   HIS C  29 
 PHE   0.009   0.001   PHE K  30 
 TYR   0.009   0.001   TYR F  58 
 ARG   0.004   0.000   ARG N  41 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 463
  time to evaluate  : 3.305 
Fit side-chains
REVERT: A   87 GLU cc_start: 0.7468 (pt0) cc_final: 0.7197 (pt0)
REVERT: A   91 ARG cc_start: 0.6370 (mtt90) cc_final: 0.6131 (mmt90)
REVERT: A  108 LYS cc_start: 0.6186 (mtmm) cc_final: 0.4920 (mtmm)
REVERT: B  132 LEU cc_start: 0.7999 (mt) cc_final: 0.7759 (mt)
REVERT: F   65 MET cc_start: 0.4711 (mtp) cc_final: 0.4299 (tmm)
REVERT: J    3 LYS cc_start: 0.7204 (pttm) cc_final: 0.6959 (ptmt)
REVERT: L   61 LYS cc_start: 0.5547 (tptt) cc_final: 0.5284 (mttm)
REVERT: N   14 ASN cc_start: 0.8676 (m-40) cc_final: 0.8472 (m-40)
REVERT: O   46 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7813 (ttm-80)
REVERT: R   24 MET cc_start: 0.7798 (mmm) cc_final: 0.7594 (mmm)
REVERT: S  201 LYS cc_start: 0.7954 (tptm) cc_final: 0.7704 (tttt)
REVERT: S  204 GLU cc_start: 0.6582 (pp20) cc_final: 0.6114 (pp20)
REVERT: V   88 ILE cc_start: 0.8087 (mp) cc_final: 0.7769 (mt)
REVERT: V  121 LYS cc_start: 0.7979 (mttm) cc_final: 0.7651 (mttp)
REVERT: Z   19 ASP cc_start: 0.5446 (m-30) cc_final: 0.5224 (m-30)
REVERT: Z   53 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6882 (mmtp)
REVERT: Z   71 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7055 (mt)
REVERT: a   43 GLN cc_start: 0.7546 (pt0) cc_final: 0.7323 (pt0)
  outliers start: 8
  outliers final: 3
  residues processed: 470
  average time/residue: 0.8803
  time to fit residues: 676.4554
Evaluate side-chains
  363 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 359
  time to evaluate  : 3.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain Z residue   71 ILE
Chi-restraints excluded: chain Z residue   78 THR
Chi-restraints excluded: chain Z residue   79 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 454 optimal weight:    6.9990
   chunk 407 optimal weight:    6.9990
   chunk 226 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9980
   chunk 275 optimal weight:    6.9990
   chunk 217 optimal weight:   10.0000
   chunk 421 optimal weight:    5.9990
   chunk 163 optimal weight:    0.3980
   chunk 256 optimal weight:    7.9990
   chunk 313 optimal weight:    6.9990
   chunk 488 optimal weight:    7.9990
   overall best weight:    4.2786

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

Flipped N/Q/H residues before XYZ refinement:
A   3 ASN
B  82 GLN
B 200 HIS
C 108 GLN
E  61 ASN
F  69 GLN
G  64 HIS
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  69 GLN
H  13 GLN
** K  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 HIS
L 187 GLN
X  27 ASN
Y  12 GLN
Z  68 ASN
Z  97 GLN
a  37 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.131  88617  Z= 0.434
  Angle     :  0.855  10.779 133480  Z= 0.422
  Chirality :  0.048   0.367  17202
  Planarity :  0.007   0.099   6446
  Dihedral  : 23.587 179.662  46385
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.43 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -3.49 (0.14), residues: 2619
  helix: -3.16 (0.15), residues: 624
  sheet: -1.32 (0.21), residues: 539
  loop : -2.35 (0.13), residues: 1456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 213 
 HIS   0.008   0.002   HIS Q  31 
 PHE   0.020   0.003   PHE S 129 
 TYR   0.022   0.003   TYR H  32 
 ARG   0.009   0.001   ARG B  87 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 350
  time to evaluate  : 3.171 
Fit side-chains
REVERT: A  108 LYS cc_start: 0.6311 (mtmm) cc_final: 0.5001 (mtmm)
REVERT: A  113 GLN cc_start: 0.7248 (tt0) cc_final: 0.7033 (tt0)
REVERT: F   25 TYR cc_start: 0.7914 (m-80) cc_final: 0.7575 (m-80)
REVERT: F   88 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5365 (m-30)
REVERT: L   61 LYS cc_start: 0.5749 (tptt) cc_final: 0.5532 (mttm)
REVERT: O   46 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7989 (ttm-80)
REVERT: Q    6 THR cc_start: 0.8477 (t) cc_final: 0.8241 (t)
REVERT: S  201 LYS cc_start: 0.7875 (tptm) cc_final: 0.7277 (tptt)
REVERT: S  204 GLU cc_start: 0.6576 (pp20) cc_final: 0.6222 (pp20)
REVERT: V    6 MET cc_start: 0.6957 (mmt) cc_final: 0.6468 (mmt)
REVERT: V   46 THR cc_start: 0.8198 (t) cc_final: 0.7666 (m)
REVERT: V   88 ILE cc_start: 0.8165 (mp) cc_final: 0.7886 (mt)
REVERT: X  139 LYS cc_start: 0.6162 (ptpp) cc_final: 0.5956 (ptpp)
REVERT: Z   53 LYS cc_start: 0.7355 (mmtt) cc_final: 0.6986 (mmtp)
  outliers start: 68
  outliers final: 51
  residues processed: 393
  average time/residue: 0.8310
  time to fit residues: 546.6839
Evaluate side-chains
  377 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 325
  time to evaluate  : 3.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain H residue   17 ASP
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   42 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain X residue   27 ASN
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain I residue   17 SER
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 271 optimal weight:    5.9990
   chunk 151 optimal weight:    1.9990
   chunk 406 optimal weight:    5.9990
   chunk 332 optimal weight:    4.9990
   chunk 134 optimal weight:    3.9990
   chunk 489 optimal weight:    5.9990
   chunk 528 optimal weight:    7.9990
   chunk 435 optimal weight:    5.9990
   chunk 485 optimal weight:    5.9990
   chunk 166 optimal weight:    5.9990
   chunk 392 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 ASN
B 194 GLN
D  65 GLN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  69 GLN
J  23 ASN
K  17 GLN
L 182 ASN
** R  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  12 GLN
Z  68 ASN
Z  79 GLN
Z  97 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.132  88617  Z= 0.462
  Angle     :  0.887  11.340 133480  Z= 0.435
  Chirality :  0.049   0.392  17202
  Planarity :  0.007   0.104   6446
  Dihedral  : 23.718 179.715  46379
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 17.56 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -3.35 (0.14), residues: 2619
  helix: -2.83 (0.16), residues: 630
  sheet: -1.30 (0.21), residues: 551
  loop : -2.34 (0.14), residues: 1438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 213 
 HIS   0.007   0.002   HIS B 230 
 PHE   0.021   0.003   PHE D   2 
 TYR   0.023   0.003   TYR Z   3 
 ARG   0.010   0.001   ARG B  87 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  451 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 119
    poor density    : 332
  time to evaluate  : 3.242 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6145 (mt-10)
REVERT: A  108 LYS cc_start: 0.6332 (mtmm) cc_final: 0.4972 (mtmm)
REVERT: C   74 MET cc_start: 0.6227 (ptm) cc_final: 0.5852 (ptm)
REVERT: C  114 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6137 (ttpp)
REVERT: E   31 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6644 (tp30)
REVERT: F   25 TYR cc_start: 0.7872 (m-80) cc_final: 0.7537 (m-10)
REVERT: F   88 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5441 (m-30)
REVERT: L   61 LYS cc_start: 0.5948 (tptt) cc_final: 0.5706 (mttm)
REVERT: M    6 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7595 (mt)
REVERT: O   46 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7999 (ttm-80)
REVERT: S  184 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7778 (mt)
REVERT: S  201 LYS cc_start: 0.7906 (tptm) cc_final: 0.7442 (tptt)
REVERT: V   46 THR cc_start: 0.8173 (t) cc_final: 0.7652 (m)
REVERT: V   88 ILE cc_start: 0.8158 (mp) cc_final: 0.7877 (mt)
REVERT: X   51 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.4474 (pm20)
REVERT: Y    1 MET cc_start: 0.6504 (tpp) cc_final: 0.6172 (tpp)
REVERT: Z   53 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6991 (mmtp)
  outliers start: 119
  outliers final: 90
  residues processed: 415
  average time/residue: 0.8708
  time to fit residues: 611.4052
Evaluate side-chains
  422 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 97
    poor density    : 325
  time to evaluate  : 3.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   17 GLN
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   42 VAL
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   97 VAL
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  117 LEU
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   39 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain I residue   17 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 483 optimal weight:    5.9990
   chunk 367 optimal weight:    6.9990
   chunk 254 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 233 optimal weight:    0.8980
   chunk 328 optimal weight:    5.9990
   chunk 491 optimal weight:    4.9990
   chunk 520 optimal weight:   10.0000
   chunk 256 optimal weight:    6.9990
   chunk 465 optimal weight:    8.9990
   chunk 140 optimal weight:    8.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  36 GLN
X  27 ASN
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.139  88617  Z= 0.478
  Angle     :  0.907  12.056 133480  Z= 0.445
  Chirality :  0.050   0.399  17202
  Planarity :  0.007   0.104   6446
  Dihedral  : 23.765 179.790  46379
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 17.83 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -3.33 (0.14), residues: 2619
  helix: -2.74 (0.17), residues: 628
  sheet: -1.31 (0.21), residues: 554
  loop : -2.37 (0.14), residues: 1437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 213 
 HIS   0.007   0.002   HIS B 230 
 PHE   0.021   0.003   PHE W 111 
 TYR   0.022   0.003   TYR a 101 
 ARG   0.010   0.001   ARG B  87 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 158
    poor density    : 326
  time to evaluate  : 3.207 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6101 (mt-10)
REVERT: A   68 SER cc_start: 0.6389 (p) cc_final: 0.5999 (m)
REVERT: A  108 LYS cc_start: 0.6362 (mtmm) cc_final: 0.4953 (mtmm)
REVERT: E   31 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6787 (tp30)
REVERT: F   14 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5796 (tp30)
REVERT: F   25 TYR cc_start: 0.7893 (m-80) cc_final: 0.7506 (m-80)
REVERT: F   88 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.5452 (m-30)
REVERT: G   58 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4797 (pm20)
REVERT: M    6 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7664 (mt)
REVERT: M   15 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7719 (mmt-90)
REVERT: O   11 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.4803 (mp0)
REVERT: O   46 ARG cc_start: 0.8238 (ttm110) cc_final: 0.8021 (ttm-80)
REVERT: S   82 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8484 (pt0)
REVERT: S  151 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7689 (mtpt)
REVERT: S  184 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7851 (mt)
REVERT: S  201 LYS cc_start: 0.7942 (tptm) cc_final: 0.7364 (tptt)
REVERT: V   88 ILE cc_start: 0.8208 (mp) cc_final: 0.7927 (mt)
REVERT: X   51 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.4528 (pm20)
REVERT: Y    1 MET cc_start: 0.6550 (tpp) cc_final: 0.6347 (tpt)
REVERT: Z   53 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6918 (mmtp)
  outliers start: 158
  outliers final: 120
  residues processed: 442
  average time/residue: 0.7914
  time to fit residues: 592.5046
Evaluate side-chains
  462 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 131
    poor density    : 331
  time to evaluate  : 3.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue   11 GLU
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   42 VAL
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue   82 GLN
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  145 THR
Chi-restraints excluded: chain S residue  151 LYS
Chi-restraints excluded: chain S residue  152 VAL
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  186 ILE
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   77 ILE
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain W residue  115 VAL
Chi-restraints excluded: chain X residue   27 ASN
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue   97 VAL
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  117 LEU
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain X residue  131 SER
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   39 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  101 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 433 optimal weight:    6.9990
   chunk 295 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 387 optimal weight:    6.9990
   chunk 214 optimal weight:    2.9990
   chunk 443 optimal weight:    3.9990
   chunk 359 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 265 optimal weight:    8.9990
   chunk 466 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  88617  Z= 0.294
  Angle     :  0.704  10.960 133480  Z= 0.357
  Chirality :  0.042   0.348  17202
  Planarity :  0.006   0.073   6446
  Dihedral  : 23.523 178.389  46379
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 19.76 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -3.05 (0.14), residues: 2619
  helix: -2.42 (0.18), residues: 630
  sheet: -1.10 (0.21), residues: 549
  loop : -2.24 (0.14), residues: 1440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 213 
 HIS   0.006   0.001   HIS C  29 
 PHE   0.014   0.002   PHE W 111 
 TYR   0.018   0.002   TYR a 101 
 ARG   0.006   0.001   ARG I  79 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 134
    poor density    : 337
  time to evaluate  : 3.376 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6010 (mt-10)
REVERT: A  108 LYS cc_start: 0.6316 (mtmm) cc_final: 0.4926 (mtmm)
REVERT: C  114 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6104 (ttpp)
REVERT: E   31 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6786 (tp30)
REVERT: F   14 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5776 (tp30)
REVERT: F   25 TYR cc_start: 0.7894 (m-80) cc_final: 0.7660 (m-80)
REVERT: F   88 ASP cc_start: 0.5475 (OUTLIER) cc_final: 0.5165 (m-30)
REVERT: G   58 GLU cc_start: 0.5190 (OUTLIER) cc_final: 0.4773 (pm20)
REVERT: M    6 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7577 (mt)
REVERT: M   15 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7870 (mmt-90)
REVERT: M   46 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7588 (mt0)
REVERT: O   46 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7895 (ttm-80)
REVERT: S  184 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (mt)
REVERT: S  201 LYS cc_start: 0.7918 (tptm) cc_final: 0.7491 (tptt)
REVERT: V   46 THR cc_start: 0.7985 (t) cc_final: 0.7528 (m)
REVERT: V   88 ILE cc_start: 0.8186 (mp) cc_final: 0.7912 (mt)
REVERT: X   51 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.4292 (pm20)
REVERT: Y    1 MET cc_start: 0.6560 (tpp) cc_final: 0.6353 (tpp)
REVERT: Z   53 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6915 (mmtp)
  outliers start: 134
  outliers final: 102
  residues processed: 433
  average time/residue: 0.7935
  time to fit residues: 577.8125
Evaluate side-chains
  444 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 112
    poor density    : 332
  time to evaluate  : 3.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   52 MET
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   11 THR
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   30 CYS
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   38 ASN
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  196 GLU
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   37 ASP
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue  116 SER
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue  117 LEU
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 174 optimal weight:    6.9990
   chunk 468 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 305 optimal weight:    6.9990
   chunk 128 optimal weight:    4.9990
   chunk 520 optimal weight:    9.9990
   chunk 432 optimal weight:    9.9990
   chunk 241 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 172 optimal weight:    5.9990
   chunk 273 optimal weight:    7.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  68 ASN
Z  97 GLN
a  43 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.153  88617  Z= 0.557
  Angle     :  0.999  12.716 133480  Z= 0.484
  Chirality :  0.054   0.411  17202
  Planarity :  0.008   0.119   6446
  Dihedral  : 23.900 179.818  46379
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 18.91 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -3.36 (0.14), residues: 2619
  helix: -2.70 (0.17), residues: 628
  sheet: -1.31 (0.21), residues: 545
  loop : -2.41 (0.14), residues: 1446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 213 
 HIS   0.008   0.002   HIS B 230 
 PHE   0.026   0.003   PHE W 111 
 TYR   0.025   0.003   TYR a 101 
 ARG   0.012   0.001   ARG B  87 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  527 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 186
    poor density    : 341
  time to evaluate  : 4.796 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6274 (mt-10)
REVERT: A  106 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6093 (ttm-80)
REVERT: A  108 LYS cc_start: 0.6526 (mtmm) cc_final: 0.5059 (mtmm)
REVERT: C  114 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6192 (ttpp)
REVERT: E   31 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6839 (tp30)
REVERT: F   14 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5866 (tp30)
REVERT: F   25 TYR cc_start: 0.7953 (m-80) cc_final: 0.7534 (m-80)
REVERT: F   88 ASP cc_start: 0.5717 (OUTLIER) cc_final: 0.5447 (m-30)
REVERT: G   58 GLU cc_start: 0.5274 (OUTLIER) cc_final: 0.4816 (pm20)
REVERT: M    6 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7684 (mt)
REVERT: M   15 ARG cc_start: 0.8231 (mmt-90) cc_final: 0.7861 (mmt-90)
REVERT: M   46 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7660 (mt0)
REVERT: S  151 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7317 (mtpt)
REVERT: S  184 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7862 (mt)
REVERT: S  201 LYS cc_start: 0.7965 (tptm) cc_final: 0.7369 (tptt)
REVERT: V   88 ILE cc_start: 0.8205 (mp) cc_final: 0.7920 (mt)
REVERT: X   51 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.4591 (pm20)
REVERT: Z   53 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6931 (mmtp)
REVERT: a    4 LYS cc_start: 0.4215 (mtpt) cc_final: 0.3304 (tppt)
  outliers start: 186
  outliers final: 151
  residues processed: 482
  average time/residue: 0.8027
  time to fit residues: 657.4026
Evaluate side-chains
  500 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 163
    poor density    : 337
  time to evaluate  : 3.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   52 MET
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   57 LEU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   68 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   17 ASP
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   62 GLU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   11 THR
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   96 VAL
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  176 ASN
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   14 ASP
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   42 VAL
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  151 LYS
Chi-restraints excluded: chain S residue  152 VAL
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  186 ILE
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain S residue  196 GLU
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   37 ASP
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   77 ILE
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain W residue  116 SER
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue   97 VAL
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  116 SER
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   31 GLU
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   39 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   34 GLU
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  101 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 501 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 296 optimal weight:    6.9990
   chunk 380 optimal weight:    3.9990
   chunk 294 optimal weight:    6.9990
   chunk 438 optimal weight:    3.9990
   chunk 290 optimal weight:    8.9990
   chunk 518 optimal weight:    4.9990
   chunk 324 optimal weight:    7.9990
   chunk 316 optimal weight:    4.9990
   chunk 239 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  90 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN
S  82 GLN
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.104  88617  Z= 0.373
  Angle     :  0.795  11.134 133480  Z= 0.400
  Chirality :  0.046   0.373  17202
  Planarity :  0.006   0.081   6446
  Dihedral  : 23.780 178.988  46379
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 20.07 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -3.23 (0.14), residues: 2619
  helix: -2.49 (0.18), residues: 629
  sheet: -1.28 (0.21), residues: 548
  loop : -2.36 (0.14), residues: 1442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP B 213 
 HIS   0.006   0.002   HIS B 230 
 PHE   0.018   0.002   PHE V   5 
 TYR   0.026   0.002   TYR a 101 
 ARG   0.008   0.001   ARG I  79 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  504 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 168
    poor density    : 336
  time to evaluate  : 3.415 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6059 (mt-10)
REVERT: A   68 SER cc_start: 0.6588 (p) cc_final: 0.6217 (m)
REVERT: A  106 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6025 (ttm-80)
REVERT: A  108 LYS cc_start: 0.6490 (mtmm) cc_final: 0.5043 (mtmm)
REVERT: C  114 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6133 (ttpp)
REVERT: E   31 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6820 (tp30)
REVERT: F   14 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5861 (tp30)
REVERT: F   25 TYR cc_start: 0.7908 (m-80) cc_final: 0.7629 (m-80)
REVERT: F   88 ASP cc_start: 0.5615 (OUTLIER) cc_final: 0.5269 (m-30)
REVERT: G   58 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4807 (pm20)
REVERT: L  210 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6690 (mp0)
REVERT: M    6 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7630 (mt)
REVERT: M   15 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7881 (mmt-90)
REVERT: M   46 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (mt0)
REVERT: O   39 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6343 (mp0)
REVERT: S  184 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7854 (mt)
REVERT: S  201 LYS cc_start: 0.7943 (tptm) cc_final: 0.7453 (tptt)
REVERT: V   46 THR cc_start: 0.8207 (t) cc_final: 0.7698 (m)
REVERT: V   88 ILE cc_start: 0.8189 (mp) cc_final: 0.7910 (mt)
REVERT: X   51 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.4425 (pm20)
REVERT: Y   31 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6590 (mm-30)
REVERT: Z   53 LYS cc_start: 0.7274 (mmtt) cc_final: 0.6849 (mmtp)
  outliers start: 168
  outliers final: 135
  residues processed: 461
  average time/residue: 0.7799
  time to fit residues: 610.0160
Evaluate side-chains
  482 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 149
    poor density    : 333
  time to evaluate  : 3.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   52 MET
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   57 LEU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   11 THR
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   96 VAL
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   14 ASP
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain O residue   39 GLU
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   42 VAL
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   38 ASN
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  145 THR
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  186 ILE
Chi-restraints excluded: chain S residue  196 GLU
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain V residue  133 HIS
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   37 ASP
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain W residue  115 VAL
Chi-restraints excluded: chain W residue  116 SER
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  116 SER
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain X residue  131 SER
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   31 GLU
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   34 GLU
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 320 optimal weight:    4.9990
   chunk 207 optimal weight:    1.9990
   chunk 309 optimal weight:    4.9990
   chunk 156 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 329 optimal weight:    5.9990
   chunk 353 optimal weight:    7.9990
   chunk 256 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 407 optimal weight:    5.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
E  61 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096  88617  Z= 0.334
  Angle     :  0.773  11.003 133480  Z= 0.387
  Chirality :  0.044   0.369  17202
  Planarity :  0.006   0.083   6446
  Dihedral  : 23.677 178.819  46379
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 20.34 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    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: -3.11 (0.14), residues: 2619
  helix: -2.38 (0.18), residues: 630
  sheet: -1.19 (0.21), residues: 543
  loop : -2.30 (0.14), residues: 1446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 213 
 HIS   0.007   0.001   HIS C  29 
 PHE   0.017   0.002   PHE V   5 
 TYR   0.023   0.002   TYR a 101 
 ARG   0.009   0.001   ARG I  79 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 165
    poor density    : 328
  time to evaluate  : 3.221 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6055 (mt-10)
REVERT: A  106 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6068 (ttm-80)
REVERT: A  108 LYS cc_start: 0.6531 (mtmm) cc_final: 0.5050 (mtmm)
REVERT: C  114 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6201 (ttpp)
REVERT: E   31 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6793 (tp30)
REVERT: F   14 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5794 (tp30)
REVERT: F   25 TYR cc_start: 0.7912 (m-80) cc_final: 0.7622 (m-80)
REVERT: F   88 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.5207 (m-30)
REVERT: G   58 GLU cc_start: 0.5229 (OUTLIER) cc_final: 0.4806 (pm20)
REVERT: L  210 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6719 (mp0)
REVERT: M    6 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7616 (mt)
REVERT: M   46 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7635 (mt0)
REVERT: S  184 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7837 (mt)
REVERT: S  201 LYS cc_start: 0.7934 (tptm) cc_final: 0.7465 (tptt)
REVERT: V   46 THR cc_start: 0.8106 (t) cc_final: 0.7611 (m)
REVERT: V   88 ILE cc_start: 0.8174 (mp) cc_final: 0.7894 (mt)
REVERT: X   51 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.4432 (pm20)
REVERT: Z   53 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6909 (mmtp)
  outliers start: 165
  outliers final: 141
  residues processed: 451
  average time/residue: 0.7927
  time to fit residues: 606.5322
Evaluate side-chains
  480 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 153
    poor density    : 327
  time to evaluate  : 3.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   52 MET
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   57 LEU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   11 THR
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   96 VAL
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  190 THR
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   14 ASP
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   24 MET
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   38 ASN
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  145 THR
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  186 ILE
Chi-restraints excluded: chain S residue  196 GLU
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain V residue  133 HIS
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   37 ASP
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   77 ILE
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain W residue  115 VAL
Chi-restraints excluded: chain W residue  116 SER
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain X residue  131 SER
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   31 GLU
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   26 ILE
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  101 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   57 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 471 optimal weight:    7.9990
   chunk 496 optimal weight:    8.9990
   chunk 453 optimal weight:    7.9990
   chunk 483 optimal weight:    6.9990
   chunk 290 optimal weight:   10.0000
   chunk 210 optimal weight:    4.9990
   chunk 379 optimal weight:    6.9990
   chunk 148 optimal weight:    3.9990
   chunk 436 optimal weight:    6.9990
   chunk 457 optimal weight:    5.9990
   chunk 481 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  61 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.160  88617  Z= 0.575
  Angle     :  1.017  13.120 133480  Z= 0.493
  Chirality :  0.055   0.424  17202
  Planarity :  0.008   0.124   6446
  Dihedral  : 23.913 179.991  46379
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  7.93 %
    Allowed  : 19.98 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -3.40 (0.14), residues: 2619
  helix: -2.69 (0.17), residues: 630
  sheet: -1.38 (0.21), residues: 547
  loop : -2.44 (0.14), residues: 1442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.004   TRP B 213 
 HIS   0.008   0.002   HIS B 230 
 PHE   0.029   0.004   PHE W 111 
 TYR   0.027   0.003   TYR a 101 
 ARG   0.012   0.001   ARG B  87 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  501 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 177
    poor density    : 324
  time to evaluate  : 3.292 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6250 (mt-10)
REVERT: A  106 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6170 (ttm-80)
REVERT: A  108 LYS cc_start: 0.6544 (mtmm) cc_final: 0.5058 (mtmm)
REVERT: C  114 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6166 (ttpp)
REVERT: E   31 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6841 (tp30)
REVERT: F   14 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5832 (tp30)
REVERT: F   25 TYR cc_start: 0.7943 (m-80) cc_final: 0.7665 (m-80)
REVERT: F   88 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5345 (m-30)
REVERT: G   58 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4799 (pm20)
REVERT: K   17 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6903 (mp10)
REVERT: M    6 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7684 (mt)
REVERT: M   46 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7674 (mt0)
REVERT: O   39 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6388 (mp0)
REVERT: S  184 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7876 (mt)
REVERT: S  201 LYS cc_start: 0.8009 (tptm) cc_final: 0.7387 (tptt)
REVERT: V   70 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6138 (pt0)
REVERT: V   88 ILE cc_start: 0.8195 (mp) cc_final: 0.7913 (mt)
REVERT: X   51 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.4745 (pm20)
REVERT: Z   53 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6874 (mmtp)
REVERT: I   25 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5735 (tt0)
  outliers start: 177
  outliers final: 153
  residues processed: 464
  average time/residue: 0.7885
  time to fit residues: 622.2083
Evaluate side-chains
  486 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 168
    poor density    : 318
  time to evaluate  : 3.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  114 LYS
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   12 ILE
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   52 MET
Chi-restraints excluded: chain F residue   14 GLU
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   23 ASP
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain J residue   14 THR
Chi-restraints excluded: chain J residue   47 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   11 THR
Chi-restraints excluded: chain K residue   17 GLN
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   40 THR
Chi-restraints excluded: chain L residue   96 VAL
Chi-restraints excluded: chain L residue  103 GLN
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  190 THR
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  209 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   14 ASP
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain O residue   39 GLU
Chi-restraints excluded: chain P residue    2 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain S residue   23 VAL
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   70 THR
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  142 VAL
Chi-restraints excluded: chain S residue  145 THR
Chi-restraints excluded: chain S residue  152 VAL
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  184 LEU
Chi-restraints excluded: chain S residue  196 GLU
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   42 LYS
Chi-restraints excluded: chain V residue   63 ILE
Chi-restraints excluded: chain V residue   70 GLU
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain V residue  133 HIS
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   37 ASP
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue   77 ILE
Chi-restraints excluded: chain W residue   85 VAL
Chi-restraints excluded: chain W residue  115 VAL
Chi-restraints excluded: chain W residue  116 SER
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   87 ASP
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  116 SER
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain X residue  131 SER
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   31 GLU
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   34 GLU
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   89 ILE
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  101 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   57 SER
Chi-restraints excluded: chain I residue   25 GLU
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 317 optimal weight:    3.9990
   chunk 510 optimal weight:    6.9990
   chunk 311 optimal weight:    0.9990
   chunk 242 optimal weight:    0.8980
   chunk 355 optimal weight:   10.0000
   chunk 535 optimal weight:    0.7980
   chunk 493 optimal weight:    1.9990
   chunk 426 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 329 optimal weight:    3.9990
   chunk 261 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
E  61 ASN
G  44 HIS
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  12 GLN
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  88617  Z= 0.201
  Angle     :  0.622   9.910 133480  Z= 0.320
  Chirality :  0.038   0.331  17202
  Planarity :  0.005   0.068   6446
  Dihedral  : 23.447 178.139  46379
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 22.09 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.14), residues: 2619
  helix: -2.15 (0.18), residues: 627
  sheet: -1.11 (0.22), residues: 540
  loop : -2.22 (0.14), residues: 1452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 213 
 HIS   0.007   0.001   HIS C  29 
 PHE   0.012   0.002   PHE S 129 
 TYR   0.017   0.002   TYR a 101 
 ARG   0.009   0.000   ARG I  79 

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

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

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5238 Ramachandran restraints generated.
    2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  469 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 129
    poor density    : 340
  time to evaluate  : 3.307 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6070 (mt-10)
REVERT: A  106 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6015 (ttm-80)
REVERT: A  108 LYS cc_start: 0.6504 (mtmm) cc_final: 0.5032 (mtmm)
REVERT: E   31 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6752 (tp30)
REVERT: F   25 TYR cc_start: 0.7790 (m-80) cc_final: 0.7463 (m-80)
REVERT: F   88 ASP cc_start: 0.5486 (OUTLIER) cc_final: 0.5210 (m-30)
REVERT: G   58 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.4694 (pm20)
REVERT: K   17 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6978 (mp10)
REVERT: L  123 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5028 (mmtt)
REVERT: L  210 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6636 (mp0)
REVERT: M    6 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7586 (mt)
REVERT: M   15 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7882 (mmt-90)
REVERT: M   46 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7610 (mt0)
REVERT: O   39 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6292 (mp0)
REVERT: S  201 LYS cc_start: 0.7897 (tptm) cc_final: 0.7399 (tptt)
REVERT: V   46 THR cc_start: 0.7842 (t) cc_final: 0.7503 (m)
REVERT: V   70 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6053 (pt0)
REVERT: V   88 ILE cc_start: 0.8125 (mp) cc_final: 0.7852 (mt)
REVERT: X   51 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.4133 (pm20)
REVERT: Y   31 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6082 (mt-10)
REVERT: Z   17 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8462 (mt)
REVERT: Z   53 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6863 (mmtp)
  outliers start: 129
  outliers final: 101
  residues processed: 435
  average time/residue: 0.8094
  time to fit residues: 598.5215
Evaluate side-chains
  447 residues out of total 2233 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 116
    poor density    : 331
  time to evaluate  : 3.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue   31 GLU
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   20 MET
Chi-restraints excluded: chain F residue   33 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   84 GLU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   20 GLN
Chi-restraints excluded: chain H residue   27 VAL
Chi-restraints excluded: chain H residue   46 VAL
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain K residue    9 LEU
Chi-restraints excluded: chain K residue   17 GLN
Chi-restraints excluded: chain K residue   37 LEU
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  123 LYS
Chi-restraints excluded: chain L residue  142 SER
Chi-restraints excluded: chain L residue  145 SER
Chi-restraints excluded: chain L residue  161 SER
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain L residue  214 SER
Chi-restraints excluded: chain M residue    6 ILE
Chi-restraints excluded: chain M residue   36 VAL
Chi-restraints excluded: chain M residue   46 GLN
Chi-restraints excluded: chain M residue   47 ILE
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   33 CYS
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   14 ASP
Chi-restraints excluded: chain O residue   20 THR
Chi-restraints excluded: chain O residue   39 GLU
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   15 LYS
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   24 MET
Chi-restraints excluded: chain S residue   49 HIS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  112 SER
Chi-restraints excluded: chain S residue  115 SER
Chi-restraints excluded: chain S residue  124 THR
Chi-restraints excluded: chain S residue  145 THR
Chi-restraints excluded: chain S residue  166 SER
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  203 GLU
Chi-restraints excluded: chain V residue   29 LEU
Chi-restraints excluded: chain V residue   70 GLU
Chi-restraints excluded: chain V residue   71 THR
Chi-restraints excluded: chain V residue   96 THR
Chi-restraints excluded: chain V residue  133 HIS
Chi-restraints excluded: chain W residue    1 MET
Chi-restraints excluded: chain W residue   32 THR
Chi-restraints excluded: chain W residue   63 VAL
Chi-restraints excluded: chain W residue   73 ASP
Chi-restraints excluded: chain W residue  115 VAL
Chi-restraints excluded: chain X residue   51 GLU
Chi-restraints excluded: chain X residue   69 ILE
Chi-restraints excluded: chain X residue   89 THR
Chi-restraints excluded: chain X residue  104 ASN
Chi-restraints excluded: chain X residue  116 SER
Chi-restraints excluded: chain X residue  118 ASP
Chi-restraints excluded: chain Y residue   31 GLU
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   94 ILE
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  132 VAL
Chi-restraints excluded: chain Z residue   17 LEU
Chi-restraints excluded: chain Z residue   23 SER
Chi-restraints excluded: chain Z residue   33 THR
Chi-restraints excluded: chain Z residue   72 LEU
Chi-restraints excluded: chain Z residue   80 THR
Chi-restraints excluded: chain Z residue   88 GLU
Chi-restraints excluded: chain Z residue   94 THR
Chi-restraints excluded: chain Z residue  101 THR
Chi-restraints excluded: chain Z residue  122 VAL
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   40 ILE
Chi-restraints excluded: chain a residue   57 SER
Chi-restraints excluded: chain I residue   45 LEU
Chi-restraints excluded: chain I residue   72 ASP
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 538
   random chunks:
   chunk 339 optimal weight:    6.9990
   chunk 454 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 393 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 427 optimal weight:   10.0000
   chunk 178 optimal weight:    0.8980
   chunk 438 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
E  61 ASN
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  68 ASN
Z  97 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.152540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.131719 restraints weight = 91870.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 0.78
r_work: 0.3095 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091  88617  Z= 0.327
  Angle     :  0.739  10.491 133480  Z= 0.371
  Chirality :  0.043   0.342  17202
  Planarity :  0.006   0.077   6446
  Dihedral  : 23.567 179.023  46379
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 21.77 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.37 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.14), residues: 2619
  helix: -2.22 (0.18), residues: 631
  sheet: -1.13 (0.22), residues: 540
  loop : -2.24 (0.14), residues: 1448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 213 
 HIS   0.006   0.001   HIS C  29 
 PHE   0.018   0.002   PHE W 111 
 TYR   0.021   0.002   TYR a 101 
 ARG   0.010   0.001   ARG I  79 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11617.70 seconds
wall clock time: 209 minutes 4.16 seconds (12544.16 seconds total)