Starting phenix.real_space_refine
on Fri Dec 15 02:54:02 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fn2_29304/12_2023/8fn2_29304.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.039
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
     Zn      2      6.06       5
     P    2874      5.49       5
     S      96      5.16       5
     C   45288      2.51       5
     N   16563      2.21       5
     O   24919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "D TYR   15": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   40": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   67": "OD1" <-> "OD2"
    Residue "D PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  100": "OD1" <-> "OD2"
    Residue "D GLU  102": "OE1" <-> "OE2"
    Residue "D PHE  187": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP   54": "OD1" <-> "OD2"
    Residue "E ASP   90": "OD1" <-> "OD2"
    Residue "E ASP  107": "OD1" <-> "OD2"
    Residue "E PHE  117": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  181": "OE1" <-> "OE2"
    Residue "E PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP   20": "OD1" <-> "OD2"
    Residue "F PHE   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   55": "OE1" <-> "OE2"
    Residue "F ASP  119": "OD1" <-> "OD2"
    Residue "F PHE  149": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  160": "OD1" <-> "OD2"
    Residue "F PHE  188": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  206": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  207": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   45": "OE1" <-> "OE2"
    Residue "G TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  117": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  150": "OE1" <-> "OE2"
    Residue "G PHE  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG    3": "NH1" <-> "NH2"
    Residue "H GLU   27": "OE1" <-> "OE2"
    Residue "H ASP   36": "OD1" <-> "OD2"
    Residue "H ASP   58": "OD1" <-> "OD2"
    Residue "H TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  113": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  137": "OD1" <-> "OD2"
    Residue "H ASP  165": "OD1" <-> "OD2"
    Residue "I PHE   25": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   22": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ASP   25": "OD1" <-> "OD2"
    Residue "L ASP   28": "OD1" <-> "OD2"
    Residue "L TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ASP   55": "OD1" <-> "OD2"
    Residue "L TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP   12": "OD1" <-> "OD2"
    Residue "M ASP   56": "OD1" <-> "OD2"
    Residue "M TYR   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP   88": "OD1" <-> "OD2"
    Residue "M PHE   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  120": "OE1" <-> "OE2"
    Residue "N PHE    2": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR    9": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O GLU   38": "OE1" <-> "OE2"
    Residue "O PHE   69": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ASP   91": "OD1" <-> "OD2"
    Residue "O PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE   69": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ASP  106": "OD1" <-> "OD2"
    Residue "P GLU  117": "OE1" <-> "OE2"
    Residue "Q PHE   35": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ASP   48": "OD1" <-> "OD2"
    Residue "Q TYR   99": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE  108": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE  115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU   37": "OE1" <-> "OE2"
    Residue "R GLU   43": "OE1" <-> "OE2"
    Residue "R TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ASP   49": "OD1" <-> "OD2"
    Residue "S PHE   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ASP   23": "OD1" <-> "OD2"
    Residue "T GLU   29": "OE1" <-> "OE2"
    Residue "T TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   95": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP   26": "OD1" <-> "OD2"
    Residue "U TYR   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP   99": "OD1" <-> "OD2"
    Residue "U PHE  109": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ASP  113": "OD1" <-> "OD2"
    Residue "V TYR    4": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU   14": "OE1" <-> "OE2"
    Residue "V TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU   45": "OE1" <-> "OE2"
    Residue "V TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   88": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W ASP   60": "OD1" <-> "OD2"
    Residue "W GLU   62": "OE1" <-> "OE2"
    Residue "W PHE   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X ASP   66": "OD1" <-> "OD2"
    Residue "X PHE   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X GLU  119": "OE1" <-> "OE2"
    Residue "X PHE  142": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU   35": "OE1" <-> "OE2"
    Residue "Y ASP   56": "OD1" <-> "OD2"
    Residue "Y GLU   68": "OE1" <-> "OE2"
    Residue "Y PHE   69": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y TYR   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z PHE   14": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z PHE   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "a ASP   11": "OD1" <-> "OD2"
    Residue "b PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "b PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "b PHE   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c GLU   33": "OE1" <-> "OE2"
    Residue "c TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "c PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d PHE    6": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "d TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "e GLU   11": "OE1" <-> "OE2"
    Residue "e GLU   36": "OE1" <-> "OE2"
    Residue "e GLU   39": "OE1" <-> "OE2"
    Residue "e TYR   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "f PHE   18": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g TYR   25": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "g PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "i GLU   15": "OE1" <-> "OE2"
  Time to flip residues: 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 89742
  Number of models: 1
  Model: ""
    Number of chains: 36
    Chain: "A"
      Number of atoms: 59248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2762, 59248
          Classifications: {'RNA': 2762}
          Modifications used: {'rna2p_pur': 288, 'rna2p_pyr': 139, 'rna3p_pur': 1337, 'rna3p_pyr': 998}
          Link IDs: {'rna2p': 427, 'rna3p': 2334}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2398
          Classifications: {'RNA': 112}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 53, 'rna3p_pyr': 40}
          Link IDs: {'rna2p': 19, 'rna3p': 92}
    Chain: "D"
      Number of atoms: 2156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2156
          Classifications: {'peptide': 277}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 261}
    Chain: "E"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1564
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
    Chain: "F"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1658
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 203}
    Chain: "G"
      Number of atoms: 1439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1439
          Classifications: {'peptide': 182}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 177}
    Chain: "H"
      Number of atoms: 1405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1405
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 174}
    Chain: "I"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 411
          Classifications: {'peptide': 63}
          Incomplete info: {'backbone_only': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 61}
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 51
    Chain: "J"
      Number of atoms: 528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 528
          Classifications: {'peptide': 132}
          Incomplete info: {'backbone_only': 125}
          Link IDs: {'PTRANS': 2, 'TRANS': 129}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 532
          Unresolved non-hydrogen angles: 761
          Unresolved non-hydrogen dihedrals: 335
          Unresolved non-hydrogen chiralities: 167
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 6, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 216
    Chain: "K"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 272
          Classifications: {'peptide': 68}
          Incomplete info: {'backbone_only': 63}
          Link IDs: {'TRANS': 67}
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 325
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 80
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 57
    Chain: "L"
      Number of atoms: 1171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1171
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 136}
    Chain: "M"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 942
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "N"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1129
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
    Chain: "O"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1092
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
    Chain: "P"
      Number of atoms: 1004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1004
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "Q"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 968
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
    Chain: "R"
      Number of atoms: 951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 951
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
    Chain: "S"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 943
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 113}
    Chain: "T"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 859
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 100}
    Chain: "U"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 918
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
    Chain: "V"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 784
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "W"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 800
          Classifications: {'peptide': 101}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 99}
    Chain: "X"
      Number of atoms: 1432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1432
          Classifications: {'peptide': 181}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 174}
    Chain: "Y"
      Number of atoms: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 571
          Classifications: {'peptide': 74}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 73}
    Chain: "Z"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 705
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "a"
      Number of atoms: 553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 553
          Classifications: {'peptide': 65}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 63}
    Chain: "b"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 814
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 99}
    Chain: "c"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 466
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 3, 'TRANS': 54}
    Chain: "d"
      Number of atoms: 484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 484
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 3, 'TRANS': 55}
    Chain: "e"
      Number of atoms: 425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 425
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 49}
    Chain: "f"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 422
          Classifications: {'peptide': 50}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "g"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 548
          Classifications: {'peptide': 66}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 64}
    Chain: "h"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 305
          Classifications: {'peptide': 37}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
    Chain: "i"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 375
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "d"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "h"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  87432  SG  CYS d  31      90.601 196.647  80.075  1.00 66.40           S
  ATOM  87452  SG  CYS d  34      92.307 196.363  76.612  1.00 78.21           S
  ATOM  87529  SG  CYS d  44      93.978 194.860  79.511  1.00 67.59           S
  ATOM  87552  SG  CYS d  47      93.744 198.614  79.314  1.00 72.45           S
  ATOM  89145  SG  CYS h  11      56.544 108.324 143.679  1.00 72.05           S
  ATOM  89169  SG  CYS h  14      57.774 109.865 140.484  1.00 77.57           S
  ATOM  89274  SG  CYS h  27      55.232 111.803 142.555  1.00 74.97           S

  Residues with excluded nonbonded symmetry interactions: 10
    residue:
      pdb=" N   ALA I  60 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   ALA I  60 " occ=0.00
    residue:
      pdb=" N   LYS I  61 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   LYS I  61 " occ=0.00
    residue:
      pdb=" N   LYS I  62 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   LYS I  62 " occ=0.00
    residue:
      pdb=" N   GLN I  63 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLN I  63 " occ=0.00
    residue:
      pdb=" N   ASN L   2 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN L   2 " occ=0.00
    residue:
      pdb=" N   LYS L   3 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS L   3 " occ=0.00
    residue:
      pdb=" N   ILE L   4 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD1 ILE L   4 " occ=0.00
    residue:
      pdb=" N   THR L   5 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR L   5 " occ=0.00
    residue:
      pdb=" N   ASN L   6 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN L   6 " occ=0.00
    residue:
      pdb=" N   ASN L   7 " occ=0.00
      ... (6 atoms not shown)
      pdb=" ND2 ASN L   7 " occ=0.00
  Time building chain proxies: 38.28, per 1000 atoms: 0.43
  Number of scatterers: 89742
  At special positions: 0
  Unit cell: (245.526, 233.469, 188.529, 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)
     Zn      2     29.99
     S      96     16.00
     P    2874     15.00
     O   24919      8.00
     N   16563      7.00
     C   45288      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS e  17 " - pdb=" SG  CYS e  44 " distance=2.05

  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: 37.78
  Conformation dependent library (CDL) restraints added in 5.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN d 101 "
        pdb="ZN    ZN d 101 " - pdb=" SG  CYS d  34 "
        pdb="ZN    ZN d 101 " - pdb=" SG  CYS d  44 "
        pdb="ZN    ZN d 101 " - pdb=" SG  CYS d  47 "
        pdb="ZN    ZN d 101 " - pdb=" SG  CYS d  31 "
      pdb="  ZN h 101 "
        pdb="ZN    ZN h 101 " - pdb=" ND1 HIS h  32 "
        pdb="ZN    ZN h 101 " - pdb=" SG  CYS h  14 "
        pdb="ZN    ZN h 101 " - pdb=" SG  CYS h  11 "
        pdb="ZN    ZN h 101 " - pdb=" SG  CYS h  27 "
      Number of angles added : 9


  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6278

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 53 sheets defined
      31.5% alpha, 22.3% beta
      732 base pairs and 1647 stacking pairs defined.
    Time for finding SS restraints: 32.57
  Creating SS restraints...
    Processing helix  chain 'D' and resid 12 through 15
      removed outlier: 4.079A  pdb=" N   TYR D  15 " --> pdb=" O   SER D  12 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 12 through 15'
    Processing helix  chain 'D' and resid 31 through 33
      No H-bonds generated for 'chain 'D' and resid 31 through 33'
    Processing helix  chain 'D' and resid 70 through 74
    Processing helix  chain 'D' and resid 209 through 216
      removed outlier: 3.543A  pdb=" N   SER D 213 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 269
      removed outlier: 3.593A  pdb=" N   ASP D 268 " --> pdb=" O   ARG D 265 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LYS D 269 " --> pdb=" O   TYR D 266 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 265 through 269'
    Processing helix  chain 'E' and resid 56 through 60
      removed outlier: 4.150A  pdb=" N   VAL E  60 " --> pdb=" O   SER E  57 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 68
      removed outlier: 3.804A  pdb=" N   TYR E  68 " --> pdb=" O   ILE E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 101
      removed outlier: 3.934A  pdb=" N   VAL E  99 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE E 100 " --> pdb=" O   VAL E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 119 through 125
    Processing helix  chain 'F' and resid 19 through 24
    Processing helix  chain 'F' and resid 28 through 42
    Processing helix  chain 'F' and resid 101 through 118
    Processing helix  chain 'F' and resid 136 through 147
    Processing helix  chain 'F' and resid 161 through 169
    Processing helix  chain 'F' and resid 180 through 182
      No H-bonds generated for 'chain 'F' and resid 180 through 182'
    Processing helix  chain 'F' and resid 183 through 190
    Processing helix  chain 'F' and resid 197 through 209
      removed outlier: 4.099A  pdb=" N   LYS F 209 " --> pdb=" O   GLU F 205 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 14
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 27 through 31
    Processing helix  chain 'G' and resid 44 through 48
    Processing helix  chain 'G' and resid 49 through 65
      removed outlier: 3.789A  pdb=" N   LEU G  53 " --> pdb=" O   ASN G  49 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 95 through 110
    Processing helix  chain 'G' and resid 137 through 141
    Processing helix  chain 'G' and resid 165 through 176
      removed outlier: 3.765A  pdb=" N   SER G 169 " --> pdb=" O   ASN G 165 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 7
      removed outlier: 3.865A  pdb=" N   ARG H   6 " --> pdb=" O   SER H   2 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 82
      removed outlier: 3.844A  pdb=" N   GLY H  66 " --> pdb=" O   LYS H  62 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL H  79 " --> pdb=" O   MET H  75 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 137 through 152
      removed outlier: 3.744A  pdb=" N   LYS H 152 " --> pdb=" O   ILE H 148 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 175 through 179
    Processing helix  chain 'I' and resid 22 through 29
    Processing helix  chain 'I' and resid 29 through 34
    Processing helix  chain 'I' and resid 43 through 54
    Processing helix  chain 'J' and resid 2 through 23
    Processing helix  chain 'J' and resid 35 through 49
    Processing helix  chain 'J' and resid 57 through 68
    Processing helix  chain 'J' and resid 73 through 77
    Processing helix  chain 'J' and resid 89 through 104
    Processing helix  chain 'J' and resid 119 through 129
    Processing helix  chain 'K' and resid 77 through 85
    Processing helix  chain 'K' and resid 103 through 114
    Processing helix  chain 'K' and resid 115 through 117
      No H-bonds generated for 'chain 'K' and resid 115 through 117'
    Processing helix  chain 'K' and resid 122 through 138
    Processing helix  chain 'L' and resid 13 through 17
      removed outlier: 3.624A  pdb=" N   VAL L  17 " --> pdb=" O   PRO L  14 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 44
      removed outlier: 3.733A  pdb=" N   GLY L  44 " --> pdb=" O   LYS L  40 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 64 through 68
      removed outlier: 4.103A  pdb=" N   VAL L  68 " --> pdb=" O   ALA L  65 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 73 through 78
    Processing helix  chain 'L' and resid 95 through 102
    Processing helix  chain 'L' and resid 104 through 115
    Processing helix  chain 'L' and resid 118 through 127
    Processing helix  chain 'L' and resid 138 through 142
      removed outlier: 3.512A  pdb=" N   ASN L 142 " --> pdb=" O   LYS L 139 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 104 through 109
      removed outlier: 3.968A  pdb=" N   ASP M 108 " --> pdb=" O   ARG M 104 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 111 through 118
    Processing helix  chain 'N' and resid 36 through 40
      removed outlier: 3.851A  pdb=" N   ASN N  40 " --> pdb=" O   LYS N  37 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 53 through 58
    Processing helix  chain 'N' and resid 77 through 84
    Processing helix  chain 'N' and resid 91 through 98
    Processing helix  chain 'N' and resid 128 through 139
    Processing helix  chain 'O' and resid 44 through 58
    Processing helix  chain 'O' and resid 110 through 123
    Processing helix  chain 'P' and resid 8 through 12
      removed outlier: 4.115A  pdb=" N   SER P  11 " --> pdb=" O   ASN P   8 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 13 through 32
    Processing helix  chain 'P' and resid 38 through 55
      removed outlier: 3.690A  pdb=" N   ARG P  50 " --> pdb=" O   ARG P  46 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 59 through 68
      removed outlier: 3.656A  pdb=" N   LYS P  68 " --> pdb=" O   ARG P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 72 through 82
    Processing helix  chain 'P' and resid 83 through 87
    Processing helix  chain 'Q' and resid 2 through 23
    Processing helix  chain 'Q' and resid 69 through 86
      removed outlier: 3.787A  pdb=" N   GLU Q  86 " --> pdb=" O   LYS Q  82 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 103 through 114
    Processing helix  chain 'R' and resid 2 through 12
    Processing helix  chain 'R' and resid 52 through 55
      removed outlier: 3.595A  pdb=" N   GLY R  55 " --> pdb=" O   LYS R  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 52 through 55'
    Processing helix  chain 'R' and resid 96 through 101
    Processing helix  chain 'R' and resid 103 through 108
      removed outlier: 3.610A  pdb=" N   ALA R 106 " --> pdb=" O   ILE R 103 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 9 through 21
    Processing helix  chain 'S' and resid 25 through 30
      removed outlier: 3.812A  pdb=" N   LYS S  29 " --> pdb=" O   GLY S  26 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER S  30 " --> pdb=" O   THR S  27 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 31 through 69
      removed outlier: 4.494A  pdb=" N   LYS S  54 " --> pdb=" O   ARG S  50 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   ARG S  55 " --> pdb=" O   LYS S  51 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 75 through 86
    Processing helix  chain 'S' and resid 91 through 102
      removed outlier: 3.720A  pdb=" N   ILE S 100 " --> pdb=" O   SER S  96 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 102 through 115
      removed outlier: 3.617A  pdb=" N   PHE S 106 " --> pdb=" O   ASP S 102 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ARG S 115 " --> pdb=" O   LEU S 111 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 26 through 30
    Processing helix  chain 'U' and resid 17 through 29
      Proline residue:  U  23  - end of helix
      removed outlier: 3.545A  pdb=" N   ILE U  28 " --> pdb=" O   ILE U  24 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 32 through 43
    Processing helix  chain 'U' and resid 45 through 66
    Processing helix  chain 'U' and resid 94 through 96
      No H-bonds generated for 'chain 'U' and resid 94 through 96'
    Processing helix  chain 'V' and resid 13 through 24
    Processing helix  chain 'V' and resid 35 through 48
    Processing helix  chain 'X' and resid 2 through 4
      No H-bonds generated for 'chain 'X' and resid 2 through 4'
    Processing helix  chain 'X' and resid 16 through 26
    Processing helix  chain 'X' and resid 47 through 55
    Processing helix  chain 'X' and resid 114 through 119
    Processing helix  chain 'X' and resid 135 through 139
    Processing helix  chain 'Z' and resid 24 through 28
    Processing helix  chain 'Z' and resid 66 through 76
    Processing helix  chain 'Z' and resid 76 through 84
    Processing helix  chain 'Z' and resid 87 through 91
    Processing helix  chain 'a' and resid 8 through 33
    Processing helix  chain 'a' and resid 39 through 61
    Processing helix  chain 'b' and resid 3 through 18
    Processing helix  chain 'b' and resid 20 through 39
    Processing helix  chain 'b' and resid 57 through 68
    Processing helix  chain 'b' and resid 81 through 91
    Processing helix  chain 'd' and resid 9 through 21
    Processing helix  chain 'f' and resid 9 through 17
    Processing helix  chain 'f' and resid 17 through 23
    Processing helix  chain 'f' and resid 24 through 38
    Processing helix  chain 'f' and resid 43 through 47
    Processing helix  chain 'g' and resid 8 through 13
    Processing helix  chain 'g' and resid 38 through 47
      removed outlier: 3.582A  pdb=" N   LYS g  47 " --> pdb=" O   ARG g  43 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 55 through 63
    Processing helix  chain 'h' and resid 29 through 32
    Processing helix  chain 'i' and resid 50 through 55
    Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 5
    Processing sheet with id=AA2, first strand: chain 'D' and resid 35 through 37
    Processing sheet with id=AA3, first strand: chain 'D' and resid 103 through 107
      removed outlier: 6.433A  pdb=" N   ILE D  93 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ILE D  83 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU D  95 " --> pdb=" O   ALA D  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133
      removed outlier: 5.713A  pdb=" N   ILE D 166 " --> pdb=" O   LYS D 177 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LYS D 177 " --> pdb=" O   ILE D 166 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA D 168 " --> pdb=" O   THR D 175 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   MET D 183 " --> pdb=" O   ILE D 272 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 15
      removed outlier: 5.551A  pdb=" N   LYS E   8 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLU E  28 " --> pdb=" O   LYS E   8 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLY E  10 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LYS E 188 " --> pdb=" O   VAL E 175 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL E 175 " --> pdb=" O   LYS E 188 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   THR E 169 " --> pdb=" O   GLY E 110 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   GLY E 110 " --> pdb=" O   THR E 169 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   GLN E 171 " --> pdb=" O   VAL E 108 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL E 108 " --> pdb=" O   GLN E 171 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   THR E 111 " --> pdb=" O   PHE E 198 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   PHE E 198 " --> pdb=" O   THR E 111 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 84
      removed outlier: 3.717A  pdb=" N   GLY E  36 " --> pdb=" O   ILE E  49 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLY E  51 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ILE E  34 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASN E  32 " --> pdb=" O   ILE E  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 118
      removed outlier: 5.402A  pdb=" N   MET E 163 " --> pdb=" O   LYS E 115 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   PHE E 117 " --> pdb=" O   GLY E 161 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   GLY E 161 " --> pdb=" O   PHE E 117 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 6
    Processing sheet with id=AA9, first strand: chain 'F' and resid 123 through 126
      removed outlier: 6.630A  pdb=" N   VAL F 153 " --> pdb=" O   LYS F 175 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   LEU F 177 " --> pdb=" O   VAL F 153 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE F 155 " --> pdb=" O   LEU F 177 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 69 through 72
      removed outlier: 3.609A  pdb=" N   GLY G  89 " --> pdb=" O   THR G  71 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS G  36 " --> pdb=" O   VAL G 160 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 120 through 121
      removed outlier: 5.596A  pdb=" N   ILE G 120 " --> pdb=" O   SER G 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 10
    Processing sheet with id=AB4, first strand: chain 'H' and resid 16 through 20
    Processing sheet with id=AB5, first strand: chain 'H' and resid 121 through 125
    Processing sheet with id=AB6, first strand: chain 'H' and resid 95 through 99
    Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20
    Processing sheet with id=AB8, first strand: chain 'J' and resid 52 through 55
      removed outlier: 6.487A  pdb=" N   ASP J  30 " --> pdb=" O   VAL J 108 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   VAL J 108 " --> pdb=" O   ASP J  30 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'K' and resid 100 through 102
      removed outlier: 6.388A  pdb=" N   GLY K 100 " --> pdb=" O   GLU K 140 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'L' and resid 128 through 130
      removed outlier: 6.724A  pdb=" N   TRP L  21 " --> pdb=" O   ILE L 144 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LEU L 146 " --> pdb=" O   TRP L  21 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   VAL L  23 " --> pdb=" O   LEU L 146 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 79 through 83
    Processing sheet with id=AC3, first strand: chain 'M' and resid 7 through 10
      removed outlier: 5.370A  pdb=" N   LYS M  17 " --> pdb=" O   ILE M  10 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   GLN M  45 " --> pdb=" O   LYS M  17 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA M  19 " --> pdb=" O   VAL M  43 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL M  43 " --> pdb=" O   ALA M  19 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   CYS M  21 " --> pdb=" O   ILE M  41 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ILE M  41 " --> pdb=" O   CYS M  21 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LYS M  23 " --> pdb=" O   ILE M  39 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ILE M  39 " --> pdb=" O   LYS M  23 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LYS M  59 " --> pdb=" O   LEU M  87 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ALA M  83 " --> pdb=" O   VAL M  63 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   CYS M  84 " --> pdb=" O   TYR M   7 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR M   9 " --> pdb=" O   CYS M  84 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ILE M  86 " --> pdb=" O   THR M   9 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'M' and resid 76 through 79
      removed outlier: 6.333A  pdb=" N   THR R  57 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   PHE R  49 " --> pdb=" O   THR R  57 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   LEU R  59 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   ILE R  63 " --> pdb=" O   GLU R  43 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   GLU R  43 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASN R  36 " --> pdb=" O   GLU R  33 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ARG R  26 " --> pdb=" O   VAL R  85 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   VAL R  85 " --> pdb=" O   ARG R  26 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   VAL R  28 " --> pdb=" O   VAL R  83 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   VAL R  83 " --> pdb=" O   VAL R  28 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   LYS R  30 " --> pdb=" O   GLU R  81 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   GLU R  81 " --> pdb=" O   LYS R  30 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 102 through 103
      removed outlier: 6.349A  pdb=" N   VAL M 102 " --> pdb=" O   ILE M 122 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'N' and resid 74 through 76
      removed outlier: 6.241A  pdb=" N   VAL N  75 " --> pdb=" O   LEU N 111 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'N' and resid 89 through 90
      removed outlier: 6.246A  pdb=" N   PHE N 122 " --> pdb=" O   GLN N 143 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'O' and resid 63 through 65
    Processing sheet with id=AC9, first strand: chain 'O' and resid 40 through 43
      removed outlier: 6.855A  pdb=" N   TYR O  74 " --> pdb=" O   ASP O  91 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   TRP O  93 " --> pdb=" O   ILE O  72 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ILE O  72 " --> pdb=" O   TRP O  93 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'P' and resid 33 through 37
      removed outlier: 6.142A  pdb=" N   MET P 110 " --> pdb=" O   LEU P 100 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'Q' and resid 52 through 58
      removed outlier: 5.739A  pdb=" N   THR Q  53 " --> pdb=" O   ASP Q  47 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ASP Q  47 " --> pdb=" O   THR Q  53 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA Q  55 " --> pdb=" O   VAL Q  45 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL Q  34 " --> pdb=" O   ASP Q  95 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'T' and resid 10 through 14
      removed outlier: 6.756A  pdb=" N   TYR T   2 " --> pdb=" O   ILE T  41 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ILE T  41 " --> pdb=" O   TYR T   2 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LEU T   4 " --> pdb=" O   LEU T  39 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'T' and resid 18 through 23
      removed outlier: 3.978A  pdb=" N   GLU T  18 " --> pdb=" O   VAL T  98 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU T  65 " --> pdb=" O   TYR T  95 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU T  97 " --> pdb=" O   TYR T  63 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   TYR T  63 " --> pdb=" O   LEU T  97 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP T  99 " --> pdb=" O   CYS T  61 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   CYS T  61 " --> pdb=" O   ASP T  99 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ILE T 101 " --> pdb=" O   ILE T  59 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE T  59 " --> pdb=" O   ILE T 101 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'T' and resid 72 through 77
    Processing sheet with id=AD6, first strand: chain 'U' and resid 8 through 14
      removed outlier: 5.995A  pdb=" N   THR U   8 " --> pdb=" O   VAL U 112 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   VAL U 112 " --> pdb=" O   THR U   8 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   LYS U  10 " --> pdb=" O   VAL U 110 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   VAL U 110 " --> pdb=" O   LYS U  10 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   LYS U  12 " --> pdb=" O   ILE U 108 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ILE U 108 " --> pdb=" O   LYS U  12 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASP U  99 " --> pdb=" O   ILE U  90 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   ILE U  90 " --> pdb=" O   ASP U  99 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU U 101 " --> pdb=" O   LYS U  88 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   LYS U  88 " --> pdb=" O   LEU U 101 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN U 103 " --> pdb=" O   ARG U  86 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG U  86 " --> pdb=" O   ASN U 103 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ASN U 105 " --> pdb=" O   GLY U  84 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ASP U 113 " --> pdb=" O   VAL U  76 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   VAL U  76 " --> pdb=" O   ASP U 113 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'V' and resid 7 through 10
      removed outlier: 4.152A  pdb=" N   LYS V  83 " --> pdb=" O   VAL V  30 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER V  53 " --> pdb=" O   TYR V  88 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'V' and resid 63 through 67
      removed outlier: 6.187A  pdb=" N   LYS V  64 " --> pdb=" O   LYS V  76 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LYS V  76 " --> pdb=" O   LYS V  64 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   VAL V  66 " --> pdb=" O   ILE V  74 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'W' and resid 65 through 66
    Processing sheet with id=AE1, first strand: chain 'W' and resid 42 through 47
    Processing sheet with id=AE2, first strand: chain 'W' and resid 81 through 85
    Processing sheet with id=AE3, first strand: chain 'X' and resid 6 through 11
      removed outlier: 7.484A  pdb=" N   SER X   8 " --> pdb=" O   LYS X  46 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   LYS X  46 " --> pdb=" O   SER X   8 " (cutoff:3.500A)
      removed outlier: 9.835A  pdb=" N   GLU X  28 " --> pdb=" O   TYR X  89 " (cutoff:3.500A)
      removed outlier: 8.855A  pdb=" N   ILE X  91 " --> pdb=" O   GLU X  28 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   PHE X  93 " --> pdb=" O   PRO X  30 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL X  32 " --> pdb=" O   PHE X  93 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   GLU X  95 " --> pdb=" O   VAL X  32 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR X  34 " --> pdb=" O   GLU X  95 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ILE X  88 " --> pdb=" O   GLU X  81 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLU X  81 " --> pdb=" O   ILE X  88 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   HIS X  90 " --> pdb=" O   ALA X  79 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA X  79 " --> pdb=" O   HIS X  90 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ASP X  92 " --> pdb=" O   LYS X  77 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   LEU X   7 " --> pdb=" O   ASP X  66 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'X' and resid 143 through 146
    Processing sheet with id=AE5, first strand: chain 'X' and resid 123 through 124
      removed outlier: 4.502A  pdb=" N   VAL X 179 " --> pdb=" O   VAL X 156 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'Y' and resid 22 through 23
      removed outlier: 6.622A  pdb=" N   ILE Y  59 " --> pdb=" O   ILE Y  37 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'Y' and resid 30 through 31
    Processing sheet with id=AE8, first strand: chain 'Z' and resid 13 through 17
    Processing sheet with id=AE9, first strand: chain 'Z' and resid 20 through 23
    Processing sheet with id=AF1, first strand: chain 'Z' and resid 46 through 53
    Processing sheet with id=AF2, first strand: chain 'b' and resid 75 through 79
    Processing sheet with id=AF3, first strand: chain 'c' and resid 22 through 27
      removed outlier: 7.541A  pdb=" N   LEU c  11 " --> pdb=" O   GLU c  42 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLU c  33 " --> pdb=" O   LEU c  45 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'd' and resid 28 through 30
    Processing sheet with id=AF5, first strand: chain 'e' and resid 25 through 30
      removed outlier: 3.743A  pdb=" N   LYS e  49 " --> pdb=" O   CYS e  44 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'g' and resid 16 through 17
    Processing sheet with id=AF7, first strand: chain 'h' and resid 2 through 4
      removed outlier: 3.895A  pdb=" N   ARG h  35 " --> pdb=" O   LYS h   2 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU h  23 " --> pdb=" O   GLN h  36 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'i' and resid 24 through 31

    1140 hydrogen bonds defined for protein.
    3129 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1703 hydrogen bonds
      2676 hydrogen bond angles
      0 basepair planarities
      732 basepair parallelities
      1647 stacking parallelities
  Total time for adding SS restraints: 133.69

  Time building geometry restraints manager: 40.66 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 10317
        1.32 -     1.45: 42169
        1.45 -     1.58: 39142
        1.58 -     1.70: 5742
        1.70 -     1.83: 165
  Bond restraints: 97535
  Sorted by residual:
  bond pdb=" CB  PHE i  30 "
       pdb=" CG  PHE i  30 "
    ideal  model  delta    sigma   weight residual
    1.502  1.412  0.090 2.30e-02 1.89e+03 1.53e+01
  bond pdb=" CB  GLU R  33 "
       pdb=" CG  GLU R  33 "
    ideal  model  delta    sigma   weight residual
    1.520  1.419  0.101 3.00e-02 1.11e+03 1.13e+01
  bond pdb=" C   ASN L 142 "
       pdb=" O   ASN L 142 "
    ideal  model  delta    sigma   weight residual
    1.235  1.220  0.015 4.70e-03 4.53e+04 1.07e+01
  bond pdb=" CA  GLN e  35 "
       pdb=" C   GLN e  35 "
    ideal  model  delta    sigma   weight residual
    1.523  1.564 -0.041 1.34e-02 5.57e+03 9.20e+00
  bond pdb=" CA  LYS O  12 "
       pdb=" C   LYS O  12 "
    ideal  model  delta    sigma   weight residual
    1.522  1.486  0.036 1.24e-02 6.50e+03 8.46e+00
  ... (remaining 97530 not shown)

  Histogram of bond angle deviations from ideal:
       71.09 -    84.74: 80
       84.74 -    98.38: 26
       98.38 -   112.03: 67443
      112.03 -   125.67: 66292
      125.67 -   139.32: 11747
  Bond angle restraints: 145588
  Sorted by residual:
  angle pdb=" OP1   G A1559 "
        pdb=" P     G A1559 "
        pdb=" OP2   G A1559 "
      ideal   model   delta    sigma   weight residual
     119.60   78.99   40.61 3.00e+00 1.11e-01 1.83e+02
  angle pdb=" O3'   C A1558 "
        pdb=" P     G A1559 "
        pdb=" OP2   G A1559 "
      ideal   model   delta    sigma   weight residual
     108.00   71.09   36.91 3.00e+00 1.11e-01 1.51e+02
  angle pdb=" CA  ARG i  52 "
        pdb=" CB  ARG i  52 "
        pdb=" CG  ARG i  52 "
      ideal   model   delta    sigma   weight residual
     114.10  136.79  -22.69 2.00e+00 2.50e-01 1.29e+02
  angle pdb=" OP1   G A1559 "
        pdb=" P     G A1559 "
        pdb=" O5'   G A1559 "
      ideal   model   delta    sigma   weight residual
     108.00   78.71   29.29 3.00e+00 1.11e-01 9.53e+01
  angle pdb=" O3'   C A1558 "
        pdb=" P     G A1559 "
        pdb=" OP1   G A1559 "
      ideal   model   delta    sigma   weight residual
     108.00  136.97  -28.97 3.00e+00 1.11e-01 9.33e+01
  ... (remaining 145583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 53212
       35.91 -    71.82: 4762
       71.82 -   107.72: 610
      107.72 -   143.63: 13
      143.63 -   179.54: 34
  Dihedral angle restraints: 58631
    sinusoidal: 48643
      harmonic: 9988
  Sorted by residual:
  dihedral pdb=" O4'   C B  41 "
           pdb=" C1'   C B  41 "
           pdb=" N1    C B  41 "
           pdb=" C2    C B  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.31  156.69     1      1.50e+01 4.44e-03 8.19e+01
  dihedral pdb=" O4'   U A1833 "
           pdb=" C1'   U A1833 "
           pdb=" N1    U A1833 "
           pdb=" C2    U A1833 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   57.28  142.72     1      1.50e+01 4.44e-03 7.66e+01
  dihedral pdb=" O4'   U A1862 "
           pdb=" C1'   U A1862 "
           pdb=" N1    U A1862 "
           pdb=" C2    U A1862 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   58.23  141.77     1      1.50e+01 4.44e-03 7.62e+01
  ... (remaining 58628 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.413: 18409
       0.413 -    0.826: 0
       0.826 -    1.239: 1
       1.239 -    1.652: 0
       1.652 -    2.065: 44
  Chirality restraints: 18454
  Sorted by residual:
  chirality pdb=" P     G A 532 "
            pdb=" OP1   G A 532 "
            pdb=" OP2   G A 532 "
            pdb=" O5'   G A 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.35    2.06 2.00e-01 2.50e+01 1.07e+02
  chirality pdb=" P     U A1620 "
            pdb=" OP1   U A1620 "
            pdb=" OP2   U A1620 "
            pdb=" O5'   U A1620 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.35    2.06 2.00e-01 2.50e+01 1.06e+02
  chirality pdb=" P     A A1520 "
            pdb=" OP1   A A1520 "
            pdb=" OP2   A A1520 "
            pdb=" O5'   A A1520 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.35    2.06 2.00e-01 2.50e+01 1.06e+02
  ... (remaining 18451 not shown)

  Planarity restraints: 7709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET E 163 "   -0.047 2.00e-02 2.50e+03   9.09e-02 8.26e+01
        pdb=" C   MET E 163 "    0.157 2.00e-02 2.50e+03
        pdb=" O   MET E 163 "   -0.059 2.00e-02 2.50e+03
        pdb=" N   ALA E 164 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE i  30 "   -0.072 2.00e-02 2.50e+03   4.73e-02 3.92e+01
        pdb=" CG  PHE i  30 "    0.090 2.00e-02 2.50e+03
        pdb=" CD1 PHE i  30 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE i  30 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE i  30 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 PHE i  30 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE i  30 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU O  80 "    0.024 2.00e-02 2.50e+03   4.90e-02 2.40e+01
        pdb=" CD  GLU O  80 "   -0.085 2.00e-02 2.50e+03
        pdb=" OE1 GLU O  80 "    0.030 2.00e-02 2.50e+03
        pdb=" OE2 GLU O  80 "    0.030 2.00e-02 2.50e+03
  ... (remaining 7706 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 1795
        2.63 -     3.20: 72965
        3.20 -     3.77: 175316
        3.77 -     4.33: 240098
        4.33 -     4.90: 320368
  Nonbonded interactions: 810542
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN G  66 "
            pdb=" O   THR G  93 "
     model   vdw
     2.063 2.520
  nonbonded pdb=" OD2 ASP c  16 "
            pdb=" OG1 THR c  51 "
     model   vdw
     2.093 2.440
  nonbonded pdb=" OD1 ASP N  81 "
            pdb=" NZ  LYS N 118 "
     model   vdw
     2.096 2.520
  nonbonded pdb=" O   ARG N  44 "
            pdb=" NH1 ARG N  44 "
     model   vdw
     2.125 2.520
  nonbonded pdb=" OG  SER X 114 "
            pdb=" O   VAL X 150 "
     model   vdw
     2.134 2.440
  ... (remaining 810537 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:             4.990
  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:          21.670
  Check model and map are aligned:         1.320
  Set scattering table:                    0.780
  Process input model:                     327.030
  Find NCS groups from input model:        1.580
  Set up NCS constraints:                  0.210
  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:2.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  360.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
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      :  0.006   0.101  97535  Z= 0.368
  Angle     :  0.885  40.614 145588  Z= 0.376
  Chirality :  0.103   2.065  18454
  Planarity :  0.005   0.099   7709
  Dihedral  : 20.789 179.538  52350
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.00 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.14), residues: 3569
  helix:  0.53 (0.16), residues: 1012
  sheet: -0.58 (0.18), residues: 775
  loop : -1.40 (0.14), residues: 1782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.047   0.003   TRP D 251 
   HIS   0.021   0.002   HIS E 140 
   PHE   0.090   0.003   PHE i  30 
   TYR   0.042   0.002   TYR T  93 
   ARG   0.032   0.002   ARG i  52 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1001 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1001
  time to evaluate  : 4.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 1001
  average time/residue: 0.9351
  time to fit residues: 1550.7789
Evaluate side-chains
  486 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 486
  time to evaluate  : 4.648 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.0484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 537 optimal weight:    1.9990
   chunk 482 optimal weight:    7.9990
   chunk 267 optimal weight:   10.0000
   chunk 164 optimal weight:   10.0000
   chunk 325 optimal weight:    0.9990
   chunk 257 optimal weight:   10.0000
   chunk 498 optimal weight:    5.9990
   chunk 192 optimal weight:   20.0000
   chunk 303 optimal weight:   20.0000
   chunk 371 optimal weight:    7.9990
   chunk 577 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 246 HIS
E  67 GLN
G   2 ASN
G  30 GLN
G 182 ASN
H 112 GLN
N 143 GLN
O  92 HIS
O  94 ASN
P   8 ASN
P  31 HIS
P  89 GLN
R 101 ASN
** V  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  69 ASN
W  88 ASN
X  10 GLN
b  46 GLN
i  32 ASN
i  46 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.125  97535  Z= 0.310
  Angle     :  0.974  39.851 145588  Z= 0.415
  Chirality :  0.102   2.078  18454
  Planarity :  0.005   0.109   7709
  Dihedral  : 21.457 179.682  45154
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.30 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.03 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.14), residues: 3569
  helix:  1.03 (0.17), residues: 1011
  sheet: -0.48 (0.18), residues: 797
  loop : -1.11 (0.14), residues: 1761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP D 251 
   HIS   0.008   0.001   HIS X  90 
   PHE   0.021   0.002   PHE G 133 
   TYR   0.022   0.002   TYR G 104 
   ARG   0.016   0.001   ARG a  16 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  656 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 101
    poor density    : 555
  time to evaluate  : 4.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 101
  outliers final: 67
  residues processed: 623
  average time/residue: 0.9418
  time to fit residues: 1025.5602
Evaluate side-chains
  537 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 470
  time to evaluate  : 4.204 
Switching outliers to nearest non-outliers
  outliers start: 67
  outliers final: 0
  residues processed: 67
  average time/residue: 0.7026
  time to fit residues: 93.6249
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 320 optimal weight:    6.9990
   chunk 179 optimal weight:   20.0000
   chunk 480 optimal weight:    3.9990
   chunk 393 optimal weight:    0.7980
   chunk 159 optimal weight:   10.0000
   chunk 578 optimal weight:    8.9990
   chunk 625 optimal weight:   10.0000
   chunk 515 optimal weight:    9.9990
   chunk 573 optimal weight:    5.9990
   chunk 197 optimal weight:   10.0000
   chunk 464 optimal weight:    6.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
N  51 GLN
O  13 GLN
Q  44 GLN
** g  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** h  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  97535  Z= 0.290
  Angle     :  0.943  39.608 145588  Z= 0.402
  Chirality :  0.103   2.079  18454
  Planarity :  0.005   0.049   7709
  Dihedral  : 21.765 179.321  45154
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.41 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.49 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.14), residues: 3569
  helix:  1.11 (0.17), residues: 1014
  sheet: -0.44 (0.18), residues: 771
  loop : -1.05 (0.14), residues: 1784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP i  20 
   HIS   0.011   0.001   HIS L  53 
   PHE   0.025   0.002   PHE N  47 
   TYR   0.029   0.002   TYR X  89 
   ARG   0.010   0.001   ARG e  31 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  610 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 80
    poor density    : 530
  time to evaluate  : 4.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 80
  outliers final: 32
  residues processed: 578
  average time/residue: 0.9024
  time to fit residues: 911.4920
Evaluate side-chains
  503 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 471
  time to evaluate  : 4.272 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 32
  outliers final: 1
  residues processed: 32
  average time/residue: 0.7729
  time to fit residues: 48.9699
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 571 optimal weight:    5.9990
   chunk 435 optimal weight:    4.9990
   chunk 300 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 276 optimal weight:   20.0000
   chunk 388 optimal weight:    3.9990
   chunk 580 optimal weight:   20.0000
   chunk 614 optimal weight:    9.9990
   chunk 303 optimal weight:    9.9990
   chunk 550 optimal weight:    6.9990
   chunk 165 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
E  32 ASN
F 162 GLN
G   2 ASN
L  53 HIS
R  11 ASN
** Z  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  32 HIS
h  34 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  97535  Z= 0.293
  Angle     :  0.946  39.921 145588  Z= 0.403
  Chirality :  0.103   2.093  18454
  Planarity :  0.005   0.080   7709
  Dihedral  : 21.933 179.979  45154
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.44 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.46 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.14), residues: 3569
  helix:  1.07 (0.17), residues: 1015
  sheet: -0.42 (0.18), residues: 749
  loop : -1.07 (0.14), residues: 1805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP i  20 
   HIS   0.009   0.001   HIS Q  52 
   PHE   0.021   0.002   PHE G 180 
   TYR   0.020   0.002   TYR M  58 
   ARG   0.010   0.001   ARG U 100 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  595 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 95
    poor density    : 500
  time to evaluate  : 4.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 95
  outliers final: 47
  residues processed: 551
  average time/residue: 0.8400
  time to fit residues: 808.1239
Evaluate side-chains
  503 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 456
  time to evaluate  : 4.164 
Switching outliers to nearest non-outliers
  outliers start: 47
  outliers final: 0
  residues processed: 47
  average time/residue: 0.7231
  time to fit residues: 66.5783
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 511 optimal weight:    0.9990
   chunk 348 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 457 optimal weight:    9.9990
   chunk 253 optimal weight:   10.0000
   chunk 524 optimal weight:   10.0000
   chunk 424 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 313 optimal weight:    3.9990
   chunk 551 optimal weight:    6.9990
   chunk 155 optimal weight:   20.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 162 GLN
G  97 ASN
P  61 HIS
R  11 ASN
R 101 ASN
** Z  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  97535  Z= 0.262
  Angle     :  0.926  40.042 145588  Z= 0.391
  Chirality :  0.102   2.100  18454
  Planarity :  0.004   0.069   7709
  Dihedral  : 22.006 179.874  45154
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.35 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.55 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.14), residues: 3569
  helix:  1.15 (0.17), residues: 1009
  sheet: -0.36 (0.19), residues: 740
  loop : -1.07 (0.14), residues: 1820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP i  20 
   HIS   0.013   0.002   HIS L  53 
   PHE   0.022   0.002   PHE Q 108 
   TYR   0.022   0.002   TYR G  25 
   ARG   0.005   0.001   ARG b  51 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  569 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 498
  time to evaluate  : 4.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 71
  outliers final: 28
  residues processed: 540
  average time/residue: 0.9455
  time to fit residues: 900.2729
Evaluate side-chains
  477 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 449
  time to evaluate  : 4.147 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 0
  residues processed: 28
  average time/residue: 0.7329
  time to fit residues: 43.2641
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 206 optimal weight:   30.0000
   chunk 553 optimal weight:    0.9990
   chunk 121 optimal weight:   10.0000
   chunk 360 optimal weight:    7.9990
   chunk 151 optimal weight:   10.0000
   chunk 615 optimal weight:   20.0000
   chunk 510 optimal weight:   10.0000
   chunk 284 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 203 optimal weight:   10.0000
   chunk 323 optimal weight:    6.9990
   overall best weight:    7.1994

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 162 GLN
G   2 ASN
G  97 ASN
** N  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  93 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.102  97535  Z= 0.388
  Angle     :  1.008  40.613 145588  Z= 0.438
  Chirality :  0.104   2.114  18454
  Planarity :  0.005   0.073   7709
  Dihedral  : 22.240 179.858  45154
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.92 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.14), residues: 3569
  helix:  0.85 (0.17), residues: 1006
  sheet: -0.61 (0.19), residues: 682
  loop : -1.22 (0.13), residues: 1881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP i  20 
   HIS   0.016   0.002   HIS L  53 
   PHE   0.024   0.002   PHE G 180 
   TYR   0.035   0.002   TYR X  89 
   ARG   0.006   0.001   ARG E 123 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  539 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 86
    poor density    : 453
  time to evaluate  : 4.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 86
  outliers final: 47
  residues processed: 518
  average time/residue: 0.8672
  time to fit residues: 786.3749
Evaluate side-chains
  480 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 433
  time to evaluate  : 4.250 
Switching outliers to nearest non-outliers
  outliers start: 47
  outliers final: 0
  residues processed: 47
  average time/residue: 0.7400
  time to fit residues: 68.8110
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 593 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 350 optimal weight:    5.9990
   chunk 449 optimal weight:    4.9990
   chunk 348 optimal weight:   10.0000
   chunk 518 optimal weight:    6.9990
   chunk 343 optimal weight:   20.0000
   chunk 613 optimal weight:    6.9990
   chunk 383 optimal weight:    8.9990
   chunk 373 optimal weight:   10.0000
   chunk 283 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 162 GLN
G  97 ASN
G 128 ASN
M 110 ASN
** N  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
e  30 ASN
h  34 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.5833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087  97535  Z= 0.363
  Angle     :  0.986  40.570 145588  Z= 0.425
  Chirality :  0.104   2.116  18454
  Planarity :  0.005   0.076   7709
  Dihedral  : 22.291 179.901  45154
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 25.21 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.14), residues: 3569
  helix:  0.79 (0.16), residues: 1005
  sheet: -0.68 (0.19), residues: 699
  loop : -1.27 (0.14), residues: 1865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP i  20 
   HIS   0.015   0.002   HIS L  53 
   PHE   0.034   0.002   PHE S  24 
   TYR   0.035   0.002   TYR f   5 
   ARG   0.016   0.001   ARG U 100 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  517 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 463
  time to evaluate  : 6.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 54
  outliers final: 28
  residues processed: 495
  average time/residue: 0.8664
  time to fit residues: 751.3551
Evaluate side-chains
  465 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 437
  time to evaluate  : 4.187 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 0
  residues processed: 28
  average time/residue: 0.7658
  time to fit residues: 43.3153
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 379 optimal weight:    2.9990
   chunk 244 optimal weight:   10.0000
   chunk 366 optimal weight:   20.0000
   chunk 184 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 118 optimal weight:   30.0000
   chunk 389 optimal weight:    6.9990
   chunk 417 optimal weight:    0.8980
   chunk 303 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 481 optimal weight:    5.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** D  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 246 HIS
F 162 GLN
G   2 ASN
G  97 ASN
** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 110 ASN
** N  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
h  34 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.5861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  97535  Z= 0.235
  Angle     :  0.932  40.521 145588  Z= 0.395
  Chirality :  0.103   2.135  18454
  Planarity :  0.004   0.075   7709
  Dihedral  : 22.224 179.800  45154
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 26.05 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.14), residues: 3569
  helix:  1.09 (0.17), residues: 1005
  sheet: -0.57 (0.19), residues: 690
  loop : -1.18 (0.14), residues: 1874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP i  20 
   HIS   0.016   0.001   HIS L  53 
   PHE   0.054   0.002   PHE S  24 
   TYR   0.034   0.002   TYR f   5 
   ARG   0.013   0.001   ARG U 100 

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

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

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7138 Ramachandran restraints generated.
    3569 Oldfield, 0 Emsley, 3569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  518 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 485
  time to evaluate  : 4.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 33
  outliers final: 23
  residues processed: 505
  average time/residue: 0.8524
  time to fit residues: 751.1753
Evaluate side-chains
  471 residues out of total 3165 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 448
  time to evaluate  : 4.209 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 0
  residues processed: 23
  average time/residue: 0.7961
  time to fit residues: 36.8006
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 636
   random chunks:
   chunk 557 optimal weight:    0.5980
   chunk 587 optimal weight:    5.9990
   chunk 535 optimal weight:    0.6980
   chunk 571 optimal weight:   20.0000
   chunk 343 optimal weight:    6.9990
   chunk 248 optimal weight:   10.0000
   chunk 448 optimal weight:    4.9990
   chunk 175 optimal weight:   10.0000
   chunk 516 optimal weight:   10.0000
   chunk 540 optimal weight:   20.0000
   chunk 569 optimal weight:    4.9990
   overall best weight:    3.4586

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