Starting phenix.real_space_refine
on Sun Mar 17 16:47:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asn_11901/03_2024/7asn_11901_updated.pdb"
  }
  resolution = 2.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P    2848      5.49       5
     S      46      5.16       5
     C   39561      2.51       5
     N   14939      2.21       5
     O   23300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "1 ARG    2": "NH1" <-> "NH2"
    Residue "1 ASP   14": "OD1" <-> "OD2"
    Residue "1 ARG   24": "NH1" <-> "NH2"
    Residue "1 TYR   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "2 PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "2 ARG   20": "NH1" <-> "NH2"
    Residue "2 ARG   22": "NH1" <-> "NH2"
    Residue "2 ARG   40": "NH1" <-> "NH2"
    Residue "3 ARG   24": "NH1" <-> "NH2"
    Residue "3 ARG   42": "NH1" <-> "NH2"
    Residue "3 ARG   57": "NH1" <-> "NH2"
    Residue "F PHE   21": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   30": "OE1" <-> "OE2"
    Residue "F ARG   43": "NH1" <-> "NH2"
    Residue "F PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   69": "NH1" <-> "NH2"
    Residue "F ASP   79": "OD1" <-> "OD2"
    Residue "F ASP   84": "OD1" <-> "OD2"
    Residue "F TYR   96": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  168": "OE1" <-> "OE2"
    Residue "F TYR  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  201": "OE1" <-> "OE2"
    Residue "F ASP  229": "OD1" <-> "OD2"
    Residue "F GLU  236": "OE1" <-> "OE2"
    Residue "F ARG  243": "NH1" <-> "NH2"
    Residue "F ASP  267": "OD1" <-> "OD2"
    Residue "D GLU   18": "OE1" <-> "OE2"
    Residue "D GLU   42": "OE1" <-> "OE2"
    Residue "D ASP   44": "OD1" <-> "OD2"
    Residue "D ASP   62": "OD1" <-> "OD2"
    Residue "D ARG   89": "NH1" <-> "NH2"
    Residue "D PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   97": "OD1" <-> "OD2"
    Residue "D PHE  110": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  149": "NH1" <-> "NH2"
    Residue "D PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  191": "OE1" <-> "OE2"
    Residue "E TYR    4": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU   18": "OE1" <-> "OE2"
    Residue "E PHE   24": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU   35": "OE1" <-> "OE2"
    Residue "E ARG   45": "NH1" <-> "NH2"
    Residue "E ARG   54": "NH1" <-> "NH2"
    Residue "E ARG  106": "NH1" <-> "NH2"
    Residue "E ARG  107": "NH1" <-> "NH2"
    Residue "E PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  160": "OD1" <-> "OD2"
    Residue "E ARG  168": "NH1" <-> "NH2"
    Residue "E ASP  190": "OD1" <-> "OD2"
    Residue "E GLU  204": "OE1" <-> "OE2"
    Residue "H ARG   14": "NH1" <-> "NH2"
    Residue "H ARG   28": "NH1" <-> "NH2"
    Residue "H TYR   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU   64": "OE1" <-> "OE2"
    Residue "H GLU   70": "OE1" <-> "OE2"
    Residue "H TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG  100": "NH1" <-> "NH2"
    Residue "H PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU  142": "OE1" <-> "OE2"
    Residue "L ARG   21": "NH1" <-> "NH2"
    Residue "L GLU   51": "OE1" <-> "OE2"
    Residue "L GLU   73": "OE1" <-> "OE2"
    Residue "L ASP   80": "OD1" <-> "OD2"
    Residue "L PHE  128": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ASP  137": "OD1" <-> "OD2"
    Residue "Y ARG   10": "NH1" <-> "NH2"
    Residue "Y ARG   20": "NH1" <-> "NH2"
    Residue "Y PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y ARG   45": "NH1" <-> "NH2"
    Residue "Y ARG   51": "NH1" <-> "NH2"
    Residue "Y ARG   56": "NH1" <-> "NH2"
    Residue "Y TYR   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE   69": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y ARG   82": "NH1" <-> "NH2"
    Residue "Y PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  112": "OE1" <-> "OE2"
    Residue "Y ARG  115": "NH1" <-> "NH2"
    Residue "Y PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG   17": "NH1" <-> "NH2"
    Residue "G ASP   73": "OD1" <-> "OD2"
    Residue "G ASP   80": "OD1" <-> "OD2"
    Residue "G ARG   88": "NH1" <-> "NH2"
    Residue "G GLU  105": "OE1" <-> "OE2"
    Residue "G PHE  111": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG   11": "NH1" <-> "NH2"
    Residue "M ARG   14": "NH1" <-> "NH2"
    Residue "M ARG   35": "NH1" <-> "NH2"
    Residue "M ASP   86": "OD1" <-> "OD2"
    Residue "M ASP   95": "OD1" <-> "OD2"
    Residue "M ARG   96": "NH1" <-> "NH2"
    Residue "M TYR  101": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG  104": "NH1" <-> "NH2"
    Residue "N ARG   16": "NH1" <-> "NH2"
    Residue "N ARG   23": "NH1" <-> "NH2"
    Residue "N ASP   26": "OD1" <-> "OD2"
    Residue "N ARG   33": "NH1" <-> "NH2"
    Residue "N PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   87": "OE1" <-> "OE2"
    Residue "N ARG   90": "NH1" <-> "NH2"
    Residue "N ARG   91": "NH1" <-> "NH2"
    Residue "N TYR  101": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ARG   48": "NH1" <-> "NH2"
    Residue "O ASP   89": "OD1" <-> "OD2"
    Residue "O GLU   97": "OE1" <-> "OE2"
    Residue "O ASP  102": "OD1" <-> "OD2"
    Residue "O PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P PHE    2": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P GLU   19": "OE1" <-> "OE2"
    Residue "P GLU   23": "OE1" <-> "OE2"
    Residue "P GLU   29": "OE1" <-> "OE2"
    Residue "P PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ARG   67": "NH1" <-> "NH2"
    Residue "P TYR   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ARG   84": "NH1" <-> "NH2"
    Residue "P TYR   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ARG    8": "NH1" <-> "NH2"
    Residue "Q ARG   11": "NH1" <-> "NH2"
    Residue "Q GLU   31": "OE1" <-> "OE2"
    Residue "Q GLU   48": "OE1" <-> "OE2"
    Residue "Q TYR   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q PHE   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ARG   86": "NH1" <-> "NH2"
    Residue "Q ARG   88": "NH1" <-> "NH2"
    Residue "Q GLU  112": "OE1" <-> "OE2"
    Residue "R GLU   18": "OE1" <-> "OE2"
    Residue "R TYR   25": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU   43": "OE1" <-> "OE2"
    Residue "R GLU   44": "OE1" <-> "OE2"
    Residue "R TYR   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG   76": "NH1" <-> "NH2"
    Residue "R PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ASP    7": "OD1" <-> "OD2"
    Residue "S GLU   20": "OE1" <-> "OE2"
    Residue "S ASP   31": "OD1" <-> "OD2"
    Residue "S ARG   32": "NH1" <-> "NH2"
    Residue "S GLU   58": "OE1" <-> "OE2"
    Residue "S TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S PHE   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ARG    9": "NH1" <-> "NH2"
    Residue "T ARG   22": "NH1" <-> "NH2"
    Residue "T TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ARG   53": "NH1" <-> "NH2"
    Residue "T ARG   57": "NH1" <-> "NH2"
    Residue "T ASP   90": "OD1" <-> "OD2"
    Residue "a ARG   22": "NH1" <-> "NH2"
    Residue "a GLU   25": "OE1" <-> "OE2"
    Residue "a ARG   28": "NH1" <-> "NH2"
    Residue "a ARG   33": "NH1" <-> "NH2"
    Residue "a ASP   35": "OD1" <-> "OD2"
    Residue "a ARG   49": "NH1" <-> "NH2"
    Residue "a PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V ARG   37": "NH1" <-> "NH2"
    Residue "W GLU   15": "OE1" <-> "OE2"
    Residue "W GLU   23": "OE1" <-> "OE2"
    Residue "W GLU   24": "OE1" <-> "OE2"
    Residue "W PHE   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W PHE   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W ARG   44": "NH1" <-> "NH2"
    Residue "W ARG   47": "NH1" <-> "NH2"
    Residue "W ARG   52": "NH1" <-> "NH2"
    Residue "W ARG   58": "NH1" <-> "NH2"
    Residue "W ARG   60": "NH1" <-> "NH2"
    Residue "X ARG   10": "NH1" <-> "NH2"
    Residue "X GLU   17": "OE1" <-> "OE2"
    Residue "X GLU   24": "OE1" <-> "OE2"
    Residue "X GLU   38": "OE1" <-> "OE2"
    Residue "X GLU   58": "OE1" <-> "OE2"
    Residue "b ARG    6": "NH1" <-> "NH2"
    Residue "b ARG    7": "NH1" <-> "NH2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 80694
  Number of models: 1
  Model: ""
    Number of chains: 25
    Chain: "A"
      Number of atoms: 58787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2742, 58787
          Classifications: {'DNA': 1, 'RNA': 2741}
          Modifications used: {'rna2p': 1, 'rna2p_pur': 291, 'rna2p_pyr': 173, 'rna3p': 2, 'rna3p_pur': 1277, 'rna3p_pyr': 997}
          Link IDs: {'rna2p': 465, 'rna3p': 2276}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  C:plan': 1, '  C:plan2': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 2260
          Classifications: {'RNA': 106}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 51, 'rna3p_pyr': 46}
          Link IDs: {'rna2p': 9, 'rna3p': 96}
          Chain breaks: 4
    Chain: "1"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 390
          Classifications: {'peptide': 47}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "2"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 367
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 1, 'TRANS': 41}
    Chain: "3"
      Number of atoms: 521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 521
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "F"
      Number of atoms: 2094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2094
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 17, 'TRANS': 256}
    Chain: "D"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1627
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 8, 'TRANS': 206}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 1572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1572
          Classifications: {'peptide': 206}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 196}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 1132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1132
          Classifications: {'peptide': 144}
          Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "L"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1086
          Classifications: {'peptide': 146}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "Y"
      Number of atoms: 1071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1071
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 129}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "G"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 918
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "M"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 872
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 1, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "N"
      Number of atoms: 878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 878
          Classifications: {'peptide': 113}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 108}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "O"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 942
          Classifications: {'peptide': 116}
          Link IDs: {'TRANS': 115}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "P"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 790
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "Q"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 854
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 715
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "S"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 770
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "T"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 722
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "a"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 597
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "V"
      Number of atoms: 379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 379
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "W"
      Number of atoms: 541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 541
          Classifications: {'peptide': 67}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 66}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "X"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 449
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "b"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 360
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 3, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 31.94, per 1000 atoms: 0.40
  Number of scatterers: 80694
  At special positions: 0
  Unit cell: (233.376, 235.95, 202.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P    2848     15.00
     O   23300      8.00
     N   14939      7.00
     C   39561      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS 1   9 " - pdb=" SG  CYS 1  12 " distance=2.01
    Simple disulfide: pdb=" SG  CYS 1  12 " - pdb=" SG  CYS 1  36 " distance=2.02

  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: 34.07
  Conformation dependent library (CDL) restraints added in 4.0 seconds
  

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4628

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      58 helices and 35 sheets defined
      20.9% alpha, 15.7% beta
      645 base pairs and 1328 stacking pairs defined.
    Time for finding SS restraints: 36.12
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 16
      removed outlier: 3.538A  pdb=" N   SER 2  14 " --> pdb=" O   LYS 2  10 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 19 through 23
    Processing helix  chain '2' and resid 26 through 37
      removed outlier: 3.571A  pdb=" N   VAL 2  31 " --> pdb=" O   ASN 2  27 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG 2  36 " --> pdb=" O   LEU 2  32 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 38 through 43
      removed outlier: 3.657A  pdb=" N   ARG 3  42 " --> pdb=" O   THR 3  38 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 52 through 62
      removed outlier: 3.536A  pdb=" N   LYS 3  56 " --> pdb=" O   LYS 3  52 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG 3  57 " --> pdb=" O   SER 3  53 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   GLN 3  60 " --> pdb=" O   LYS 3  56 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   LEU 3  61 " --> pdb=" O   ARG 3  57 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU 3  62 " --> pdb=" O   VAL 3  58 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 132 through 134
      No H-bonds generated for 'chain 'F' and resid 132 through 134'
    Processing helix  chain 'F' and resid 208 through 214
    Processing helix  chain 'D' and resid 41 through 44
      No H-bonds generated for 'chain 'D' and resid 41 through 44'
    Processing helix  chain 'D' and resid 71 through 75
    Processing helix  chain 'D' and resid 107 through 109
      No H-bonds generated for 'chain 'D' and resid 107 through 109'
    Processing helix  chain 'D' and resid 131 through 134
      No H-bonds generated for 'chain 'D' and resid 131 through 134'
    Processing helix  chain 'E' and resid 30 through 44
      removed outlier: 3.601A  pdb=" N   GLU E  35 " --> pdb=" O   SER E  31 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU E  44 " --> pdb=" O   GLN E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 56
      No H-bonds generated for 'chain 'E' and resid 54 through 56'
    Processing helix  chain 'E' and resid 103 through 116
    Processing helix  chain 'E' and resid 136 through 143
    Processing helix  chain 'E' and resid 161 through 164
      No H-bonds generated for 'chain 'E' and resid 161 through 164'
    Processing helix  chain 'E' and resid 178 through 180
      No H-bonds generated for 'chain 'E' and resid 178 through 180'
    Processing helix  chain 'E' and resid 183 through 187
    Processing helix  chain 'E' and resid 196 through 206
    Processing helix  chain 'H' and resid 26 through 38
    Processing helix  chain 'H' and resid 90 through 95
    Processing helix  chain 'H' and resid 98 through 109
      removed outlier: 3.645A  pdb=" N   SER H 105 " --> pdb=" O   LEU H 101 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET H 109 " --> pdb=" O   SER H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 114 through 122
      removed outlier: 3.763A  pdb=" N   LYS H 121 " --> pdb=" O   GLU H 117 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS H 122 " --> pdb=" O   LYS H 118 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 38 through 40
      No H-bonds generated for 'chain 'L' and resid 38 through 40'
    Processing helix  chain 'L' and resid 57 through 60
      No H-bonds generated for 'chain 'L' and resid 57 through 60'
    Processing helix  chain 'L' and resid 93 through 98
      removed outlier: 3.524A  pdb=" N   VAL L  97 " --> pdb=" O   PRO L  93 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU L  98 " --> pdb=" O   ALA L  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 93 through 98'
    Processing helix  chain 'L' and resid 130 through 139
    Processing helix  chain 'Y' and resid 44 through 58
    Processing helix  chain 'Y' and resid 111 through 123
      removed outlier: 4.012A  pdb=" N   ARG Y 119 " --> pdb=" O   ARG Y 115 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA Y 121 " --> pdb=" O   ALA Y 117 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER Y 122 " --> pdb=" O   LEU Y 118 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   HIS Y 123 " --> pdb=" O   ARG Y 119 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 104 through 108
    Processing helix  chain 'G' and resid 112 through 117
      removed outlier: 3.860A  pdb=" N   SER G 116 " --> pdb=" O   MET G 112 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU G 117 " --> pdb=" O   LYS G 113 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 112 through 117'
    Processing helix  chain 'M' and resid 7 through 18
    Processing helix  chain 'M' and resid 71 through 86
      removed outlier: 3.858A  pdb=" N   LYS M  82 " --> pdb=" O   GLU M  78 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS M  83 " --> pdb=" O   ALA M  79 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 104 through 113
    Processing helix  chain 'N' and resid 5 through 14
      removed outlier: 3.599A  pdb=" N   THR N  11 " --> pdb=" O   ILE N   7 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER N  13 " --> pdb=" O   ALA N   9 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   GLN N  14 " --> pdb=" O   VAL N  10 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 56 through 58
      No H-bonds generated for 'chain 'N' and resid 56 through 58'
    Processing helix  chain 'O' and resid 9 through 20
      removed outlier: 3.732A  pdb=" N   THR O  17 " --> pdb=" O   ARG O  13 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 26 through 29
    Processing helix  chain 'O' and resid 32 through 72
      removed outlier: 3.525A  pdb=" N   PHE O  47 " --> pdb=" O   GLY O  43 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG O  48 " --> pdb=" O   GLN O  44 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LYS O  54 " --> pdb=" O   ARG O  50 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ARG O  55 " --> pdb=" O   ARG O  51 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN O  71 " --> pdb=" O   ALA O  67 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   HIS O  72 " --> pdb=" O   ALA O  68 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 76 through 86
    Processing helix  chain 'O' and resid 92 through 101
    Processing helix  chain 'O' and resid 103 through 116
      removed outlier: 3.552A  pdb=" N   GLN O 108 " --> pdb=" O   LYS O 104 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 14 through 21
      removed outlier: 4.074A  pdb=" N   LEU Q  19 " --> pdb=" O   ARG Q  15 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   VAL Q  20 " --> pdb=" O   LYS Q  16 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 29 through 38
      removed outlier: 3.658A  pdb=" N   LEU Q  38 " --> pdb=" O   ALA Q  34 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 44 through 60
      removed outlier: 3.675A  pdb=" N   GLU Q  59 " --> pdb=" O   LEU Q  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 14 through 21
      removed outlier: 3.562A  pdb=" N   ALA R  21 " --> pdb=" O   SER R  17 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 46
      removed outlier: 3.630A  pdb=" N   LYS R  39 " --> pdb=" O   LYS R  35 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   MET R  40 " --> pdb=" O   THR R  36 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 65 through 67
      No H-bonds generated for 'chain 'S' and resid 65 through 67'
    Processing helix  chain 'T' and resid 15 through 24
      removed outlier: 3.942A  pdb=" N   LYS T  23 " --> pdb=" O   LYS T  19 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER T  24 " --> pdb=" O   GLN T  20 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 46 through 52
    Processing helix  chain 'V' and resid 51 through 55
    Processing helix  chain 'W' and resid 6 through 8
      No H-bonds generated for 'chain 'W' and resid 6 through 8'
    Processing helix  chain 'W' and resid 13 through 33
      removed outlier: 3.809A  pdb=" N   SER W  20 " --> pdb=" O   GLU W  16 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU W  23 " --> pdb=" O   LYS W  19 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA W  33 " --> pdb=" O   ARG W  29 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 43 through 64
      removed outlier: 3.550A  pdb=" N   LYS W  48 " --> pdb=" O   ARG W  44 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   THR W  49 " --> pdb=" O   THR W  45 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 17 through 25
    Processing helix  chain 'X' and resid 41 through 49
      removed outlier: 3.720A  pdb=" N   GLN X  46 " --> pdb=" O   ALA X  42 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 51 through 53
      No H-bonds generated for 'chain 'X' and resid 51 through 53'
    Processing helix  chain 'b' and resid 10 through 18
      removed outlier: 3.857A  pdb=" N   THR b  18 " --> pdb=" O   ASN b  14 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain '1' and resid 17 through 21
      removed outlier: 4.575A  pdb=" N   TYR 1  17 " --> pdb=" O   LEU 1   7 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain '3' and resid 14 through 16
    Processing sheet with id=  C, first strand: chain 'F' and resid 3 through 5
    Processing sheet with id=  D, first strand: chain 'F' and resid 34 through 36
    Processing sheet with id=  E, first strand: chain 'F' and resid 101 through 105
      removed outlier: 3.737A  pdb=" N   SER F  80 " --> pdb=" O   LEU F  93 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL F  95 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL F  78 " --> pdb=" O   VAL F  95 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'F' and resid 129 through 131
      removed outlier: 3.921A  pdb=" N   LEU F 130 " --> pdb=" O   ALA F 190 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR F 191 " --> pdb=" O   ASN F 143 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   ASN F 143 " --> pdb=" O   THR F 191 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'F' and resid 180 through 184
      removed outlier: 3.719A  pdb=" N   GLU F 180 " --> pdb=" O   LEU F 176 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR F 171 " --> pdb=" O   GLU F 168 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   ARG F 175 " --> pdb=" O   VAL F 164 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL F 164 " --> pdb=" O   ARG F 175 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'D' and resid 9 through 17
      removed outlier: 6.673A  pdb=" N   VAL D  27 " --> pdb=" O   ILE D  10 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   MET D  12 " --> pdb=" O   VAL D  25 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL D  25 " --> pdb=" O   MET D  12 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   GLN D  14 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE D  23 " --> pdb=" O   GLN D  14 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   PHE D  16 " --> pdb=" O   GLU D  21 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   GLU D  21 " --> pdb=" O   PHE D  16 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN D 187 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LYS D 198 " --> pdb=" O   VAL D 185 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL D 185 " --> pdb=" O   LYS D 198 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'D' and resid 87 through 91
      removed outlier: 4.192A  pdb=" N   PHE D  87 " --> pdb=" O   PHE D  53 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN D  37 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLY D  52 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   VAL D  35 " --> pdb=" O   GLY D  52 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'D' and resid 210 through 213
    Processing sheet with id=  K, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.823A  pdb=" N   GLY E  15 " --> pdb=" O   VAL E   6 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'E' and resid 123 through 126
      removed outlier: 6.374A  pdb=" N   LEU E 192 " --> pdb=" O   THR E 124 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL E 126 " --> pdb=" O   LEU E 192 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   ILE E 194 " --> pdb=" O   VAL E 126 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'H' and resid 16 through 19
      removed outlier: 6.663A  pdb=" N   TYR H  54 " --> pdb=" O   TYR H  17 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ILE H  19 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   ILE H  56 " --> pdb=" O   ILE H  19 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'H' and resid 74 through 78
    Processing sheet with id=  O, first strand: chain 'L' and resid 75 through 77
    Processing sheet with id=  P, first strand: chain 'Y' and resid 131 through 133
      removed outlier: 3.955A  pdb=" N   VAL Y 132 " --> pdb=" O   GLY Y  33 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LYS Y  63 " --> pdb=" O   ALA Y 107 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'Y' and resid 40 through 43
      removed outlier: 6.899A  pdb=" N   TYR Y  74 " --> pdb=" O   GLU Y  91 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   TRP Y  93 " --> pdb=" O   THR Y  72 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR Y  72 " --> pdb=" O   TRP Y  93 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'G' and resid 7 through 9
      removed outlier: 3.657A  pdb=" N   ASN G  45 " --> pdb=" O   GLU G  18 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU G  20 " --> pdb=" O   VAL G  43 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   VAL G  43 " --> pdb=" O   LEU G  20 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE G  39 " --> pdb=" O   ALA G  60 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL G  63 " --> pdb=" O   ALA G  83 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'M' and resid 29 through 31
    Processing sheet with id=  T, first strand: chain 'N' and resid 85 through 90
      removed outlier: 3.979A  pdb=" N   LYS N  85 " --> pdb=" O   HIS N  31 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   THR N  27 " --> pdb=" O   LYS N  89 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   THR N  62 " --> pdb=" O   ILE N  50 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ARG N  52 " --> pdb=" O   THR N  60 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR N  60 " --> pdb=" O   ARG N  52 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE N  61 " --> pdb=" O   PHE N  76 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'P' and resid 10 through 15
      removed outlier: 3.834A  pdb=" N   PHE P  40 " --> pdb=" O   ILE P   4 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLU P   6 " --> pdb=" O   VAL P  38 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL P  38 " --> pdb=" O   GLU P   6 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'P' and resid 19 through 22
    Processing sheet with id=  W, first strand: chain 'P' and resid 32 through 35
      removed outlier: 3.507A  pdb=" N   LYS P  99 " --> pdb=" O   THR P  59 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR P  61 " --> pdb=" O   ILE P  97 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ILE P  97 " --> pdb=" O   THR P  61 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'P' and resid 71 through 76
    Processing sheet with id=  Y, first strand: chain 'Q' and resid 3 through 7
      removed outlier: 6.123A  pdb=" N   SER Q 108 " --> pdb=" O   VAL Q  71 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   VAL Q  71 " --> pdb=" O   SER Q 108 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'Q' and resid 82 through 87
    Processing sheet with id= AA, first strand: chain 'R' and resid 52 through 58
      removed outlier: 4.276A  pdb=" N   ARG R  76 " --> pdb=" O   VAL R  29 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG R   9 " --> pdb=" O   ASP R  28 " (cutoff:3.500A)
    Processing sheet with id= AB, first strand: chain 'S' and resid 20 through 22
    Processing sheet with id= AC, first strand: chain 'S' and resid 82 through 84
    Processing sheet with id= AD, first strand: chain 'T' and resid 6 through 8
      removed outlier: 3.796A  pdb=" N   VAL T  41 " --> pdb=" O   ALA T  29 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   LEU T  92 " --> pdb=" O   VAL T  74 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   VAL T  74 " --> pdb=" O   LEU T  92 " (cutoff:3.500A)
    Processing sheet with id= AE, first strand: chain 'a' and resid 59 through 61
    Processing sheet with id= AF, first strand: chain 'a' and resid 74 through 79
    Processing sheet with id= AG, first strand: chain 'V' and resid 13 through 16
      removed outlier: 4.295A  pdb=" N   SER V  13 " --> pdb=" O   TRP V  29 " (cutoff:3.500A)
    Processing sheet with id= AH, first strand: chain 'V' and resid 33 through 39
      removed outlier: 3.832A  pdb=" N   VAL V  36 " --> pdb=" O   VAL V  47 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL V  47 " --> pdb=" O   VAL V  36 " (cutoff:3.500A)
    Processing sheet with id= AI, first strand: chain 'X' and resid 3 through 7

    471 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1608 hydrogen bonds
      2584 hydrogen bond angles
      0 basepair planarities
      645 basepair parallelities
      1328 stacking parallelities
  Total time for adding SS restraints: 101.84

  Time building geometry restraints manager: 36.78 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 6353
        1.30 -     1.43: 40753
        1.43 -     1.56: 35377
        1.56 -     1.69: 5685
        1.69 -     1.82: 85
  Bond restraints: 88253
  Sorted by residual:
  bond pdb=" C5  5MU A1966 "
       pdb=" C6  5MU A1966 "
    ideal  model  delta    sigma   weight residual
    1.155  1.450 -0.295 2.00e-02 2.50e+03 2.18e+02
  bond pdb=" C5  5MU A 792 "
       pdb=" C6  5MU A 792 "
    ideal  model  delta    sigma   weight residual
    1.155  1.443 -0.288 2.00e-02 2.50e+03 2.07e+02
  bond pdb=" C4  5MU A 792 "
       pdb=" C5  5MU A 792 "
    ideal  model  delta    sigma   weight residual
    1.802  1.611  0.191 2.00e-02 2.50e+03 9.15e+01
  bond pdb=" C4  5MU A1966 "
       pdb=" C5  5MU A1966 "
    ideal  model  delta    sigma   weight residual
    1.802  1.617  0.185 2.00e-02 2.50e+03 8.52e+01
  bond pdb=" N1  5MU A1966 "
       pdb=" C2  5MU A1966 "
    ideal  model  delta    sigma   weight residual
    1.436  1.581 -0.145 2.00e-02 2.50e+03 5.28e+01
  ... (remaining 88248 not shown)

  Histogram of bond angle deviations from ideal:
       97.79 -   106.18: 17076
      106.18 -   114.58: 56352
      114.58 -   122.97: 43815
      122.97 -   131.37: 15140
      131.37 -   139.77: 837
  Bond angle restraints: 133220
  Sorted by residual:
  angle pdb=" CA  CYS 1  12 "
        pdb=" CB  CYS 1  12 "
        pdb=" SG  CYS 1  12 "
      ideal   model   delta    sigma   weight residual
     114.40  130.24  -15.84 2.30e+00 1.89e-01 4.74e+01
  angle pdb=" N   VAL F 224 "
        pdb=" CA  VAL F 224 "
        pdb=" C   VAL F 224 "
      ideal   model   delta    sigma   weight residual
     112.83  106.17    6.66 9.90e-01 1.02e+00 4.53e+01
  angle pdb=" N   ARG E 168 "
        pdb=" CA  ARG E 168 "
        pdb=" C   ARG E 168 "
      ideal   model   delta    sigma   weight residual
     114.75  107.45    7.30 1.26e+00 6.30e-01 3.36e+01
  angle pdb=" N   ARG 1  38 "
        pdb=" CA  ARG 1  38 "
        pdb=" C   ARG 1  38 "
      ideal   model   delta    sigma   weight residual
     114.04  106.96    7.08 1.24e+00 6.50e-01 3.26e+01
  angle pdb=" N   ARG R   4 "
        pdb=" CA  ARG R   4 "
        pdb=" C   ARG R   4 "
      ideal   model   delta    sigma   weight residual
     114.56  107.41    7.15 1.27e+00 6.20e-01 3.17e+01
  ... (remaining 133215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.66: 48369
       35.66 -    71.33: 7201
       71.33 -   106.99: 811
      106.99 -   142.66: 39
      142.66 -   178.32: 29
  Dihedral angle restraints: 56449
    sinusoidal: 49244
      harmonic: 7205
  Sorted by residual:
  dihedral pdb=" C5'   A A 775 "
           pdb=" C4'   A A 775 "
           pdb=" C3'   A A 775 "
           pdb=" O3'   A A 775 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   68.56   78.44     1      8.00e+00 1.56e-02 1.20e+02
  dihedral pdb=" CA  ILE H  58 "
           pdb=" C   ILE H  58 "
           pdb=" N   ASN H  59 "
           pdb=" CA  ASN H  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  128.71   51.29     0      5.00e+00 4.00e-02 1.05e+02
  dihedral pdb=" C4'   A A 775 "
           pdb=" C3'   A A 775 "
           pdb=" C2'   A A 775 "
           pdb=" C1'   A A 775 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   32.82  -67.82     1      8.00e+00 1.56e-02 9.34e+01
  ... (remaining 56446 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 15575
       0.088 -    0.176: 1472
       0.176 -    0.265: 134
       0.265 -    0.353: 37
       0.353 -    0.441: 10
  Chirality restraints: 17228
  Sorted by residual:
  chirality pdb=" C3'   A A 775 "
            pdb=" C4'   A A 775 "
            pdb=" O3'   A A 775 "
            pdb=" C2'   A A 775 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.30   -0.44 2.00e-01 2.50e+01 4.86e+00
  chirality pdb=" C3'   U A1706 "
            pdb=" C4'   U A1706 "
            pdb=" O3'   U A1706 "
            pdb=" C2'   U A1706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.06   -0.41 2.00e-01 2.50e+01 4.27e+00
  chirality pdb=" C3'   C A 572 "
            pdb=" C4'   C A 572 "
            pdb=" O3'   C A 572 "
            pdb=" C2'   C A 572 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.34   -0.41 2.00e-01 2.50e+01 4.13e+00
  ... (remaining 17225 not shown)

  Planarity restraints: 6262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 5MU A 792 "    0.013 2.00e-02 2.50e+03   4.86e-01 5.32e+03
        pdb=" C4' 5MU A 792 "    0.398 2.00e-02 2.50e+03
        pdb=" O4' 5MU A 792 "    0.477 2.00e-02 2.50e+03
        pdb=" C3' 5MU A 792 "   -0.571 2.00e-02 2.50e+03
        pdb=" O3' 5MU A 792 "   -0.413 2.00e-02 2.50e+03
        pdb=" C2' 5MU A 792 "   -0.260 2.00e-02 2.50e+03
        pdb=" O2' 5MU A 792 "    0.793 2.00e-02 2.50e+03
        pdb=" C1' 5MU A 792 "    0.256 2.00e-02 2.50e+03
        pdb=" N1  5MU A 792 "   -0.694 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 5MU A1966 "    0.166 2.00e-02 2.50e+03   2.99e-01 2.01e+03
        pdb=" C4' 5MU A1966 "   -0.312 2.00e-02 2.50e+03
        pdb=" O4' 5MU A1966 "   -0.219 2.00e-02 2.50e+03
        pdb=" C3' 5MU A1966 "    0.469 2.00e-02 2.50e+03
        pdb=" O3' 5MU A1966 "   -0.190 2.00e-02 2.50e+03
        pdb=" C2' 5MU A1966 "    0.420 2.00e-02 2.50e+03
        pdb=" O2' 5MU A1966 "   -0.242 2.00e-02 2.50e+03
        pdb=" C1' 5MU A1966 "   -0.308 2.00e-02 2.50e+03
        pdb=" N1  5MU A1966 "    0.216 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 557 "    0.070 2.00e-02 2.50e+03   2.88e-02 2.49e+01
        pdb=" N9    G A 557 "   -0.062 2.00e-02 2.50e+03
        pdb=" C8    G A 557 "   -0.009 2.00e-02 2.50e+03
        pdb=" N7    G A 557 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    G A 557 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 557 "    0.017 2.00e-02 2.50e+03
        pdb=" O6    G A 557 "    0.015 2.00e-02 2.50e+03
        pdb=" N1    G A 557 "    0.010 2.00e-02 2.50e+03
        pdb=" C2    G A 557 "   -0.010 2.00e-02 2.50e+03
        pdb=" N2    G A 557 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G A 557 "   -0.017 2.00e-02 2.50e+03
        pdb=" C4    G A 557 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 6259 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 676
        2.54 -     3.13: 55803
        3.13 -     3.72: 151152
        3.72 -     4.31: 221929
        4.31 -     4.90: 293252
  Nonbonded interactions: 722812
  Sorted by model distance:
  nonbonded pdb=" O4    U A 163 "
            pdb=" O2'   G A2244 "
     model   vdw
     1.953 2.440
  nonbonded pdb=" O2'   A A1745 "
            pdb=" OP1   C A1793 "
     model   vdw
     1.995 2.440
  nonbonded pdb=" N2    G A2866 "
            pdb=" O6    G A2889 "
     model   vdw
     2.024 2.520
  nonbonded pdb=" O2'   G A1490 "
            pdb=" OP2   C A1491 "
     model   vdw
     2.044 2.440
  nonbonded pdb=" OG1 THR D   2 "
            pdb=" O   ASN D  93 "
     model   vdw
     2.046 2.440
  ... (remaining 722807 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  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:          10.490
  Check model and map are aligned:         0.890
  Set scattering table:                    0.550
  Process input model:                     257.670
  Find NCS groups from input model:        1.220
  Set up NCS constraints:                  0.180
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  284.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2123
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      :  0.008   0.295  88253  Z= 0.465
  Angle     :  1.044  17.817 133220  Z= 0.542
  Chirality :  0.055   0.441  17228
  Planarity :  0.010   0.486   6262
  Dihedral  : 25.085 178.319  51815
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.26 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.48 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.14), residues: 2496
  helix: -1.75 (0.20), residues: 566
  sheet: -1.29 (0.24), residues: 413
  loop : -2.74 (0.13), residues: 1517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP F 213 
 HIS   0.023   0.003   HIS E  49 
 PHE   0.059   0.004   PHE D 147 
 TYR   0.030   0.004   TYR N 101 
 ARG   0.027   0.002   ARG P  79 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  813 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 803
  time to evaluate  : 3.184 
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
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   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
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   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
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "THR V  60 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU X  58 " (corrupted residue). Skipping it.
  outliers start: 10
  outliers final: 8
  residues processed: 809
  average time/residue: 1.8370
  time to fit residues: 1925.9302
Evaluate side-chains
  417 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 409
  time to evaluate  : 3.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  216 LYS
Chi-restraints excluded: chain H residue   45 TYR
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain Q residue  112 GLU
Chi-restraints excluded: chain R residue   90 PHE
Chi-restraints excluded: chain V residue   60 THR
Chi-restraints excluded: chain X residue   58 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 444 optimal weight:    5.9990
   chunk 398 optimal weight:    1.9990
   chunk 221 optimal weight:   20.0000
   chunk 136 optimal weight:   30.0000
   chunk 268 optimal weight:   10.0000
   chunk 212 optimal weight:   20.0000
   chunk 412 optimal weight:    3.9990
   chunk 159 optimal weight:   30.0000
   chunk 250 optimal weight:   40.0000
   chunk 306 optimal weight:    3.9990
   chunk 477 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
2   9 ASN
2  13 HIS
3   7 HIS
** F  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  61 GLN
F  82 GLN
F 153 GLN
D  19 ASN
D  33 ASN
D 134 HIS
** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  78 ASN
Y  12 GLN
Y  46 GLN
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  37 GLN
O  52 GLN
** P  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  60 HIS
Q  61 ASN
Q 102 HIS
R  54 ASN
S  39 ASN
S  45 GLN
V  23 ASN
** W  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2741
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120  88253  Z= 0.238
  Angle     :  0.776  15.512 133220  Z= 0.397
  Chirality :  0.040   0.323  17228
  Planarity :  0.007   0.109   6262
  Dihedral  : 25.092 179.383  46882
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.45 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 20.13 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.15), residues: 2496
  helix: -0.68 (0.21), residues: 535
  sheet: -1.04 (0.24), residues: 439
  loop : -2.28 (0.13), residues: 1522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP Y  41 
 HIS   0.006   0.001   HIS T  88 
 PHE   0.032   0.004   PHE N  76 
 TYR   0.028   0.002   TYR F 103 
 ARG   0.016   0.001   ARG D   8 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  663 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 131
    poor density    : 532
  time to evaluate  : 3.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU O 117 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU X  58 " (corrupted residue). Skipping it.
REVERT: F    6 TYR cc_start: 0.5711 (m-80) cc_final: 0.5483 (m-80)
  outliers start: 131
  outliers final: 47
  residues processed: 597
  average time/residue: 1.6740
  time to fit residues: 1325.8837
Evaluate side-chains
  430 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 383
  time to evaluate  : 3.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 2 residue   13 HIS
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  183 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain Y residue   43 THR
Chi-restraints excluded: chain Y residue   48 GLU
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain Y residue  115 ARG
Chi-restraints excluded: chain G residue   77 ILE
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue   29 ARG
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   60 THR
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain O residue   17 THR
Chi-restraints excluded: chain O residue   79 LEU
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   84 ARG
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue  112 GLU
Chi-restraints excluded: chain R residue   73 ASN
Chi-restraints excluded: chain T residue   21 LEU
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   65 VAL
Chi-restraints excluded: chain X residue   18 THR
Chi-restraints excluded: chain X residue   33 SER
Chi-restraints excluded: chain X residue   37 VAL
Chi-restraints excluded: chain X residue   58 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 265 optimal weight:   30.0000
   chunk 148 optimal weight:   30.0000
   chunk 397 optimal weight:   20.0000
   chunk 325 optimal weight:   10.0000
   chunk 131 optimal weight:   30.0000
   chunk 478 optimal weight:   30.0000
   chunk 516 optimal weight:    5.9990
   chunk 426 optimal weight:    9.9990
   chunk 474 optimal weight:    2.9990
   chunk 163 optimal weight:   20.0000
   chunk 383 optimal weight:    0.4980
   overall best weight:    5.8990

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

Flipped N/Q/H residues before XYZ refinement:
3   7 HIS
F  44 ASN
F  90 ASN
F 153 GLN
F 226 ASN
D 176 ASN
** E  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 148 GLN
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
** H   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  97 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 136 GLN
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   4 GLN
M  55 GLN
** N  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  79 HIS
** S   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 ASN
S  64 HIS
V  16 ASN
** W  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X  32 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3347
moved from start:          0.7668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111  88253  Z= 0.267
  Angle     :  0.752  13.923 133220  Z= 0.387
  Chirality :  0.039   0.314  17228
  Planarity :  0.007   0.122   6262
  Dihedral  : 25.115 178.974  46873
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  7.86 %
    Allowed  : 24.10 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.15), residues: 2496
  helix: -1.14 (0.20), residues: 553
  sheet: -1.23 (0.22), residues: 476
  loop : -2.18 (0.14), residues: 1467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 250 
 HIS   0.090   0.003   HIS 2  13 
 PHE   0.037   0.004   PHE O  47 
 TYR   0.038   0.003   TYR 2   6 
 ARG   0.021   0.001   ARG W  42 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  740 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 162
    poor density    : 578
  time to evaluate  : 3.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   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
TARDY: cannot create tardy model for: "GLU X  58 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: E  184 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4267 (tm)
REVERT: L   39 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5275 (ptmt)
REVERT: N   85 LYS cc_start: 0.3870 (OUTLIER) cc_final: 0.2723 (ptmm)
REVERT: P   12 ILE cc_start: 0.4679 (OUTLIER) cc_final: 0.4403 (pt)
REVERT: a   33 ARG cc_start: 0.5248 (OUTLIER) cc_final: 0.4967 (mpp-170)
  outliers start: 162
  outliers final: 44
  residues processed: 658
  average time/residue: 1.7745
  time to fit residues: 1559.3615
Evaluate side-chains
  482 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 433
  time to evaluate  : 3.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   10 LYS
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain D residue    3 LYS
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  211 ILE
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   43 THR
Chi-restraints excluded: chain Y residue  115 ARG
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   77 ILE
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue  119 PHE
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   29 ARG
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   70 VAL
Chi-restraints excluded: chain N residue   85 LYS
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain O residue   79 LEU
Chi-restraints excluded: chain P residue   12 ILE
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   28 ASN
Chi-restraints excluded: chain Q residue   50 VAL
Chi-restraints excluded: chain Q residue   75 TYR
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain Q residue  107 VAL
Chi-restraints excluded: chain S residue   63 ILE
Chi-restraints excluded: chain S residue   92 ARG
Chi-restraints excluded: chain T residue   39 VAL
Chi-restraints excluded: chain T residue   48 PHE
Chi-restraints excluded: chain T residue   65 VAL
Chi-restraints excluded: chain a residue   33 ARG
Chi-restraints excluded: chain a residue   39 VAL
Chi-restraints excluded: chain W residue   12 SER
Chi-restraints excluded: chain X residue   37 VAL
Chi-restraints excluded: chain X residue   58 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 472 optimal weight:   40.0000
   chunk 359 optimal weight:    1.9990
   chunk 248 optimal weight:   20.0000
   chunk 52 optimal weight:   20.0000
   chunk 228 optimal weight:   30.0000
   chunk 321 optimal weight:   40.0000
   chunk 480 optimal weight:   10.0000
   chunk 508 optimal weight:   20.0000
   chunk 250 optimal weight:   50.0000
   chunk 455 optimal weight:   20.0000
   chunk 137 optimal weight:   50.0000
   overall best weight:   14.3998

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

Flipped N/Q/H residues before XYZ refinement:
3  35 ASN
F 226 ASN
F 228 ASN
** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 GLN
D 181 GLN
** E  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  46 GLN
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  11 ASN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  37 GLN
O  44 GLN
O  72 HIS
Q  97 ASN
R  47 ASN
** S   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  85 GLN
** W  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X  32 ASN
b  19 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3922
moved from start:          1.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.101  88253  Z= 0.421
  Angle     :  0.966  16.913 133220  Z= 0.487
  Chirality :  0.049   0.393  17228
  Planarity :  0.008   0.112   6262
  Dihedral  : 25.801 178.905  46870
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 32.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.54 %
    Favored  : 90.38 %
  Rotamer:
    Outliers : 10.23 %
    Allowed  : 27.26 %
    Favored  : 62.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.15), residues: 2496
  helix: -1.91 (0.19), residues: 521
  sheet: -1.35 (0.21), residues: 525
  loop : -2.31 (0.14), residues: 1450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP E  65 
 HIS   0.014   0.003   HIS D 134 
 PHE   0.043   0.004   PHE a  77 
 TYR   0.037   0.004   TYR F 103 
 ARG   0.024   0.002   ARG M  11 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  788 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 211
    poor density    : 577
  time to evaluate  : 3.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   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
TARDY: cannot create tardy model for: "GLU X  58 " (corrupted residue). Skipping it.
REVERT: S   76 ASN cc_start: 0.4257 (p0) cc_final: 0.3970 (p0)
REVERT: T   42 LYS cc_start: 0.3897 (OUTLIER) cc_final: 0.3574 (ptmm)
  outliers start: 211
  outliers final: 75
  residues processed: 695
  average time/residue: 1.6431
  time to fit residues: 1519.9694
Evaluate side-chains
  518 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 442
  time to evaluate  : 3.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   35 TYR
Chi-restraints excluded: chain 2 residue    9 ASN
Chi-restraints excluded: chain 2 residue   13 HIS
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue   20 ASP
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  221 ARG
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   51 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   77 ARG
Chi-restraints excluded: chain H residue   88 ILE
Chi-restraints excluded: chain H residue   96 THR
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  123 VAL
Chi-restraints excluded: chain Y residue   48 GLU
Chi-restraints excluded: chain Y residue  113 VAL
Chi-restraints excluded: chain Y residue  122 SER
Chi-restraints excluded: chain Y residue  129 THR
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   77 ILE
Chi-restraints excluded: chain G residue   85 VAL
Chi-restraints excluded: chain G residue   98 ILE
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue    9 LYS
Chi-restraints excluded: chain M residue   10 VAL
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain O residue    4 VAL
Chi-restraints excluded: chain O residue   39 VAL
Chi-restraints excluded: chain O residue   52 GLN
Chi-restraints excluded: chain O residue  109 LEU
Chi-restraints excluded: chain O residue  114 LYS
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   63 ASN
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   47 ILE
Chi-restraints excluded: chain Q residue   63 ASP
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain Q residue  104 THR
Chi-restraints excluded: chain R residue    5 ASP
Chi-restraints excluded: chain R residue   13 THR
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain S residue   33 VAL
Chi-restraints excluded: chain S residue   63 ILE
Chi-restraints excluded: chain S residue   97 SER
Chi-restraints excluded: chain T residue   42 LYS
Chi-restraints excluded: chain T residue   46 VAL
Chi-restraints excluded: chain T residue   60 VAL
Chi-restraints excluded: chain T residue   65 VAL
Chi-restraints excluded: chain a residue   58 ASN
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain V residue   40 VAL
Chi-restraints excluded: chain X residue   58 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 423 optimal weight:   30.0000
   chunk 288 optimal weight:    5.9990
   chunk 7 optimal weight:   30.0000
   chunk 378 optimal weight:    5.9990
   chunk 209 optimal weight:   20.0000
   chunk 433 optimal weight:    7.9990
   chunk 351 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 259 optimal weight:   50.0000
   chunk 456 optimal weight:   10.0000
   chunk 128 optimal weight:   20.0000
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
** 3  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 ASN
** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 ASN
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  49 HIS
E  53 ASN
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
** H   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  24 GLN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  97 ASN
Y  35 GLN
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  47 ASN
R  57 ASN
S   8 ASN
** W  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3844
moved from start:          1.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  88253  Z= 0.219
  Angle     :  0.694  13.667 133220  Z= 0.358
  Chirality :  0.038   0.331  17228
  Planarity :  0.006   0.113   6262
  Dihedral  : 25.289 179.429  46870
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 20.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 35.16 %
    Favored  : 57.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.15), residues: 2496
  helix: -0.89 (0.21), residues: 534
  sheet: -1.21 (0.22), residues: 512
  loop : -2.12 (0.15), residues: 1450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  16 
 HIS   0.006   0.001   HIS S  64 
 PHE   0.025   0.002   PHE O 106 
 TYR   0.023   0.002   TYR M  34 
 ARG   0.013   0.001   ARG O  53 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  649 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 143
    poor density    : 506
  time to evaluate  : 3.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU X  58 " (corrupted residue). Skipping it.
REVERT: E   84 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6396 (mtp-110)
REVERT: H   17 TYR cc_start: 0.4731 (m-10) cc_final: 0.4402 (m-80)
REVERT: N   76 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.5108 (p90)
  outliers start: 143
  outliers final: 64
  residues processed: 584
  average time/residue: 1.6385
  time to fit residues: 1285.0416
Evaluate side-chains
  503 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 437
  time to evaluate  : 3.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue   20 ASP
Chi-restraints excluded: chain F residue  121 GLU
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain E residue   13 LYS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   84 ARG
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  194 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   38 THR
Chi-restraints excluded: chain Y residue   48 GLU
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain Y residue  129 THR
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   77 ILE
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue   98 ILE
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue    9 LYS
Chi-restraints excluded: chain M residue   66 THR
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   11 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   76 PHE
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain O residue   95 LEU
Chi-restraints excluded: chain O residue   96 SER
Chi-restraints excluded: chain O residue  109 LEU
Chi-restraints excluded: chain P residue   14 VAL
Chi-restraints excluded: chain P residue   26 ASP
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   21 LEU
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain Q residue  105 ILE
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue    9 VAL
Chi-restraints excluded: chain S residue   33 VAL
Chi-restraints excluded: chain S residue   68 VAL
Chi-restraints excluded: chain T residue   22 ARG
Chi-restraints excluded: chain T residue   65 VAL
Chi-restraints excluded: chain a residue   33 ARG
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain W residue   12 SER
Chi-restraints excluded: chain X residue   58 GLU
Chi-restraints excluded: chain b residue   11 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 171 optimal weight:   50.0000
   chunk 457 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 298 optimal weight:    6.9990
   chunk 125 optimal weight:   30.0000
   chunk 508 optimal weight:   20.0000
   chunk 422 optimal weight:   50.0000
   chunk 235 optimal weight:   30.0000
   chunk 42 optimal weight:   40.0000
   chunk 168 optimal weight:   30.0000
   chunk 267 optimal weight:   20.0000
   overall best weight:   17.3998

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

Flipped N/Q/H residues before XYZ refinement:
F  82 GLN
F 230 HIS
D 128 GLN
D 134 HIS
D 200 ASN
** E  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  24 GLN
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  46 GLN
** M  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  28 ASN
V  34 GLN
W  36 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4056
moved from start:          1.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.166  88253  Z= 0.447
  Angle     :  0.924  14.868 133220  Z= 0.461
  Chirality :  0.047   0.371  17228
  Planarity :  0.007   0.115   6262
  Dihedral  : 25.662 178.557  46870
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 33.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  8.34 %
    Allowed  : 35.45 %
    Favored  : 56.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.15), residues: 2496
  helix: -1.27 (0.20), residues: 560
  sheet: -1.50 (0.23), residues: 474
  loop : -2.28 (0.15), residues: 1462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  16 
 HIS   0.013   0.002   HIS X  52 
 PHE   0.033   0.003   PHE W  26 
 TYR   0.031   0.003   TYR 2   6 
 ARG   0.015   0.001   ARG R  32 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  646 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 172
    poor density    : 474
  time to evaluate  : 3.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   76 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5332 (p90)
REVERT: N   85 LYS cc_start: 0.4231 (ptmm) cc_final: 0.3428 (pttp)
REVERT: N   86 ILE cc_start: 0.5221 (OUTLIER) cc_final: 0.4312 (pp)
REVERT: Q   65 ASN cc_start: 0.3910 (OUTLIER) cc_final: 0.3675 (p0)
REVERT: R   30 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4898 (p0)
REVERT: R   68 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.2191 (m-10)
REVERT: S    4 LYS cc_start: 0.5076 (OUTLIER) cc_final: 0.4487 (pmtt)
REVERT: X   24 GLU cc_start: 0.4049 (tp30) cc_final: 0.3810 (tp30)
REVERT: X   59 LYS cc_start: 0.3253 (pmtt) cc_final: 0.2970 (pmtt)
  outliers start: 172
  outliers final: 78
  residues processed: 582
  average time/residue: 1.6630
  time to fit residues: 1296.8796
Evaluate side-chains
  499 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 415
  time to evaluate  : 3.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 1 residue   41 LYS
Chi-restraints excluded: chain 2 residue    9 ASN
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain 3 residue   19 SER
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue   70 ASN
Chi-restraints excluded: chain F residue  121 GLU
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain D residue   19 ASN
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   13 LYS
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  194 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   88 ILE
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue  115 ARG
Chi-restraints excluded: chain Y residue  122 SER
Chi-restraints excluded: chain Y residue  129 THR
Chi-restraints excluded: chain G residue    2 ILE
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   42 THR
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   73 ASP
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue   66 THR
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   70 VAL
Chi-restraints excluded: chain N residue   76 PHE
Chi-restraints excluded: chain N residue   86 ILE
Chi-restraints excluded: chain N residue  113 GLN
Chi-restraints excluded: chain O residue    4 VAL
Chi-restraints excluded: chain O residue   96 SER
Chi-restraints excluded: chain P residue   26 ASP
Chi-restraints excluded: chain P residue   36 ASP
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   21 LEU
Chi-restraints excluded: chain Q residue   65 ASN
Chi-restraints excluded: chain Q residue   66 THR
Chi-restraints excluded: chain Q residue   86 ARG
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain Q residue  104 THR
Chi-restraints excluded: chain Q residue  105 ILE
Chi-restraints excluded: chain R residue   17 SER
Chi-restraints excluded: chain R residue   30 ASP
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue   68 TYR
Chi-restraints excluded: chain R residue   90 PHE
Chi-restraints excluded: chain S residue    4 LYS
Chi-restraints excluded: chain S residue    9 VAL
Chi-restraints excluded: chain T residue   22 ARG
Chi-restraints excluded: chain T residue   60 VAL
Chi-restraints excluded: chain a residue   58 ASN
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain X residue   23 VAL
Chi-restraints excluded: chain b residue   11 THR
Chi-restraints excluded: chain b residue   18 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 490 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 289 optimal weight:    6.9990
   chunk 371 optimal weight:    6.9990
   chunk 287 optimal weight:   10.0000
   chunk 428 optimal weight:   30.0000
   chunk 284 optimal weight:    0.0670
   chunk 506 optimal weight:    6.9990
   chunk 317 optimal weight:   20.0000
   chunk 309 optimal weight:   10.0000
   chunk 234 optimal weight:   20.0000
   overall best weight:    6.2128

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

Flipped N/Q/H residues before XYZ refinement:
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** Y  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 HIS
N 113 GLN
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  18 GLN
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  37 GLN
V  34 GLN
W  36 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3921
moved from start:          1.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  88253  Z= 0.210
  Angle     :  0.700  16.262 133220  Z= 0.360
  Chirality :  0.038   0.345  17228
  Planarity :  0.006   0.113   6262
  Dihedral  : 25.277 179.116  46867
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 21.36
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.93 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 38.89 %
    Favored  : 56.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.15), residues: 2496
  helix: -0.85 (0.21), residues: 540
  sheet: -1.26 (0.24), residues: 465
  loop : -2.10 (0.15), residues: 1491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP V  48 
 HIS   0.005   0.001   HIS X  52 
 PHE   0.022   0.002   PHE O 106 
 TYR   0.024   0.002   TYR P  76 
 ARG   0.011   0.001   ARG H  95 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  568 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 103
    poor density    : 465
  time to evaluate  : 3.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  228 ASN cc_start: 0.0235 (OUTLIER) cc_final: -0.0597 (t0)
REVERT: N   76 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.5237 (p90)
REVERT: R   30 ASP cc_start: 0.5134 (OUTLIER) cc_final: 0.4882 (p0)
REVERT: R   68 TYR cc_start: 0.2403 (OUTLIER) cc_final: 0.2122 (m-10)
REVERT: a   65 ASP cc_start: 0.5078 (m-30) cc_final: 0.4867 (m-30)
  outliers start: 103
  outliers final: 65
  residues processed: 526
  average time/residue: 1.6521
  time to fit residues: 1167.0687
Evaluate side-chains
  497 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 428
  time to evaluate  : 3.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 1 residue   35 TYR
Chi-restraints excluded: chain 1 residue   41 LYS
Chi-restraints excluded: chain 2 residue    9 ASN
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain 3 residue   62 LEU
Chi-restraints excluded: chain F residue   70 ASN
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  228 ASN
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain E residue   13 LYS
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue  129 THR
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   73 ASP
Chi-restraints excluded: chain G residue   75 SER
Chi-restraints excluded: chain G residue   77 ILE
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue    9 LYS
Chi-restraints excluded: chain M residue   66 THR
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   70 VAL
Chi-restraints excluded: chain N residue   76 PHE
Chi-restraints excluded: chain O residue   18 ILE
Chi-restraints excluded: chain P residue   26 ASP
Chi-restraints excluded: chain P residue   32 THR
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   63 ASN
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   21 LEU
Chi-restraints excluded: chain Q residue   66 THR
Chi-restraints excluded: chain Q residue   86 ARG
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain Q residue  105 ILE
Chi-restraints excluded: chain R residue   30 ASP
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue   68 TYR
Chi-restraints excluded: chain S residue    9 VAL
Chi-restraints excluded: chain S residue   16 ASP
Chi-restraints excluded: chain T residue   60 VAL
Chi-restraints excluded: chain a residue   33 ARG
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain X residue   23 VAL
Chi-restraints excluded: chain b residue   11 THR
Chi-restraints excluded: chain b residue   18 THR
Chi-restraints excluded: chain b residue   41 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 313 optimal weight:   40.0000
   chunk 202 optimal weight:   90.0000
   chunk 302 optimal weight:   20.0000
   chunk 152 optimal weight:   30.0000
   chunk 99 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 322 optimal weight:    0.0070
   chunk 345 optimal weight:    9.9990
   chunk 250 optimal weight:   40.0000
   chunk 47 optimal weight:   30.0000
   chunk 398 optimal weight:   30.0000
   overall best weight:   14.0012

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

Flipped N/Q/H residues before XYZ refinement:
F  46 GLN
** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  19 ASN
** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  59 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 ASN
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  65 ASN
V  34 GLN
** W  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4057
moved from start:          1.5217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.107  88253  Z= 0.371
  Angle     :  0.850  16.474 133220  Z= 0.428
  Chirality :  0.044   0.378  17228
  Planarity :  0.006   0.115   6262
  Dihedral  : 25.550 178.187  46864
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 31.05
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 11.06 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 37.92 %
    Favored  : 55.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.15), residues: 2496
  helix: -0.99 (0.21), residues: 542
  sheet: -1.64 (0.23), residues: 475
  loop : -2.09 (0.15), residues: 1479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP V  48 
 HIS   0.011   0.002   HIS b  40 
 PHE   0.030   0.003   PHE O  47 
 TYR   0.033   0.003   TYR F 171 
 ARG   0.024   0.001   ARG Q  25 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  586 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 135
    poor density    : 451
  time to evaluate  : 3.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  228 ASN cc_start: 0.0458 (OUTLIER) cc_final: -0.0341 (t0)
REVERT: M    8 ASN cc_start: 0.2946 (m110) cc_final: 0.2719 (m-40)
REVERT: N   76 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5266 (p90)
REVERT: O   90 ILE cc_start: 0.5801 (tp) cc_final: 0.5566 (tp)
REVERT: R    6 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3752 (pp)
REVERT: R   68 TYR cc_start: 0.2797 (OUTLIER) cc_final: 0.2404 (m-10)
REVERT: S    4 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.5208 (pmtt)
REVERT: T   79 PHE cc_start: 0.4742 (t80) cc_final: 0.4537 (t80)
  outliers start: 135
  outliers final: 84
  residues processed: 531
  average time/residue: 1.5963
  time to fit residues: 1149.1405
Evaluate side-chains
  510 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 89
    poor density    : 421
  time to evaluate  : 3.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 1 residue   41 LYS
Chi-restraints excluded: chain 2 residue    9 ASN
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain F residue   70 ASN
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  220 VAL
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  228 ASN
Chi-restraints excluded: chain D residue   19 ASN
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  147 PHE
Chi-restraints excluded: chain D residue  176 ASN
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  197 VAL
Chi-restraints excluded: chain D residue  200 ASN
Chi-restraints excluded: chain D residue  215 ILE
Chi-restraints excluded: chain E residue    6 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  194 ILE
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   88 ILE
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   17 THR
Chi-restraints excluded: chain Y residue   66 ILE
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain Y residue  122 SER
Chi-restraints excluded: chain Y residue  129 THR
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   73 ASP
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue   98 ILE
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain M residue   66 THR
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   10 VAL
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   50 ILE
Chi-restraints excluded: chain N residue   70 VAL
Chi-restraints excluded: chain N residue   76 PHE
Chi-restraints excluded: chain N residue   88 VAL
Chi-restraints excluded: chain O residue   18 ILE
Chi-restraints excluded: chain O residue   96 SER
Chi-restraints excluded: chain P residue   26 ASP
Chi-restraints excluded: chain P residue   32 THR
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   62 VAL
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   21 LEU
Chi-restraints excluded: chain Q residue   71 VAL
Chi-restraints excluded: chain Q residue   86 ARG
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain R residue    6 ILE
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue   68 TYR
Chi-restraints excluded: chain R residue   87 ILE
Chi-restraints excluded: chain R residue   90 PHE
Chi-restraints excluded: chain S residue    4 LYS
Chi-restraints excluded: chain S residue    9 VAL
Chi-restraints excluded: chain S residue   33 VAL
Chi-restraints excluded: chain S residue   79 THR
Chi-restraints excluded: chain T residue   22 ARG
Chi-restraints excluded: chain T residue   60 VAL
Chi-restraints excluded: chain a residue   33 ARG
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain V residue   19 SER
Chi-restraints excluded: chain W residue   32 LEU
Chi-restraints excluded: chain b residue   11 THR
Chi-restraints excluded: chain b residue   18 THR
Chi-restraints excluded: chain b residue   41 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 461 optimal weight:    5.9990
   chunk 485 optimal weight:    0.5980
   chunk 443 optimal weight:    2.9990
   chunk 472 optimal weight:   20.0000
   chunk 284 optimal weight:    7.9990
   chunk 205 optimal weight:   50.0000
   chunk 370 optimal weight:    1.9990
   chunk 144 optimal weight:   20.0000
   chunk 426 optimal weight:   50.0000
   chunk 446 optimal weight:    5.9990
   chunk 470 optimal weight:   40.0000
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
F  61 GLN
D  93 ASN
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  41 ASN
Y  35 GLN
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 113 GLN
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  34 GLN
W  36 GLN
b  19 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3871
moved from start:          1.5199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  88253  Z= 0.170
  Angle     :  0.677  17.543 133220  Z= 0.348
  Chirality :  0.036   0.358  17228
  Planarity :  0.005   0.113   6262
  Dihedral  : 25.141 179.570  46864
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 41.32 %
    Favored  : 55.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.16), residues: 2496
  helix: -0.78 (0.22), residues: 538
  sheet: -1.14 (0.24), residues: 446
  loop : -1.95 (0.15), residues: 1512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 213 
 HIS   0.005   0.001   HIS T  88 
 PHE   0.022   0.002   PHE O 106 
 TYR   0.026   0.002   TYR P  76 
 ARG   0.011   0.001   ARG S  32 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  540 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 468
  time to evaluate  : 3.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE R  90 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   32 MET cc_start: 0.0480 (mmt) cc_final: -0.0190 (tpt)
  outliers start: 72
  outliers final: 46
  residues processed: 507
  average time/residue: 1.6443
  time to fit residues: 1119.3982
Evaluate side-chains
  475 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 429
  time to evaluate  : 3.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain F residue  121 GLU
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  220 VAL
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  200 ASN
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   66 ILE
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain G residue   13 ASN
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASP
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain N residue   51 LYS
Chi-restraints excluded: chain O residue  102 ASP
Chi-restraints excluded: chain P residue   36 ASP
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   62 VAL
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue   66 THR
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain T residue   17 ASP
Chi-restraints excluded: chain T residue   22 ARG
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain X residue   23 VAL
Chi-restraints excluded: chain b residue   18 THR
Chi-restraints excluded: chain b residue   41 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 310 optimal weight:   30.0000
   chunk 499 optimal weight:    7.9990
   chunk 304 optimal weight:    0.8980
   chunk 236 optimal weight:   30.0000
   chunk 347 optimal weight:   30.0000
   chunk 524 optimal weight:    2.9990
   chunk 482 optimal weight:    5.9990
   chunk 417 optimal weight:   20.0000
   chunk 43 optimal weight:   40.0000
   chunk 322 optimal weight:   40.0000
   chunk 255 optimal weight:   30.0000
   overall best weight:    7.5790

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

Flipped N/Q/H residues before XYZ refinement:
** 3  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  93 ASN
** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  41 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 113 GLN
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  37 GLN
V  34 GLN
W  27 ASN
X  19 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3942
moved from start:          1.5363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  88253  Z= 0.226
  Angle     :  0.705  17.519 133220  Z= 0.361
  Chirality :  0.037   0.361  17228
  Planarity :  0.006   0.113   6262
  Dihedral  : 25.144 179.358  46864
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 22.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 42.53 %
    Favored  : 54.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.16), residues: 2496
  helix: -0.71 (0.22), residues: 543
  sheet: -1.12 (0.24), residues: 445
  loop : -1.97 (0.15), residues: 1508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP V  48 
 HIS   0.007   0.001   HIS X  52 
 PHE   0.037   0.002   PHE O 106 
 TYR   0.049   0.002   TYR O  32 
 ARG   0.013   0.001   ARG S  32 

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

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

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4992 Ramachandran restraints generated.
    2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  492 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 432
  time to evaluate  : 3.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU G 122 " (corrupted residue). Skipping it.
   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: Q    1 MET cc_start: 0.4937 (OUTLIER) cc_final: 0.4708 (ppp)
REVERT: R   30 ASP cc_start: 0.5387 (OUTLIER) cc_final: 0.5114 (p0)
  outliers start: 60
  outliers final: 51
  residues processed: 467
  average time/residue: 1.6804
  time to fit residues: 1054.0409
Evaluate side-chains
  462 residues out of total 2123 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 409
  time to evaluate  : 3.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   12 CYS
Chi-restraints excluded: chain 1 residue   41 LYS
Chi-restraints excluded: chain 2 residue    9 ASN
Chi-restraints excluded: chain 2 residue   25 THR
Chi-restraints excluded: chain 3 residue   44 LEU
Chi-restraints excluded: chain F residue  140 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  220 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  139 PHE
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 HIS
Chi-restraints excluded: chain L residue   67 THR
Chi-restraints excluded: chain L residue   72 LYS
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain Y residue   66 ILE
Chi-restraints excluded: chain Y residue   75 THR
Chi-restraints excluded: chain G residue   13 ASN
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   22 ILE
Chi-restraints excluded: chain G residue   56 ASP
Chi-restraints excluded: chain G residue   73 ASP
Chi-restraints excluded: chain G residue   96 THR
Chi-restraints excluded: chain G residue  122 LEU
Chi-restraints excluded: chain N residue    2 THR
Chi-restraints excluded: chain N residue   30 VAL
Chi-restraints excluded: chain N residue   34 ILE
Chi-restraints excluded: chain O residue   18 ILE
Chi-restraints excluded: chain P residue   26 ASP
Chi-restraints excluded: chain P residue   36 ASP
Chi-restraints excluded: chain P residue   61 THR
Chi-restraints excluded: chain P residue   62 VAL
Chi-restraints excluded: chain P residue   96 THR
Chi-restraints excluded: chain Q residue    1 MET
Chi-restraints excluded: chain Q residue   21 LEU
Chi-restraints excluded: chain Q residue   92 ARG
Chi-restraints excluded: chain R residue   30 ASP
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   16 ASP
Chi-restraints excluded: chain S residue   57 LEU
Chi-restraints excluded: chain T residue   17 ASP
Chi-restraints excluded: chain T residue   22 ARG
Chi-restraints excluded: chain a residue   75 VAL
Chi-restraints excluded: chain b residue   18 THR
Chi-restraints excluded: chain b residue   41 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 526
   random chunks:
   chunk 331 optimal weight:   30.0000
   chunk 444 optimal weight:    6.9990
   chunk 127 optimal weight:   30.0000
   chunk 384 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 115 optimal weight:   20.0000
   chunk 417 optimal weight:    9.9990
   chunk 174 optimal weight:   70.0000
   chunk 429 optimal weight:    7.9990
   chunk 52 optimal weight:   30.0000
   chunk 76 optimal weight:   30.0000
   overall best weight:   10.1992

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

Flipped N/Q/H residues before XYZ refinement:
** 3  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  14 GLN
N 113 GLN
** O  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  65 ASN
a  37 GLN
V  34 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.076639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.054696 restraints weight = 468909.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.59
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          1.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  88253  Z= 0.280
  Angle     :  0.752  17.306 133220  Z= 0.384
  Chirality :  0.039   0.360  17228
  Planarity :  0.006   0.114   6262
  Dihedral  : 25.269 178.776  46864
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 42.29 %
    Favored  : 54.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.15), residues: 2496
  helix: -0.93 (0.21), residues: 549
  sheet: -1.21 (0.24), residues: 459
  loop : -2.02 (0.15), residues: 1488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP V  48 
 HIS   0.009   0.001   HIS b  40 
 PHE   0.153   0.003   PHE E 139 
 TYR   0.033   0.002   TYR M  34 
 ARG   0.015   0.001   ARG V  17 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 21455.52 seconds
wall clock time: 378 minutes 1.63 seconds (22681.63 seconds total)