Starting phenix.real_space_refine
on Fri Dec 15 23:47:41 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2023/6xz7_10655_updated.pdb"
  }
  resolution = 2.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P    3170      5.49       5
     Mg    178      5.21       5
     S      85      5.16       5
     C   46777      2.51       5
     N   17508      2.21       5
     O   27197      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C ARG   52": "NH1" <-> "NH2"
    Residue "C ARG   63": "NH1" <-> "NH2"
    Residue "C ARG   80": "NH1" <-> "NH2"
    Residue "C GLU   82": "OE1" <-> "OE2"
    Residue "C GLU  100": "OE1" <-> "OE2"
    Residue "C ARG  133": "NH1" <-> "NH2"
    Residue "C ARG  167": "NH1" <-> "NH2"
    Residue "C ARG  177": "NH1" <-> "NH2"
    Residue "C ARG  182": "NH1" <-> "NH2"
    Residue "C GLU  185": "OE1" <-> "OE2"
    Residue "C ARG  189": "NH1" <-> "NH2"
    Residue "C ARG  203": "NH1" <-> "NH2"
    Residue "C ARG  212": "NH1" <-> "NH2"
    Residue "C GLU  236": "OE1" <-> "OE2"
    Residue "D ARG   13": "NH1" <-> "NH2"
    Residue "D GLU   28": "OE1" <-> "OE2"
    Residue "D ARG   33": "NH1" <-> "NH2"
    Residue "D ARG   59": "NH1" <-> "NH2"
    Residue "D GLU   64": "OE1" <-> "OE2"
    Residue "D GLU   74": "OE1" <-> "OE2"
    Residue "D ARG   77": "NH1" <-> "NH2"
    Residue "D GLU   81": "OE1" <-> "OE2"
    Residue "D ARG   83": "NH1" <-> "NH2"
    Residue "D GLU   86": "OE1" <-> "OE2"
    Residue "D GLU   88": "OE1" <-> "OE2"
    Residue "D ARG  169": "NH1" <-> "NH2"
    Residue "D ARG  184": "NH1" <-> "NH2"
    Residue "E GLU    2": "OE1" <-> "OE2"
    Residue "E ARG   21": "NH1" <-> "NH2"
    Residue "E ARG   44": "NH1" <-> "NH2"
    Residue "E ARG   49": "NH1" <-> "NH2"
    Residue "E ARG   61": "NH1" <-> "NH2"
    Residue "E ARG   88": "NH1" <-> "NH2"
    Residue "E ARG  102": "NH1" <-> "NH2"
    Residue "E GLU  111": "OE1" <-> "OE2"
    Residue "E GLU  122": "OE1" <-> "OE2"
    Residue "E GLU  127": "OE1" <-> "OE2"
    Residue "E GLU  144": "OE1" <-> "OE2"
    Residue "E GLU  152": "OE1" <-> "OE2"
    Residue "E GLU  155": "OE1" <-> "OE2"
    Residue "E ARG  162": "NH1" <-> "NH2"
    Residue "E ARG  170": "NH1" <-> "NH2"
    Residue "F GLU   11": "OE1" <-> "OE2"
    Residue "F GLU   32": "OE1" <-> "OE2"
    Residue "F GLU   42": "OE1" <-> "OE2"
    Residue "F ARG   71": "NH1" <-> "NH2"
    Residue "F ARG   92": "NH1" <-> "NH2"
    Residue "F GLU   94": "OE1" <-> "OE2"
    Residue "F ARG  102": "NH1" <-> "NH2"
    Residue "F ARG  110": "NH1" <-> "NH2"
    Residue "F ARG  115": "NH1" <-> "NH2"
    Residue "F ARG  133": "NH1" <-> "NH2"
    Residue "F GLU  164": "OE1" <-> "OE2"
    Residue "F GLU  165": "OE1" <-> "OE2"
    Residue "G ARG    3": "NH1" <-> "NH2"
    Residue "G GLU   42": "OE1" <-> "OE2"
    Residue "G PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  153": "NH1" <-> "NH2"
    Residue "G GLU  155": "OE1" <-> "OE2"
    Residue "G ARG  163": "NH1" <-> "NH2"
    Residue "G ARG  170": "NH1" <-> "NH2"
    Residue "G GLU  173": "OE1" <-> "OE2"
    Residue "H GLU   87": "OE1" <-> "OE2"
    Residue "H PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU  114": "OE1" <-> "OE2"
    Residue "H GLU  133": "OE1" <-> "OE2"
    Residue "J GLU    9": "OE1" <-> "OE2"
    Residue "J ARG   13": "NH1" <-> "NH2"
    Residue "J ARG   37": "NH1" <-> "NH2"
    Residue "J GLU   90": "OE1" <-> "OE2"
    Residue "J GLU   91": "OE1" <-> "OE2"
    Residue "J ARG   96": "NH1" <-> "NH2"
    Residue "J GLU  102": "OE1" <-> "OE2"
    Residue "J ARG  120": "NH1" <-> "NH2"
    Residue "K GLU    4": "OE1" <-> "OE2"
    Residue "K GLU  106": "OE1" <-> "OE2"
    Residue "K GLU  110": "OE1" <-> "OE2"
    Residue "L GLU   10": "OE1" <-> "OE2"
    Residue "L ARG   21": "NH1" <-> "NH2"
    Residue "L ARG   33": "NH1" <-> "NH2"
    Residue "L ARG   41": "NH1" <-> "NH2"
    Residue "L ARG   47": "NH1" <-> "NH2"
    Residue "L ARG   60": "NH1" <-> "NH2"
    Residue "L GLU   76": "OE1" <-> "OE2"
    Residue "L ARG   78": "NH1" <-> "NH2"
    Residue "L GLU  106": "OE1" <-> "OE2"
    Residue "L ARG  126": "NH1" <-> "NH2"
    Residue "M ARG   10": "NH1" <-> "NH2"
    Residue "M ARG   18": "NH1" <-> "NH2"
    Residue "M ARG   40": "NH1" <-> "NH2"
    Residue "M ARG   44": "NH1" <-> "NH2"
    Residue "M GLU   47": "OE1" <-> "OE2"
    Residue "M ARG   50": "NH1" <-> "NH2"
    Residue "M ARG   59": "NH1" <-> "NH2"
    Residue "M GLU   90": "OE1" <-> "OE2"
    Residue "M GLU  104": "OE1" <-> "OE2"
    Residue "M ARG  114": "NH1" <-> "NH2"
    Residue "N ARG    8": "NH1" <-> "NH2"
    Residue "N ARG   12": "NH1" <-> "NH2"
    Residue "N ARG   17": "NH1" <-> "NH2"
    Residue "N ARG   22": "NH1" <-> "NH2"
    Residue "N GLU   32": "OE1" <-> "OE2"
    Residue "N GLU   43": "OE1" <-> "OE2"
    Residue "N ARG   46": "NH1" <-> "NH2"
    Residue "N GLU   49": "OE1" <-> "OE2"
    Residue "N ARG   63": "NH1" <-> "NH2"
    Residue "N ARG   64": "NH1" <-> "NH2"
    Residue "N ARG   69": "NH1" <-> "NH2"
    Residue "N ARG   71": "NH1" <-> "NH2"
    Residue "N GLU   82": "OE1" <-> "OE2"
    Residue "N ARG   96": "NH1" <-> "NH2"
    Residue "N ARG  118": "NH1" <-> "NH2"
    Residue "N GLU  120": "OE1" <-> "OE2"
    Residue "O ARG   10": "NH1" <-> "NH2"
    Residue "O ARG   16": "NH1" <-> "NH2"
    Residue "O ARG   25": "NH1" <-> "NH2"
    Residue "O GLU   55": "OE1" <-> "OE2"
    Residue "O GLU   60": "OE1" <-> "OE2"
    Residue "O GLU   80": "OE1" <-> "OE2"
    Residue "O ARG   81": "NH1" <-> "NH2"
    Residue "O ARG   94": "NH1" <-> "NH2"
    Residue "O ARG  102": "NH1" <-> "NH2"
    Residue "O ARG  111": "NH1" <-> "NH2"
    Residue "O GLU  112": "OE1" <-> "OE2"
    Residue "P ARG   21": "NH1" <-> "NH2"
    Residue "P ARG   39": "NH1" <-> "NH2"
    Residue "P ARG   62": "NH1" <-> "NH2"
    Residue "P ARG   89": "NH1" <-> "NH2"
    Residue "P ARG  101": "NH1" <-> "NH2"
    Residue "P ARG  109": "NH1" <-> "NH2"
    Residue "Q ARG    3": "NH1" <-> "NH2"
    Residue "Q ARG    6": "NH1" <-> "NH2"
    Residue "Q ARG   13": "NH1" <-> "NH2"
    Residue "Q ARG   33": "NH1" <-> "NH2"
    Residue "Q ARG   48": "NH1" <-> "NH2"
    Residue "Q ARG   70": "NH1" <-> "NH2"
    Residue "Q GLU   89": "OE1" <-> "OE2"
    Residue "Q GLU  111": "OE1" <-> "OE2"
    Residue "R ARG   21": "NH1" <-> "NH2"
    Residue "R GLU   23": "OE1" <-> "OE2"
    Residue "R GLU   31": "OE1" <-> "OE2"
    Residue "R GLU   37": "OE1" <-> "OE2"
    Residue "R ARG   68": "NH1" <-> "NH2"
    Residue "R GLU   70": "OE1" <-> "OE2"
    Residue "R ARG   78": "NH1" <-> "NH2"
    Residue "R ARG   79": "NH1" <-> "NH2"
    Residue "R ARG   84": "NH1" <-> "NH2"
    Residue "S ARG   84": "NH1" <-> "NH2"
    Residue "S ARG   88": "NH1" <-> "NH2"
    Residue "S ARG   95": "NH1" <-> "NH2"
    Residue "S ARG  110": "NH1" <-> "NH2"
    Residue "T GLU   56": "OE1" <-> "OE2"
    Residue "T ARG   73": "NH1" <-> "NH2"
    Residue "U ARG    6": "NH1" <-> "NH2"
    Residue "U ARG    7": "NH1" <-> "NH2"
    Residue "U GLU   10": "OE1" <-> "OE2"
    Residue "U GLU   62": "OE1" <-> "OE2"
    Residue "U ARG   82": "NH1" <-> "NH2"
    Residue "U ARG   86": "NH1" <-> "NH2"
    Residue "U ARG   94": "NH1" <-> "NH2"
    Residue "W GLU   29": "OE1" <-> "OE2"
    Residue "W GLU   70": "OE1" <-> "OE2"
    Residue "W GLU   83": "OE1" <-> "OE2"
    Residue "W GLU   85": "OE1" <-> "OE2"
    Residue "X ARG    3": "NH1" <-> "NH2"
    Residue "X ARG   11": "NH1" <-> "NH2"
    Residue "X ARG   18": "NH1" <-> "NH2"
    Residue "X ARG   37": "NH1" <-> "NH2"
    Residue "X GLU   41": "OE1" <-> "OE2"
    Residue "X ARG   50": "NH1" <-> "NH2"
    Residue "X ARG   57": "NH1" <-> "NH2"
    Residue "X ARG   74": "NH1" <-> "NH2"
    Residue "X TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU    5": "OE1" <-> "OE2"
    Residue "Y GLU   24": "OE1" <-> "OE2"
    Residue "Y ARG   29": "NH1" <-> "NH2"
    Residue "Y ARG   47": "NH1" <-> "NH2"
    Residue "Y ARG   52": "NH1" <-> "NH2"
    Residue "Y GLU   59": "OE1" <-> "OE2"
    Residue "Z ARG   11": "NH1" <-> "NH2"
    Residue "Z ARG   30": "NH1" <-> "NH2"
    Residue "Z ARG   45": "NH1" <-> "NH2"
    Residue "Z GLU   58": "OE1" <-> "OE2"
    Residue "a ARG   10": "NH1" <-> "NH2"
    Residue "a ARG   16": "NH1" <-> "NH2"
    Residue "a ARG   52": "NH1" <-> "NH2"
    Residue "b ARG   44": "NH1" <-> "NH2"
    Residue "b GLU   51": "OE1" <-> "OE2"
    Residue "c ARG    3": "NH1" <-> "NH2"
    Residue "c ARG   12": "NH1" <-> "NH2"
    Residue "c ARG   14": "NH1" <-> "NH2"
    Residue "c ARG   19": "NH1" <-> "NH2"
    Residue "c ARG   21": "NH1" <-> "NH2"
    Residue "c ARG   33": "NH1" <-> "NH2"
    Residue "c ARG   41": "NH1" <-> "NH2"
    Residue "d ARG   13": "NH1" <-> "NH2"
    Residue "d ARG   30": "NH1" <-> "NH2"
    Residue "d ARG   40": "NH1" <-> "NH2"
    Residue "d ARG   42": "NH1" <-> "NH2"
    Residue "e ARG   24": "NH1" <-> "NH2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 94915
  Number of models: 1
  Model: ""
    Number of chains: 45
    Chain: "A"
      Number of atoms: 62252
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 2897, 62209
          Classifications: {'RNA': 2897}
          Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063}
          Link IDs: {'rna2p': 429, 'rna3p': 2467}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 15
      Conformer: "B"
        Number of residues, atoms: 2897, 62209
          Classifications: {'RNA': 2897}
          Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063}
          Link IDs: {'rna2p': 429, 'rna3p': 2467}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 15
          bond proxies already assigned to first conformer: 69623
    Chain: "B"
      Number of atoms: 2569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 2569
          Classifications: {'RNA': 120}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50}
          Link IDs: {'rna2p': 13, 'rna3p': 106}
    Chain: "C"
      Number of atoms: 2083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2083
          Classifications: {'peptide': 271}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 209, 1566
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 202}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MEQ:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1552
          Classifications: {'peptide': 201}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 1411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1411
          Classifications: {'peptide': 177}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 170}
    Chain: "G"
      Number of atoms: 1323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1323
          Classifications: {'peptide': 176}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 167}
    Chain: "H"
      Number of atoms: 1023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1023
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 129}
    Chain: "I"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 979
          Classifications: {'peptide': 134}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
    Chain: "J"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1129
          Classifications: {'peptide': 142}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
    Chain: "K"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 946
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 1053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1053
          Classifications: {'peptide': 144}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 139}
    Chain: "M"
      Number of atoms: 1075
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 136, 1075
          Classifications: {'peptide': 136}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'4D4:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 993
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 4, 'TRANS': 120}
    Chain: "O"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 900
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
    Chain: "P"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 857
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 107}
    Chain: "T"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 739
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
    Chain: "U"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 780
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "V"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 753
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
    Chain: "W"
      Number of atoms: 580
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 76, 580
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 74}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "X"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "Y"
      Number of atoms: 501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 501
          Classifications: {'peptide': 62}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 61}
    Chain: "Z"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 58, 449
          Classifications: {'peptide': 58}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
    Chain: "a"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 444
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 54}
    Chain: "b"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 414
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "c"
      Number of atoms: 377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 377
          Classifications: {'peptide': 46}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "d"
      Number of atoms: 504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 504
          Classifications: {'peptide': 64}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 61}
    Chain: "e"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 302
          Classifications: {'peptide': 38}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
    Chain: "f"
      Number of atoms: 1625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1625
          Classifications: {'RNA': 76}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 9, 'rna3p': 66}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
    Chain: "g"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1667
          Classifications: {'RNA': 75, 'peptide': 1}
          Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p': 12, 'rna3p_pur': 30, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 10, 'rna3p': 64, None: 1}
            Not linked:
              pdbres="  C g  75 "
              pdbres="31M g  76 "
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 13
    Chain: "A"
      Number of atoms: 232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 232
          Unusual residues: {' MG': 174, 'DI0': 1}
          Classifications: {'undetermined': 175}
          Link IDs: {None: 174}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "U"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 498
          Classifications: {'water': 498}
          Link IDs: {None: 497}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "L"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "d"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" P  A  C A2888 " occ=0.53
      ... (38 atoms not shown)
      pdb=" C6 B  C A2888 " occ=0.47
    residue:
      pdb=" N  AMEQ D 150 " occ=0.49
      ... (8 atoms not shown)
      pdb=" NE2AMEQ D 150 " occ=0.49
    residue:
      pdb=" N  AARG W  41 " occ=0.51
      ... (9 atoms not shown)
      pdb=" NH2AARG W  41 " occ=0.51
    residue:
      pdb=" N  AALA Z   2 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB AALA Z   2 " occ=0.50
    residue:
      pdb=" N  ALYS Z   3 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ ALYS Z   3 " occ=0.50
  Time building chain proxies: 60.06, per 1000 atoms: 0.63
  Number of scatterers: 94915
  At special positions: 0
  Unit cell: (251.12, 227.9, 208.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      85     16.00
     P    3170     15.00
     Mg    178     11.99
     O   27197      8.00
     N   17508      7.00
     C   46777      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 46.61
  Conformation dependent library (CDL) restraints added in 4.1 seconds
  

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6118

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      102 helices and 49 sheets defined
      27.7% alpha, 19.8% beta
      1041 base pairs and 1710 stacking pairs defined.
    Time for finding SS restraints: 55.65
  Creating SS restraints...
    Processing helix  chain 'C' and resid 31 through 33
      No H-bonds generated for 'chain 'C' and resid 31 through 33'
    Processing helix  chain 'C' and resid 132 through 134
      No H-bonds generated for 'chain 'C' and resid 132 through 134'
    Processing helix  chain 'C' and resid 198 through 202
      removed outlier: 3.920A  pdb=" N   MET C 201 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 214
      removed outlier: 3.819A  pdb=" N   ARG C 214 " --> pdb=" O   ALA C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 224
      No H-bonds generated for 'chain 'C' and resid 222 through 224'
    Processing helix  chain 'C' and resid 264 through 266
      No H-bonds generated for 'chain 'C' and resid 264 through 266'
    Processing helix  chain 'D' and resid 62 through 71
      removed outlier: 3.525A  pdb=" N   ALA D  71 " --> pdb=" O   HIS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 101
    Processing helix  chain 'D' and resid 121 through 125
    Processing helix  chain 'E' and resid 16 through 19
      No H-bonds generated for 'chain 'E' and resid 16 through 19'
    Processing helix  chain 'E' and resid 25 through 39
    Processing helix  chain 'E' and resid 98 through 114
    Processing helix  chain 'E' and resid 131 through 140
    Processing helix  chain 'E' and resid 155 through 160
    Processing helix  chain 'E' and resid 172 through 174
      No H-bonds generated for 'chain 'E' and resid 172 through 174'
    Processing helix  chain 'E' and resid 177 through 182
      removed outlier: 3.575A  pdb=" N   ILE E 181 " --> pdb=" O   PRO E 177 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'F' and resid 3 through 10
      removed outlier: 3.550A  pdb=" N   ASP F  10 " --> pdb=" O   ASP F   6 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 19
      removed outlier: 3.576A  pdb=" N   THR F  18 " --> pdb=" O   LYS F  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 27
      No H-bonds generated for 'chain 'F' and resid 25 through 27'
    Processing helix  chain 'F' and resid 42 through 44
      No H-bonds generated for 'chain 'F' and resid 42 through 44'
    Processing helix  chain 'F' and resid 48 through 61
      removed outlier: 3.874A  pdb=" N   ASN F  52 " --> pdb=" O   LYS F  48 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER F  61 " --> pdb=" O   LEU F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 104
      removed outlier: 3.708A  pdb=" N   ARG F 102 " --> pdb=" O   GLU F  98 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE F 104 " --> pdb=" O   PHE F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 172
    Processing helix  chain 'G' and resid 59 through 80
      removed outlier: 4.573A  pdb=" N   TRP G  62 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY G  66 " --> pdb=" O   ALA G  63 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ARG G  69 " --> pdb=" O   GLY G  66 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU G  72 " --> pdb=" O   ARG G  69 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL G  76 " --> pdb=" O   ASN G  73 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL G  79 " --> pdb=" O   VAL G  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 138 through 151
    Processing helix  chain 'H' and resid 5 through 21
      removed outlier: 3.571A  pdb=" N   GLY H  21 " --> pdb=" O   GLU H  17 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 47
    Processing helix  chain 'H' and resid 57 through 65
      removed outlier: 3.744A  pdb=" N   ALA H  63 " --> pdb=" O   LEU H  59 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 71 through 75
      removed outlier: 3.888A  pdb=" N   ASP H  74 " --> pdb=" O   CYS H  71 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 103
      removed outlier: 3.665A  pdb=" N   LYS H  97 " --> pdb=" O   ALA H  93 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU H  98 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 121 through 128
      removed outlier: 3.740A  pdb=" N   ASP H 124 " --> pdb=" O   SER H 121 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA H 127 " --> pdb=" O   ASP H 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 132 through 134
      No H-bonds generated for 'chain 'H' and resid 132 through 134'
    Processing helix  chain 'I' and resid 25 through 31
      removed outlier: 4.635A  pdb=" N   GLN I  31 " --> pdb=" O   ALA I  27 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 35 through 48
      removed outlier: 5.220A  pdb=" N   SER I  48 " --> pdb=" O   ALA I  44 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 76 through 83
    Processing helix  chain 'I' and resid 103 through 116
    Processing helix  chain 'I' and resid 122 through 135
    Processing helix  chain 'J' and resid 25 through 37
      removed outlier: 4.034A  pdb=" N   GLU J  31 " --> pdb=" O   ARG J  27 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 59 through 61
      No H-bonds generated for 'chain 'J' and resid 59 through 61'
    Processing helix  chain 'J' and resid 68 through 71
      No H-bonds generated for 'chain 'J' and resid 68 through 71'
    Processing helix  chain 'J' and resid 89 through 95
    Processing helix  chain 'J' and resid 97 through 108
      removed outlier: 4.234A  pdb=" N   ILE J 101 " --> pdb=" O   PRO J  97 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET J 108 " --> pdb=" O   ALA J 104 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 113 through 121
      removed outlier: 3.917A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 133 through 135
      No H-bonds generated for 'chain 'J' and resid 133 through 135'
    Processing helix  chain 'K' and resid 105 through 107
      No H-bonds generated for 'chain 'K' and resid 105 through 107'
    Processing helix  chain 'K' and resid 113 through 118
    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 71 through 73
      No H-bonds generated for 'chain 'L' and resid 71 through 73'
    Processing helix  chain 'L' and resid 79 through 81
      No H-bonds generated for 'chain 'L' and resid 79 through 81'
    Processing helix  chain 'L' and resid 92 through 97
    Processing helix  chain 'L' and resid 129 through 138
    Processing helix  chain 'M' and resid 43 through 56
    Processing helix  chain 'M' and resid 110 through 123
      removed outlier: 3.603A  pdb=" N   GLU M 115 " --> pdb=" O   GLU M 111 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LYS M 123 " --> pdb=" O   LEU M 119 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 14 through 31
    Processing helix  chain 'N' and resid 38 through 56
      removed outlier: 4.270A  pdb=" N   ARG N  46 " --> pdb=" O   LYS N  42 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL N  47 " --> pdb=" O   GLU N  43 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 60 through 70
    Processing helix  chain 'N' and resid 73 through 81
    Processing helix  chain 'N' and resid 83 through 87
    Processing helix  chain 'N' and resid 122 through 124
      No H-bonds generated for 'chain 'N' and resid 122 through 124'
    Processing helix  chain 'O' and resid 3 through 21
      removed outlier: 3.537A  pdb=" N   ARG O  10 " --> pdb=" O   ALA O   6 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ARG O  13 " --> pdb=" O   ARG O   9 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   ALA O  14 " --> pdb=" O   ARG O  10 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 56 through 61
      removed outlier: 5.846A  pdb=" N   GLN O  61 " --> pdb=" O   ALA O  57 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 68 through 83
    Processing helix  chain 'O' and resid 102 through 112
    Processing helix  chain 'P' and resid 3 through 10
    Processing helix  chain 'P' and resid 54 through 56
      No H-bonds generated for 'chain 'P' and resid 54 through 56'
    Processing helix  chain 'P' and resid 98 through 102
    Processing helix  chain 'P' and resid 105 through 108
    Processing helix  chain 'Q' and resid 7 through 20
      removed outlier: 3.568A  pdb=" N   GLN Q  20 " --> pdb=" O   LYS Q  16 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 26 through 29
    Processing helix  chain 'Q' and resid 32 through 72
      removed outlier: 3.651A  pdb=" N   GLN Q  37 " --> pdb=" O   ARG Q  33 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ARG Q  51 " --> pdb=" O   TYR Q  47 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LYS Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG Q  55 " --> pdb=" O   ARG Q  51 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG Q  58 " --> pdb=" O   LYS Q  54 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN Q  72 " --> pdb=" O   ALA Q  68 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 76 through 85
    Processing helix  chain 'Q' and resid 92 through 101
    Processing helix  chain 'Q' and resid 103 through 117
    Processing helix  chain 'S' and resid 14 through 24
      removed outlier: 3.762A  pdb=" N   LEU S  19 " --> pdb=" O   GLN S  15 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   VAL S  20 " --> pdb=" O   LYS S  16 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU S  23 " --> pdb=" O   LEU S  19 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ILE S  24 " --> pdb=" O   VAL S  20 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 29 through 37
      removed outlier: 3.574A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 42 through 60
    Processing helix  chain 'S' and resid 66 through 68
      No H-bonds generated for 'chain 'S' and resid 66 through 68'
    Processing helix  chain 'S' and resid 89 through 91
      No H-bonds generated for 'chain 'S' and resid 89 through 91'
    Processing helix  chain 'T' and resid 4 through 10
      removed outlier: 3.980A  pdb=" N   LYS T   9 " --> pdb=" O   GLU T   5 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL T  10 " --> pdb=" O   ARG T   6 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 18 through 26
    Processing helix  chain 'T' and resid 40 through 50
    Processing helix  chain 'U' and resid 51 through 53
      No H-bonds generated for 'chain 'U' and resid 51 through 53'
    Processing helix  chain 'U' and resid 67 through 69
      No H-bonds generated for 'chain 'U' and resid 67 through 69'
    Processing helix  chain 'V' and resid 14 through 23
    Processing helix  chain 'V' and resid 44 through 52
      removed outlier: 3.533A  pdb=" N   MET V  50 " --> pdb=" O   LYS V  46 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA V  52 " --> pdb=" O   MET V  48 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 54 through 57
    Processing helix  chain 'X' and resid 53 through 62
    Processing helix  chain 'X' and resid 64 through 74
    Processing helix  chain 'Y' and resid 6 through 8
      No H-bonds generated for 'chain 'Y' and resid 6 through 8'
    Processing helix  chain 'Y' and resid 11 through 34
    Processing helix  chain 'Y' and resid 40 through 62
      removed outlier: 3.726A  pdb=" N   VAL Y  46 " --> pdb=" O   LEU Y  43 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP Y  49 " --> pdb=" O   VAL Y  46 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL Y  50 " --> pdb=" O   ARG Y  47 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS Y  54 " --> pdb=" O   ALA Y  51 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU Y  57 " --> pdb=" O   LYS Y  54 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS Y  60 " --> pdb=" O   LEU Y  57 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA Y  61 " --> pdb=" O   ASN Y  58 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 18 through 27
    Processing helix  chain 'Z' and resid 42 through 50
    Processing helix  chain 'a' and resid 10 through 19
      removed outlier: 4.811A  pdb=" N   HIS a  19 " --> pdb=" O   MET a  15 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 9 through 16
    Processing helix  chain 'c' and resid 18 through 23
    Processing helix  chain 'c' and resid 25 through 37
    Processing helix  chain 'd' and resid 8 through 11
      No H-bonds generated for 'chain 'd' and resid 8 through 11'
    Processing helix  chain 'd' and resid 38 through 44
    Processing helix  chain 'd' and resid 52 through 61
      removed outlier: 4.784A  pdb=" N   GLY d  56 " --> pdb=" O   GLY d  53 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE d  59 " --> pdb=" O   GLY d  56 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 31 through 33
      No H-bonds generated for 'chain 'e' and resid 31 through 33'
    Processing sheet with id=  A, first strand: chain 'C' and resid 3 through 5
    Processing sheet with id=  B, first strand: chain 'C' and resid 34 through 36
    Processing sheet with id=  C, first strand: chain 'C' and resid 101 through 105
      removed outlier: 3.641A  pdb=" N   ARG C  80 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU C  95 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   VAL C  78 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'C' and resid 129 through 131
    Processing sheet with id=  E, first strand: chain 'C' and resid 181 through 185
      removed outlier: 3.528A  pdb=" N   ALA C 166 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ARG C 175 " --> pdb=" O   ILE C 164 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ILE C 164 " --> pdb=" O   ARG C 175 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'D' and resid 169 through 172
      removed outlier: 4.772A  pdb=" N   THR D 112 " --> pdb=" O   ASP D 200 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ASP D 200 " --> pdb=" O   THR D 112 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL D  26 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   MET D  11 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL D  24 " --> pdb=" O   MET D  11 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ARG D  13 " --> pdb=" O   ILE D  22 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE D  22 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE D  15 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   VAL D  20 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   LYS D 190 " --> pdb=" O   VAL D 177 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL D 177 " --> pdb=" O   LYS D 190 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'D' and resid 79 through 83
      removed outlier: 6.371A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'D' and resid 115 through 119
      removed outlier: 5.725A  pdb=" N   MET D 165 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   PHE D 118 " --> pdb=" O   GLY D 163 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   GLY D 163 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=  J, first strand: chain 'E' and resid 118 through 121
      removed outlier: 6.131A  pdb=" N   VAL E 186 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   VAL E 121 " --> pdb=" O   VAL E 186 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   MET E 188 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'F' and resid 128 through 132
      removed outlier: 3.590A  pdb=" N   THR F 155 " --> pdb=" O   THR F  35 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR F  35 " --> pdb=" O   THR F 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS F  33 " --> pdb=" O   THR F 157 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   THR F  68 " --> pdb=" O   ILE F  85 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   CYS F  87 " --> pdb=" O   LEU F  66 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU F  66 " --> pdb=" O   CYS F  87 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'G' and resid 16 through 20
    Processing sheet with id=  M, first strand: chain 'G' and resid 41 through 45
    Processing sheet with id=  N, first strand: chain 'G' and resid 161 through 164
      removed outlier: 3.544A  pdb=" N   ARG G 163 " --> pdb=" O   GLN G  88 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'G' and resid 95 through 99
      removed outlier: 3.615A  pdb=" N   ARG G  95 " --> pdb=" O   SER G 106 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL G 113 " --> pdb=" O   LEU G 105 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'H' and resid 24 through 28
      removed outlier: 3.907A  pdb=" N   SER H  24 " --> pdb=" O   VAL H  85 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'H' and resid 111 through 113
    Processing sheet with id=  R, first strand: chain 'I' and resid 9 through 14
    Processing sheet with id=  S, first strand: chain 'J' and resid 15 through 19
      removed outlier: 6.708A  pdb=" N   TYR J  53 " --> pdb=" O   TYR J  16 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   VAL J  18 " --> pdb=" O   TYR J  53 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ILE J  55 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'J' and resid 73 through 77
    Processing sheet with id=  U, first strand: chain 'K' and resid 7 through 9
      removed outlier: 6.474A  pdb=" N   LYS K  40 " --> pdb=" O   ILE K  22 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   VAL K  24 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   ILE K  38 " --> pdb=" O   VAL K  24 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS K  59 " --> pdb=" O   LEU K  87 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ALA K  83 " --> pdb=" O   VAL K  63 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'L' and resid 74 through 78
      removed outlier: 6.636A  pdb=" N   PHE L 107 " --> pdb=" O   ALA L  75 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   ILE L  77 " --> pdb=" O   PHE L 107 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LYS L 109 " --> pdb=" O   ILE L  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  V
    Processing sheet with id=  W, first strand: chain 'L' and resid 121 through 123
      removed outlier: 6.477A  pdb=" N   LYS L 141 " --> pdb=" O   VAL L 122 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  W
    Processing sheet with id=  X, first strand: chain 'M' and resid 128 through 132
      removed outlier: 3.698A  pdb=" N   TYR M 103 " --> pdb=" O   LEU M  33 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA M  35 " --> pdb=" O   VAL M 101 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL M 101 " --> pdb=" O   ALA M  35 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'M' and resid 39 through 42
      removed outlier: 6.945A  pdb=" N   ILE M  73 " --> pdb=" O   GLU M  90 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   TRP M  92 " --> pdb=" O   LYS M  71 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LYS M  71 " --> pdb=" O   TRP M  92 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'N' and resid 33 through 37
    Processing sheet with id= AA, first strand: chain 'O' and resid 91 through 93
      removed outlier: 3.788A  pdb=" N   VAL O  49 " --> pdb=" O   VAL O  39 " (cutoff:3.500A)
    Processing sheet with id= AB, first strand: chain 'P' and resid 83 through 88
      removed outlier: 6.800A  pdb=" N   THR P  25 " --> pdb=" O   LYS P  87 " (cutoff:3.500A)
      removed outlier: 8.967A  pdb=" N   GLU P  44 " --> pdb=" O   ILE P  64 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   ILE P  64 " --> pdb=" O   GLU P  44 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR P  60 " --> pdb=" O   ILE P  48 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ILE P  50 " --> pdb=" O   ALA P  58 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ALA P  58 " --> pdb=" O   ILE P  50 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'R' and resid 10 through 15
      removed outlier: 7.299A  pdb=" N   GLN R   6 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL R  38 " --> pdb=" O   GLN R   6 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'R' and resid 19 through 23
    Processing sheet with id= AE, first strand: chain 'R' and resid 32 through 35
      removed outlier: 6.425A  pdb=" N   GLU R  62 " --> pdb=" O   ILE R  98 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   ILE R  98 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'R' and resid 72 through 78
      removed outlier: 4.149A  pdb=" N   TYR R  83 " --> pdb=" O   ARG R  78 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'S' and resid 3 through 7
      removed outlier: 6.808A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id= AH, first strand: chain 'S' and resid 82 through 87
    Processing sheet with id= AI, first strand: chain 'T' and resid 11 through 14
      removed outlier: 6.615A  pdb=" N   LYS T  33 " --> pdb=" O   ARG T  12 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   VAL T  31 " --> pdb=" O   PRO T  14 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
    Processing sheet with id= AJ, first strand: chain 'T' and resid 67 through 70
    Processing sheet with id= AK, first strand: chain 'U' and resid 22 through 24
      removed outlier: 6.076A  pdb=" N   GLU U  10 " --> pdb=" O   PHE U  73 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ILE U  72 " --> pdb=" O   ASP U  81 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'U' and resid 41 through 46
    Processing sheet with id= AM, first strand: chain 'U' and resid 83 through 87
    Processing sheet with id= AN, first strand: chain 'U' and resid 25 through 28
      removed outlier: 6.802A  pdb=" N   ILE U  35 " --> pdb=" O   LYS U  26 " (cutoff:3.500A)
    Processing sheet with id= AO, first strand: chain 'V' and resid 62 through 65
      removed outlier: 7.988A  pdb=" N   ASN V   5 " --> pdb=" O   ASP V  43 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ASP V  43 " --> pdb=" O   ASN V   5 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ILE V  89 " --> pdb=" O   ILE V  29 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   TYR V  31 " --> pdb=" O   ILE V  89 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   PHE V  91 " --> pdb=" O   TYR V  31 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   VAL V  92 " --> pdb=" O   ALA V  74 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ALA V  74 " --> pdb=" O   VAL V  92 " (cutoff:3.500A)
    Processing sheet with id= AP, first strand: chain 'W' and resid 51 through 53
    Processing sheet with id= AQ, first strand: chain 'W' and resid 66 through 72
    Processing sheet with id= AR, first strand: chain 'X' and resid 13 through 18
    Processing sheet with id= AS, first strand: chain 'X' and resid 33 through 40
    Processing sheet with id= AT, first strand: chain 'Z' and resid 35 through 39
    Processing sheet with id= AU, first strand: chain 'b' and resid 20 through 25
    Processing sheet with id= AV, first strand: chain 'e' and resid 2 through 4
    Processing sheet with id= AW, first strand: chain 'e' and resid 14 through 19

    873 hydrogen bonds defined for protein.
    2355 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      2614 hydrogen bonds
      4046 hydrogen bond angles
      0 basepair planarities
      1041 basepair parallelities
      1712 stacking parallelities
  Total time for adding SS restraints: 252.87

  Time building geometry restraints manager: 49.61 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 7234
        1.27 -     1.40: 32553
        1.40 -     1.54: 56259
        1.54 -     1.68: 6524
        1.68 -     1.82: 153
  Bond restraints: 102723
  Sorted by residual:
  bond pdb=" O3' 3TD A1915 "
       pdb=" P     A A1916 "
    ideal  model  delta    sigma   weight residual
    1.607  1.315  0.292 1.50e-02 4.44e+03 3.80e+02
  bond pdb=" C4  5MU A1939 "
       pdb=" C5  5MU A1939 "
    ideal  model  delta    sigma   weight residual
    1.802  1.422  0.380 2.00e-02 2.50e+03 3.60e+02
  bond pdb=" C4  5MU A 747 "
       pdb=" C5  5MU A 747 "
    ideal  model  delta    sigma   weight residual
    1.802  1.424  0.378 2.00e-02 2.50e+03 3.57e+02
  bond pdb=" C4  5MU f  54 "
       pdb=" C5  5MU f  54 "
    ideal  model  delta    sigma   weight residual
    1.802  1.427  0.375 2.00e-02 2.50e+03 3.52e+02
  bond pdb=" C2' 31M g  76 "
       pdb=" C1' 31M g  76 "
    ideal  model  delta    sigma   weight residual
    1.623  1.276  0.347 2.00e-02 2.50e+03 3.00e+02
  ... (remaining 102718 not shown)

  Histogram of bond angle deviations from ideal:
       86.98 -    97.95: 38
       97.95 -   108.92: 40384
      108.92 -   119.89: 71889
      119.89 -   130.86: 41120
      130.86 -   141.83: 1003
  Bond angle restraints: 154434
  Sorted by residual:
  angle pdb=" C3' 3TD A1915 "
        pdb=" O3' 3TD A1915 "
        pdb=" P     A A1916 "
      ideal   model   delta    sigma   weight residual
     120.20   89.07   31.13 1.50e+00 4.44e-01 4.31e+02
  angle pdb=" C1' 31M g  76 "
        pdb=" N9  31M g  76 "
        pdb=" C8  31M g  76 "
      ideal   model   delta    sigma   weight residual
      79.05  125.79  -46.74 3.00e+00 1.11e-01 2.43e+02
  angle pdb=" O2'   C f  51 "
        pdb=" C2'   C f  51 "
        pdb=" C1'   C f  51 "
      ideal   model   delta    sigma   weight residual
     108.40   86.98   21.42 1.50e+00 4.44e-01 2.04e+02
  angle pdb=" O2'   C f  40 "
        pdb=" C2'   C f  40 "
        pdb=" C1'   C f  40 "
      ideal   model   delta    sigma   weight residual
     108.40   87.97   20.43 1.50e+00 4.44e-01 1.86e+02
  angle pdb=" C4'   U g  47 "
        pdb=" C3'   U g  47 "
        pdb=" O3'   U g  47 "
      ideal   model   delta    sigma   weight residual
     109.40  129.72  -20.32 1.50e+00 4.44e-01 1.84e+02
  ... (remaining 154429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.85: 56094
       35.85 -    71.71: 6363
       71.71 -   107.56: 919
      107.56 -   143.41: 21
      143.41 -   179.26: 13
  Dihedral angle restraints: 63410
    sinusoidal: 53909
      harmonic: 9501
  Sorted by residual:
  dihedral pdb=" O4'   U A 545 "
           pdb=" C1'   U A 545 "
           pdb=" N1    U A 545 "
           pdb=" C2    U A 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   23.09  176.91     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U A1779 "
           pdb=" C1'   U A1779 "
           pdb=" N1    U A1779 "
           pdb=" C2    U A1779 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   57.47  142.53     1      1.50e+01 4.44e-03 7.65e+01
  dihedral pdb=" O4'   U A2321 "
           pdb=" C1'   U A2321 "
           pdb=" N1    U A2321 "
           pdb=" C2    U A2321 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   60.67  139.33     1      1.50e+01 4.44e-03 7.50e+01
  ... (remaining 63407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.195: 19536
       0.195 -    0.390: 119
       0.390 -    0.585: 23
       0.585 -    0.780: 6
       0.780 -    0.975: 2
  Chirality restraints: 19686
  Sorted by residual:
  chirality pdb=" C3'   C g  13 "
            pdb=" C4'   C g  13 "
            pdb=" O3'   C g  13 "
            pdb=" C2'   C g  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.50   -0.97 2.00e-01 2.50e+01 2.37e+01
  chirality pdb=" C2'   G g  18 "
            pdb=" C3'   G g  18 "
            pdb=" O2'   G g  18 "
            pdb=" C1'   G g  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -1.72   -0.80 2.00e-01 2.50e+01 1.60e+01
  chirality pdb=" C3'   U g  47 "
            pdb=" C4'   U g  47 "
            pdb=" O3'   U g  47 "
            pdb=" C2'   U g  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -1.97   -0.77 2.00e-01 2.50e+01 1.50e+01
  ... (remaining 19683 not shown)

  Planarity restraints: 7773
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 1MA g  58 "    0.876 2.00e-02 2.50e+03   6.96e-01 1.09e+04
        pdb=" C4' 1MA g  58 "   -0.306 2.00e-02 2.50e+03
        pdb=" O4' 1MA g  58 "   -0.433 2.00e-02 2.50e+03
        pdb=" C3' 1MA g  58 "   -0.098 2.00e-02 2.50e+03
        pdb=" O3' 1MA g  58 "   -1.346 2.00e-02 2.50e+03
        pdb=" C2' 1MA g  58 "    0.737 2.00e-02 2.50e+03
        pdb=" O2' 1MA g  58 "    0.932 2.00e-02 2.50e+03
        pdb=" C1' 1MA g  58 "   -0.241 2.00e-02 2.50e+03
        pdb=" N9  1MA g  58 "   -0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 2MG g  10 "   -0.001 2.00e-02 2.50e+03   6.54e-01 9.62e+03
        pdb=" C4' 2MG g  10 "    0.476 2.00e-02 2.50e+03
        pdb=" O4' 2MG g  10 "    0.766 2.00e-02 2.50e+03
        pdb=" C3' 2MG g  10 "   -0.561 2.00e-02 2.50e+03
        pdb=" O3' 2MG g  10 "   -0.686 2.00e-02 2.50e+03
        pdb=" C2' 2MG g  10 "   -0.188 2.00e-02 2.50e+03
        pdb=" O2' 2MG g  10 "    1.063 2.00e-02 2.50e+03
        pdb=" C1' 2MG g  10 "    0.160 2.00e-02 2.50e+03
        pdb=" N9  2MG g  10 "   -1.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' YYG g  37 "    0.072 2.00e-02 2.50e+03   6.35e-01 9.06e+03
        pdb=" C4' YYG g  37 "    0.367 2.00e-02 2.50e+03
        pdb=" O4' YYG g  37 "    0.596 2.00e-02 2.50e+03
        pdb=" C3' YYG g  37 "   -0.703 2.00e-02 2.50e+03
        pdb=" O3' YYG g  37 "   -0.642 2.00e-02 2.50e+03
        pdb=" C2' YYG g  37 "   -0.116 2.00e-02 2.50e+03
        pdb=" O2' YYG g  37 "    1.107 2.00e-02 2.50e+03
        pdb=" C1' YYG g  37 "    0.272 2.00e-02 2.50e+03
        pdb=" N9  YYG g  37 "   -0.954 2.00e-02 2.50e+03
  ... (remaining 7770 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 397
        2.23 -     2.90: 34443
        2.90 -     3.57: 150445
        3.57 -     4.23: 315400
        4.23 -     4.90: 405152
  Nonbonded interactions: 905837
  Sorted by model distance:
  nonbonded pdb=" N2    G A 883 "
            pdb=" O2    U A 894 "
     model   vdw
     1.564 2.496
  nonbonded pdb=" OP1   A A2268 "
            pdb="MG    MG A3044 "
     model   vdw
     1.586 2.170
  nonbonded pdb=" OP1   A A 751 "
            pdb="MG    MG A3012 "
     model   vdw
     1.589 2.170
  nonbonded pdb=" OP2   A A1189 "
            pdb="MG    MG A3088 "
     model   vdw
     1.606 2.170
  nonbonded pdb=" OP2   G A1828 "
            pdb="MG    MG A3072 "
     model   vdw
     1.620 2.170
  ... (remaining 905832 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.47 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:             7.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          28.740
  Check model and map are aligned:         1.120
  Set scattering table:                    0.690
  Process input model:                     475.980
  Find NCS groups from input model:        1.690
  Set up NCS constraints:                  0.280
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  528.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
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      :  0.010   0.380 102723  Z= 0.589
  Angle     :  0.837  46.739 154434  Z= 0.480
  Chirality :  0.048   0.975  19686
  Planarity :  0.036   0.696   7773
  Dihedral  : 22.590 179.265  57292
  Min Nonbonded Distance : 1.564

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  2.83 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.73 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.03 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.13), residues: 3287
  helix: -2.05 (0.13), residues: 904
  sheet: -1.33 (0.18), residues: 695
  loop : -1.04 (0.14), residues: 1688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP C 248 
   HIS   0.005   0.001   HIS C 230 
   PHE   0.026   0.001   PHE H 106 
   TYR   0.010   0.001   TYR S  38 
   ARG   0.007   0.001   ARG G 170 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  730 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 642
  time to evaluate  : 4.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 88
  outliers final: 31
  residues processed: 708
  average time/residue: 2.2018
  time to fit residues: 2030.9486
Evaluate side-chains
  576 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 545
  time to evaluate  : 3.960 
Switching outliers to nearest non-outliers
  outliers start: 31
  outliers final: 25
  residues processed: 6
  average time/residue: 1.2326
  time to fit residues: 15.5596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 537 optimal weight:    2.9990
   chunk 482 optimal weight:    0.6980
   chunk 267 optimal weight:    5.9990
   chunk 164 optimal weight:    5.9990
   chunk 325 optimal weight:    1.9990
   chunk 257 optimal weight:    0.8980
   chunk 499 optimal weight:    6.9990
   chunk 193 optimal weight:    0.7980
   chunk 303 optimal weight:    1.9990
   chunk 371 optimal weight:    7.9990
   chunk 578 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
C 134 ASN
D  42 ASN
G 104 ASN
G 111 HIS
N  18 GLN
N  23 ASN
P   7 GLN
P  41 GLN
P  75 GLN
T  70 HIS
U  66 GLN
Y  58 ASN
Z  49 ASN
c  26 ASN
d  28 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074 102723  Z= 0.180
  Angle     :  0.772  26.207 154434  Z= 0.430
  Chirality :  0.036   0.410  19686
  Planarity :  0.009   0.137   7773
  Dihedral  : 22.874 178.873  50774
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.25 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.28 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.14), residues: 3287
  helix: -0.21 (0.16), residues: 934
  sheet: -0.65 (0.19), residues: 683
  loop : -0.51 (0.14), residues: 1670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP C 248 
   HIS   0.005   0.001   HIS L  35 
   PHE   0.013   0.001   PHE H  99 
   TYR   0.013   0.001   TYR Q  32 
   ARG   0.007   0.001   ARG F 125 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  640 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 90
    poor density    : 550
  time to evaluate  : 4.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 90
  outliers final: 48
  residues processed: 612
  average time/residue: 2.0334
  time to fit residues: 1651.8188
Evaluate side-chains
  586 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 538
  time to evaluate  : 4.244 
Switching outliers to nearest non-outliers
  outliers start: 48
  outliers final: 35
  residues processed: 14
  average time/residue: 0.9167
  time to fit residues: 26.3821
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 321 optimal weight:    0.9980
   chunk 179 optimal weight:    6.9990
   chunk 481 optimal weight:    2.9990
   chunk 393 optimal weight:    6.9990
   chunk 159 optimal weight:    7.9990
   chunk 579 optimal weight:    2.9990
   chunk 626 optimal weight:   50.0000
   chunk 516 optimal weight:    0.9980
   chunk 574 optimal weight:    0.8980
   chunk 197 optimal weight:    5.9990
   chunk 464 optimal weight:    7.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
F  37 ASN
N  18 GLN
N  23 ASN
Q  59 GLN
U  74 ASN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065 102723  Z= 0.209
  Angle     :  0.767  25.991 154434  Z= 0.430
  Chirality :  0.037   0.410  19686
  Planarity :  0.009   0.142   7773
  Dihedral  : 22.712 179.034  50774
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.28 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.31 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.14), residues: 3287
  helix:  0.41 (0.17), residues: 935
  sheet: -0.34 (0.18), residues: 687
  loop : -0.30 (0.14), residues: 1665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP C 248 
   HIS   0.007   0.001   HIS L  35 
   PHE   0.018   0.002   PHE F  20 
   TYR   0.014   0.001   TYR Q  32 
   ARG   0.008   0.001   ARG F 112 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  639 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 548
  time to evaluate  : 3.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 91
  outliers final: 60
  residues processed: 601
  average time/residue: 2.1610
  time to fit residues: 1741.2304
Evaluate side-chains
  594 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 534
  time to evaluate  : 4.096 
Switching outliers to nearest non-outliers
  outliers start: 60
  outliers final: 41
  residues processed: 20
  average time/residue: 1.4152
  time to fit residues: 47.5439
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 572 optimal weight:    9.9990
   chunk 435 optimal weight:    9.9990
   chunk 300 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 276 optimal weight:    7.9990
   chunk 389 optimal weight:    0.3980
   chunk 581 optimal weight:    4.9990
   chunk 615 optimal weight:    0.5980
   chunk 303 optimal weight:    1.9990
   chunk 551 optimal weight:    3.9990
   chunk 165 optimal weight:    5.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
K  29 HIS
N  18 GLN
N  23 ASN
Q  72 ASN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065 102723  Z= 0.256
  Angle     :  0.804  27.721 154434  Z= 0.445
  Chirality :  0.038   0.414  19686
  Planarity :  0.009   0.147   7773
  Dihedral  : 22.678 179.817  50774
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.16 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.35 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.14), residues: 3287
  helix:  0.61 (0.17), residues: 928
  sheet: -0.29 (0.18), residues: 704
  loop : -0.14 (0.15), residues: 1655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP C 248 
   HIS   0.010   0.001   HIS L  35 
   PHE   0.015   0.002   PHE N  21 
   TYR   0.015   0.002   TYR Q  32 
   ARG   0.008   0.001   ARG F 125 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  631 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 97
    poor density    : 534
  time to evaluate  : 4.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 97
  outliers final: 59
  residues processed: 598
  average time/residue: 2.1389
  time to fit residues: 1683.0497
Evaluate side-chains
  578 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 519
  time to evaluate  : 4.005 
Switching outliers to nearest non-outliers
  outliers start: 59
  outliers final: 43
  residues processed: 17
  average time/residue: 1.1901
  time to fit residues: 35.1915
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 512 optimal weight:    9.9990
   chunk 349 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 458 optimal weight:    3.9990
   chunk 254 optimal weight:    5.9990
   chunk 525 optimal weight:    0.7980
   chunk 425 optimal weight:   50.0000
   chunk 0 optimal weight:   10.0000
   chunk 314 optimal weight:    0.0770
   chunk 552 optimal weight:    0.2980
   chunk 155 optimal weight:    7.9990
   overall best weight:    2.2342

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
K  29 HIS
N  18 GLN
N  23 ASN
P  75 GLN
U  66 GLN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058 102723  Z= 0.240
  Angle     :  0.785  27.004 154434  Z= 0.437
  Chirality :  0.037   0.404  19686
  Planarity :  0.009   0.144   7773
  Dihedral  : 22.634 179.284  50774
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.19 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.87 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.14), residues: 3287
  helix:  0.73 (0.17), residues: 930
  sheet: -0.23 (0.19), residues: 700
  loop : -0.05 (0.15), residues: 1657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP C 248 
   HIS   0.011   0.001   HIS L  35 
   PHE   0.014   0.002   PHE N  21 
   TYR   0.016   0.002   TYR S  38 
   ARG   0.007   0.001   ARG F 112 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  630 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 97
    poor density    : 533
  time to evaluate  : 4.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 97
  outliers final: 64
  residues processed: 594
  average time/residue: 2.0905
  time to fit residues: 1639.8804
Evaluate side-chains
  592 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 528
  time to evaluate  : 4.030 
Switching outliers to nearest non-outliers
  outliers start: 64
  outliers final: 45
  residues processed: 19
  average time/residue: 1.2016
  time to fit residues: 39.1830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 207 optimal weight:    6.9990
   chunk 554 optimal weight:    9.9990
   chunk 121 optimal weight:    6.9990
   chunk 361 optimal weight:    6.9990
   chunk 151 optimal weight:    9.9990
   chunk 616 optimal weight:    8.9990
   chunk 511 optimal weight:    3.9990
   chunk 285 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 203 optimal weight:    6.9990
   chunk 323 optimal weight:    2.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
C 243 HIS
K  29 HIS
N  18 GLN
P  75 GLN
Q  72 ASN
U  66 GLN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.095 102723  Z= 0.520
  Angle     :  1.020  29.688 154434  Z= 0.529
  Chirality :  0.049   0.413  19686
  Planarity :  0.011   0.168   7773
  Dihedral  : 22.734 177.741  50774
  Min Nonbonded Distance : 1.679

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.56 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.50 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.14), residues: 3287
  helix:  0.47 (0.17), residues: 935
  sheet: -0.25 (0.18), residues: 698
  loop : -0.12 (0.15), residues: 1654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.003   TRP C 248 
   HIS   0.029   0.002   HIS L  35 
   PHE   0.024   0.003   PHE Q  36 
   TYR   0.023   0.003   TYR S  38 
   ARG   0.016   0.001   ARG D 141 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  640 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 106
    poor density    : 534
  time to evaluate  : 4.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 106
  outliers final: 64
  residues processed: 601
  average time/residue: 2.0962
  time to fit residues: 1665.2885
Evaluate side-chains
  597 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 533
  time to evaluate  : 3.972 
Switching outliers to nearest non-outliers
  outliers start: 64
  outliers final: 46
  residues processed: 18
  average time/residue: 0.9542
  time to fit residues: 33.0128
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 594 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 351 optimal weight:    3.9990
   chunk 450 optimal weight:    0.9990
   chunk 348 optimal weight:    0.0870
   chunk 518 optimal weight:    0.9990
   chunk 344 optimal weight:    0.9990
   chunk 613 optimal weight:    1.9990
   chunk 384 optimal weight:   20.0000
   chunk 374 optimal weight:   10.0000
   chunk 283 optimal weight:    4.9990
   overall best weight:    1.0166

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
K  29 HIS
K  90 ASN
N  18 GLN
P  75 GLN
Q  72 ASN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053 102723  Z= 0.141
  Angle     :  0.719  25.516 154434  Z= 0.412
  Chirality :  0.034   0.406  19686
  Planarity :  0.009   0.132   7773
  Dihedral  : 22.614 177.921  50774
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.16 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.68 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.14), residues: 3287
  helix:  0.88 (0.17), residues: 937
  sheet: -0.13 (0.19), residues: 700
  loop :  0.02 (0.15), residues: 1650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP C 248 
   HIS   0.005   0.001   HIS L  35 
   PHE   0.011   0.001   PHE H 106 
   TYR   0.015   0.001   TYR R   2 
   ARG   0.004   0.000   ARG F 125 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  638 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 560
  time to evaluate  : 4.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 78
  outliers final: 59
  residues processed: 612
  average time/residue: 2.1068
  time to fit residues: 1705.4683
Evaluate side-chains
  602 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 543
  time to evaluate  : 4.034 
Switching outliers to nearest non-outliers
  outliers start: 59
  outliers final: 46
  residues processed: 13
  average time/residue: 1.2993
  time to fit residues: 29.4762
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 637
   random chunks:
   chunk 379 optimal weight:   20.0000
   chunk 245 optimal weight:    7.9990
   chunk 366 optimal weight:    9.9990
   chunk 184 optimal weight:    8.9990
   chunk 120 optimal weight:    7.9990
   chunk 118 optimal weight:    5.9990
   chunk 390 optimal weight:    0.0370
   chunk 418 optimal weight:   30.0000
   chunk 303 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 482 optimal weight:    3.9990
   overall best weight:    4.4066

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C 134 ASN
K  29 HIS
N  18 GLN
P  75 GLN
Q  72 ASN
U  54 GLN
Z  49 ASN
d  28 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082 102723  Z= 0.417
  Angle     :  0.926  29.055 154434  Z= 0.492
  Chirality :  0.044   0.405  19686
  Planarity :  0.010   0.155   7773
  Dihedral  : 22.669 178.627  50774
  Min Nonbonded Distance : 1.724

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.46 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.05 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.91 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.14), residues: 3287
  helix:  0.69 (0.17), residues: 937
  sheet: -0.16 (0.19), residues: 695
  loop : -0.02 (0.15), residues: 1655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.003   TRP C 248 
   HIS   0.021   0.002   HIS L  35 
   PHE   0.022   0.002   PHE Q  36 
   TYR   0.022   0.002   TYR S  38 
   ARG   0.012   0.001   ARG D 141 

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

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

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6574 Ramachandran restraints generated.
    3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  602 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 527
  time to evaluate  : 4.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 75
  outliers final: 61
  residues processed: 581
  average time/residue: 2.1149
  time to fit residues: 1629.6027
Evaluate side-chains
  585 residues out of total 2705 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 524
  time to evaluate  : 4.031 
Switching outliers to nearest non-outliers
  outliers start: 61
  outliers final: 47
  residues processed: 14
  average time/residue: 1.2082
  time to fit residues: 30.4756
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2054 > 50:
  distance: 79 - 84:  33.779
  distance: 84 - 85:  40.678
  distance: 85 - 86:  41.448
  distance: 85 - 88:  68.660
  distance: 86 - 87:  57.280
  distance: 86 - 95:  38.936
  distance: 88 - 89:  39.536
  distance: 89 - 90:  39.436
  distance: 90 - 91:  56.865
  distance: 92 - 93:  39.765
  distance: 92 - 94:  57.363
  distance: 96 - 99:  58.035
  distance: 97 - 98:  56.077
  distance: 97 - 106:  38.851
  distance: 99 - 100:  57.240
  distance: 100 - 101:  68.061
  distance: 101 - 102:  23.239
  distance: 102 - 103:  46.792
  distance: 103 - 104:  46.509
  distance: 103 - 105:  16.427
  distance: 106 - 107:  41.220
  distance: 106 - 112:  39.651
  distance: 107 - 108:  57.428
  distance: 107 - 110:  41.193
  distance: 108 - 109:  39.434
  distance: 108 - 113:  55.401
  distance: 110 - 111:   7.953
  distance: 111 - 112:  65.412
  distance: 113 - 114:  57.550
  distance: 114 - 115:  56.861
  distance: 114 - 117:  67.962
  distance: 115 - 116:  40.128
  distance: 115 - 121:  56.646
  distance: 117 - 118:  56.114
  distance: 118 - 120:  55.621
  distance: 121 - 122:  57.891
  distance: 122 - 123:  56.159
  distance: 123 - 125:  55.823
  distance: 125 - 126:  39.735
  distance: 126 - 127:  38.707
  distance: 127 - 131:  39.959
  distance: 129 - 130:  56.693
  distance: 131 - 132:  39.559
  distance: 132 - 133:  57.791
  distance: 132 - 135:  39.269
  distance: 133 - 134:  38.877
  distance: 133 - 138:  69.933
  distance: 135 - 136:  66.139
  distance: 135 - 137:  57.467
  distance: 138 - 139:  56.245
  distance: 139 - 140:  41.153
  distance: 139 - 142:  39.172
  distance: 140 - 141:  40.266
  distance: 140 - 146:  68.947
  distance: 142 - 143:  56.068
  distance: 142 - 144:  43.611
  distance: 143 - 145:  55.544
  distance: 146 - 147:  38.863
  distance: 147 - 148:  39.844
  distance: 147 - 150:  39.814
  distance: 148 - 157:  56.004
  distance: 150 - 151:  57.978
  distance: 151 - 152:  39.231
  distance: 152 - 153:  55.663
  distance: 153 - 154:  39.144
  distance: 154 - 155:  39.091
  distance: 154 - 156:  40.425
  distance: 157 - 158:  41.169
  distance: 158 - 159:  57.892
  distance: 158 - 161:  69.078
  distance: 159 - 160:  39.589
  distance: 159 - 168:  34.778
  distance: 161 - 162:  40.609
  distance: 162 - 164:  41.162
  distance: 163 - 165:  40.334
  distance: 164 - 166:  68.417
  distance: 165 - 167:  57.363
  distance: 166 - 167:  39.134