Starting phenix.real_space_refine (version: dev)
on Fri Feb 24 18:06:45 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj5_22894/02_2023/7kj5_22894.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.001
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
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  170": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  191": "OE1" <-> "OE2"
    Residue "A PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  329": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  421": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  428": "OD1" <-> "OD2"
    Residue "A TYR  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  454": "NH1" <-> "NH2"
    Residue "A ASP  467": "OD1" <-> "OD2"
    Residue "A TYR  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  543": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  660": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  782": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  789": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  797": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  817": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  868": "OE1" <-> "OE2"
    Residue "A TYR  873": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  888": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  904": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  917": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1107": "NH1" <-> "NH2"
    Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1144": "OE1" <-> "OE2"
    Residue "B TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   88": "OD1" <-> "OD2"
    Residue "B PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  170": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  329": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  347": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  396": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  406": "OE1" <-> "OE2"
    Residue "B PHE  429": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  508": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  718": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  782": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  789": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  797": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  817": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  855": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  873": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  888": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  917": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  170": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  191": "OE1" <-> "OE2"
    Residue "C PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  329": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  421": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  428": "OD1" <-> "OD2"
    Residue "C TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  495": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  619": "OE1" <-> "OE2"
    Residue "C PHE  718": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  748": "OE1" <-> "OE2"
    Residue "C PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  782": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  789": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  797": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  802": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  815": "NH1" <-> "NH2"
    Residue "C PHE  817": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  873": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  888": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  917": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  950": "OD1" <-> "OD2"
    Residue "C PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG 1019": "NH1" <-> "NH2"
    Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU 1111": "OE1" <-> "OE2"
    Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 23562
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 7569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 967, 7569
          Classifications: {'peptide': 967}
          Link IDs: {'PTRANS': 48, 'TRANS': 918}
          Chain breaks: 11
    Chain: "B"
      Number of atoms: 7662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 981, 7662
          Classifications: {'peptide': 981}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 48, 'TRANS': 932}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 7505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 961, 7505
          Classifications: {'peptide': 961}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 48, 'TRANS': 912}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "N"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "O"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen chiralities: 10
    Chain: "B"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 182
          Unusual residues: {'NAG': 13}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen chiralities: 13
    Chain: "C"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 168
          Unusual residues: {'NAG': 12}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen chiralities: 12
  Time building chain proxies: 12.33, per 1000 atoms: 0.52
  Number of scatterers: 23562
  At special positions: 0
  Unit cell: (129.525, 137.775, 193.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     101     16.00
     O    4632      8.00
     N    3830      7.00
     C   14999      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=37, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.84
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.97
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.95
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.14
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.24
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.46
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.51
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.95
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.84
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM22776  O5  NAG E   1 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG L   1 " - " NAG L   2 "
      " NAG M   1 " - " NAG M   2 "
      " NAG N   1 " - " NAG N   2 "
      " NAG O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 122 "
      " NAG A1303 " - " ASN A 282 "
      " NAG A1304 " - " ASN A 331 "
      " NAG A1305 " - " ASN A 343 "
      " NAG A1307 " - " ASN A 616 "
      " NAG A1308 " - " ASN A 657 "
      " NAG A1309 " - " ASN A 709 "
      " NAG A1310 " - " ASN A1074 "
      " NAG B1301 " - " ASN B  61 "
      " NAG B1302 " - " ASN B 122 "
      " NAG B1304 " - " ASN B 282 "
      " NAG B1305 " - " ASN B 331 "
      " NAG B1306 " - " ASN B 343 "
      " NAG B1307 " - " ASN B 603 "
      " NAG B1308 " - " ASN B 616 "
      " NAG B1309 " - " ASN B 657 "
      " NAG B1310 " - " ASN B 709 "
      " NAG B1311 " - " ASN B 717 "
      " NAG B1312 " - " ASN B1074 "
      " NAG C1301 " - " ASN C  61 "
      " NAG C1302 " - " ASN C 122 "
      " NAG C1303 " - " ASN C 234 "
      " NAG C1304 " - " ASN C 282 "
      " NAG C1305 " - " ASN C 331 "
      " NAG C1306 " - " ASN C 343 "
      " NAG C1307 " - " ASN C 603 "
      " NAG C1308 " - " ASN C 616 "
      " NAG C1309 " - " ASN C 657 "
      " NAG C1310 " - " ASN C 709 "
      " NAG C1311 " - " ASN C1074 "
      " NAG C1312 " - " ASN C 165 "
      " NAG D   1 " - " ASN A 234 "
      " NAG E   1 " - " ASN A 717 "
      " NAG F   1 " - " ASN A 801 "
      " NAG G   1 " - " ASN A1098 "
      " NAG H   1 " - " ASN A1134 "
      " NAG I   1 " - " ASN B 801 "
      " NAG J   1 " - " ASN B1098 "
      " NAG K   1 " - " ASN B1134 "
      " NAG L   1 " - " ASN C 717 "
      " NAG M   1 " - " ASN C 801 "
      " NAG N   1 " - " ASN C1098 "
      " NAG O   1 " - " ASN C1134 "
  Time building additional restraints: 9.57
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5466

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 42 sheets defined
      27.7% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.543A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASN A 343 " --> pdb=" O   GLY A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.986A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.598A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 737 through 743
    Processing helix  chain 'A' and resid 746 through 754
    Processing helix  chain 'A' and resid 755 through 757
      No H-bonds generated for 'chain 'A' and resid 755 through 757'
    Processing helix  chain 'A' and resid 758 through 783
      removed outlier: 3.644A  pdb=" N   LEU A 763 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASN A 764 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP A 775 " --> pdb=" O   ALA A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 805
      removed outlier: 4.071A  pdb=" N   GLN A 804 " --> pdb=" O   ASN A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 3.577A  pdb=" N   LEU A 821 " --> pdb=" O   PHE A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 885
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 897 through 909
    Processing helix  chain 'A' and resid 913 through 918
    Processing helix  chain 'A' and resid 919 through 941
    Processing helix  chain 'A' and resid 945 through 965
      removed outlier: 4.231A  pdb=" N   VAL A 951 " --> pdb=" O   LYS A 947 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN A 955 " --> pdb=" O   VAL A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 985 through 1033
      removed outlier: 4.621A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ASP A 994 " --> pdb=" O   GLU A 990 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 996 " --> pdb=" O   GLN A 992 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A1007 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A1016 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A1021 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1147
      removed outlier: 4.302A  pdb=" N   GLU A1144 " --> pdb=" O   PRO A1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 303
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.753A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.622A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.222A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.991A  pdb=" N   ARG B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 404 through 408'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'B' and resid 737 through 744
      removed outlier: 3.563A  pdb=" N   ILE B 742 " --> pdb=" O   CYS B 738 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 746 through 754
      removed outlier: 4.422A  pdb=" N   LEU B 752 " --> pdb=" O   GLU B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 757
      No H-bonds generated for 'chain 'B' and resid 755 through 757'
    Processing helix  chain 'B' and resid 758 through 783
      removed outlier: 3.610A  pdb=" N   LEU B 767 " --> pdb=" O   LEU B 763 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASP B 775 " --> pdb=" O   ALA B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 801 through 805
      removed outlier: 3.653A  pdb=" N   GLN B 804 " --> pdb=" O   ASN B 801 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 824
    Processing helix  chain 'B' and resid 866 through 885
      removed outlier: 3.659A  pdb=" N   GLY B 885 " --> pdb=" O   THR B 881 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 886 through 891
    Processing helix  chain 'B' and resid 897 through 909
    Processing helix  chain 'B' and resid 912 through 918
      removed outlier: 3.952A  pdb=" N   LEU B 916 " --> pdb=" O   THR B 912 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR B 917 " --> pdb=" O   GLN B 913 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 919 through 939
    Processing helix  chain 'B' and resid 942 through 944
      No H-bonds generated for 'chain 'B' and resid 942 through 944'
    Processing helix  chain 'B' and resid 945 through 965
      removed outlier: 4.485A  pdb=" N   VAL B 951 " --> pdb=" O   LYS B 947 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 952 " --> pdb=" O   LEU B 948 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU B 959 " --> pdb=" O   ASN B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 976 through 984
    Processing helix  chain 'B' and resid 985 through 1032
      removed outlier: 4.625A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN B 992 " --> pdb=" O   GLU B 988 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG B 995 " --> pdb=" O   VAL B 991 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU B1017 " --> pdb=" O   ILE B1013 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1140 through 1147
      removed outlier: 4.109A  pdb=" N   GLU B1144 " --> pdb=" O   PRO B1140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 303
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.731A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 369
      removed outlier: 3.914A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 389
      removed outlier: 3.615A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.631A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
      removed outlier: 3.604A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 502 through 505
    Processing helix  chain 'C' and resid 616 through 620
    Processing helix  chain 'C' and resid 737 through 744
    Processing helix  chain 'C' and resid 746 through 754
      removed outlier: 4.269A  pdb=" N   LEU C 752 " --> pdb=" O   GLU C 748 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 755 through 757
      No H-bonds generated for 'chain 'C' and resid 755 through 757'
    Processing helix  chain 'C' and resid 760 through 783
      removed outlier: 3.768A  pdb=" N   ASN C 764 " --> pdb=" O   CYS C 760 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASP C 775 " --> pdb=" O   ALA C 771 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 801 through 805
      removed outlier: 4.094A  pdb=" N   GLN C 804 " --> pdb=" O   ASN C 801 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 816 through 826
      removed outlier: 3.713A  pdb=" N   VAL C 826 " --> pdb=" O   LEU C 822 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 866 through 885
    Processing helix  chain 'C' and resid 886 through 891
    Processing helix  chain 'C' and resid 897 through 909
    Processing helix  chain 'C' and resid 913 through 918
    Processing helix  chain 'C' and resid 919 through 941
      removed outlier: 3.771A  pdb=" N   THR C 941 " --> pdb=" O   SER C 937 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 942 through 944
      No H-bonds generated for 'chain 'C' and resid 942 through 944'
    Processing helix  chain 'C' and resid 945 through 965
      removed outlier: 3.878A  pdb=" N   VAL C 951 " --> pdb=" O   LYS C 947 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   LEU C 959 " --> pdb=" O   ASN C 955 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 977 through 982
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 4.346A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ARG C 995 " --> pdb=" O   VAL C 991 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA C1020 " --> pdb=" O   ALA C1016 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1140 through 1147
      removed outlier: 4.102A  pdb=" N   GLU C1144 " --> pdb=" O   PRO C1140 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 8.173A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA A 264 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
      removed outlier: 5.633A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   GLU C 324 " --> pdb=" O   ASN C 540 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.613A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.545A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319
      removed outlier: 5.510A  pdb=" N   ILE A 312 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   THR A 599 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   GLN A 314 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL A 597 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 316 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY A 594 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.875A  pdb=" N   GLU A 324 " --> pdb=" O   CYS A 538 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE A 565 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.768A  pdb=" N   ALA A 348 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 9.071A  pdb=" N   ARG A 403 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.768A  pdb=" N   ALA A 348 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 9.071A  pdb=" N   ARG A 403 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.041A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655
      removed outlier: 6.098A  pdb=" N   GLU A 654 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   THR A 696 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728
      removed outlier: 6.397A  pdb=" N   GLN A1071 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   PHE A 718 " --> pdb=" O   PRO A1069 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE A 720 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR A1067 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL A 722 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL A1065 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR A 724 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU A1063 " --> pdb=" O   THR A 724 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A1061 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL A1061 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   GLY A1059 " --> pdb=" O   PRO A 728 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   TYR A1067 " --> pdb=" O   HIS A1048 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   HIS A1048 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790
      removed outlier: 6.149A  pdb=" N   ILE A 788 " --> pdb=" O   ASN C 703 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125
      removed outlier: 4.197A  pdb=" N   ALA A1087 " --> pdb=" O   SER A1123 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097
    Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30
      removed outlier: 8.663A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
      removed outlier: 9.678A  pdb=" N   HIS B 207 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 9.819A  pdb=" N   LEU B 223 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   VAL B  36 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55
      removed outlier: 7.205A  pdb=" N   THR B 274 " --> pdb=" O   ASP B 290 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   ASP B 290 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU B 276 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ALA B 288 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LYS B 278 " --> pdb=" O   THR B 286 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.628A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319
      removed outlier: 7.129A  pdb=" N   VAL B 595 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   ASN B 317 " --> pdb=" O   GLY B 593 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY B 593 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   GLY B 594 " --> pdb=" O   GLN B 613 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328
      removed outlier: 6.706A  pdb=" N   GLU B 324 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ASN B 542 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE B 326 " --> pdb=" O   ASN B 542 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   PHE B 565 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.450A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655
      removed outlier: 5.573A  pdb=" N   GLU B 654 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   THR B 696 " --> pdb=" O   GLU B 654 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704
      removed outlier: 6.635A  pdb=" N   ASN B 703 " --> pdb=" O   LYS C 790 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715
    Processing sheet with id=AD1, first strand: chain 'B' and resid 721 through 728
      removed outlier: 6.197A  pdb=" N   TYR B1067 " --> pdb=" O   HIS B1048 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   HIS B1048 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125
      removed outlier: 3.742A  pdb=" N   ALA B1087 " --> pdb=" O   SER B1123 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30
      removed outlier: 8.795A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
      removed outlier: 9.390A  pdb=" N   HIS C 207 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
      removed outlier: 9.363A  pdb=" N   LEU C 223 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL C  36 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55
      removed outlier: 4.034A  pdb=" N   ASP C  53 " --> pdb=" O   ARG C 273 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG C 273 " --> pdb=" O   ASP C  53 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   THR C 274 " --> pdb=" O   ASP C 290 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ASP C 290 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LEU C 276 " --> pdb=" O   ALA C 288 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ALA C 288 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LYS C 278 " --> pdb=" O   THR C 286 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85
    Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319
      removed outlier: 6.990A  pdb=" N   VAL C 595 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ASN C 317 " --> pdb=" O   GLY C 593 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLY C 593 " --> pdb=" O   ASN C 317 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLY C 594 " --> pdb=" O   GLN C 613 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.767A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453
    Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655
      removed outlier: 6.642A  pdb=" N   ILE C 670 " --> pdb=" O   ILE C 666 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715
      removed outlier: 3.644A  pdb=" N   THR C1076 " --> pdb=" O   SER C1097 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA C1078 " --> pdb=" O   PHE C1095 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   PHE C1095 " --> pdb=" O   ALA C1078 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728
      removed outlier: 5.791A  pdb=" N   TYR C1067 " --> pdb=" O   HIS C1048 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   HIS C1048 " --> pdb=" O   TYR C1067 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736
      removed outlier: 4.333A  pdb=" N   LYS C 733 " --> pdb=" O   LEU C 861 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1123
      removed outlier: 3.658A  pdb=" N   ALA C1087 " --> pdb=" O   SER C1123 " (cutoff:3.500A)

    980 hydrogen bonds defined for protein.
    2676 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 10.67

  Time building geometry restraints manager: 10.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 5701
        1.33 -     1.46: 5446
        1.46 -     1.58: 12784
        1.58 -     1.71: 6
        1.71 -     1.83: 125
  Bond restraints: 24062
  Sorted by residual:
  bond pdb=" C5  NAG K   2 "
       pdb=" O5  NAG K   2 "
    ideal  model  delta    sigma   weight residual
    1.435  1.504 -0.069 1.10e-02 8.26e+03 3.89e+01
  bond pdb=" C4  NAG G   1 "
       pdb=" O4  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.423  1.485 -0.062 1.00e-02 1.00e+04 3.80e+01
  bond pdb=" C5  NAG C1311 "
       pdb=" O5  NAG C1311 "
    ideal  model  delta    sigma   weight residual
    1.435  1.501 -0.066 1.10e-02 8.26e+03 3.61e+01
  bond pdb=" C5  NAG B1312 "
       pdb=" O5  NAG B1312 "
    ideal  model  delta    sigma   weight residual
    1.435  1.499 -0.064 1.10e-02 8.26e+03 3.42e+01
  bond pdb=" C4  NAG N   1 "
       pdb=" O4  NAG N   1 "
    ideal  model  delta    sigma   weight residual
    1.423  1.481 -0.058 1.00e-02 1.00e+04 3.34e+01
  ... (remaining 24057 not shown)

  Histogram of bond angle deviations from ideal:
       95.67 -   103.75: 238
      103.75 -   111.82: 9686
      111.82 -   119.90: 11919
      119.90 -   127.98: 10780
      127.98 -   136.05: 105
  Bond angle restraints: 32728
  Sorted by residual:
  angle pdb=" N   ARG C 328 "
        pdb=" CA  ARG C 328 "
        pdb=" C   ARG C 328 "
      ideal   model   delta    sigma   weight residual
     109.54  122.06  -12.52 1.37e+00 5.33e-01 8.35e+01
  angle pdb=" N   LEU C 390 "
        pdb=" CA  LEU C 390 "
        pdb=" C   LEU C 390 "
      ideal   model   delta    sigma   weight residual
     110.53  121.99  -11.46 1.32e+00 5.74e-01 7.53e+01
  angle pdb=" N   ARG A 214 "
        pdb=" CA  ARG A 214 "
        pdb=" C   ARG A 214 "
      ideal   model   delta    sigma   weight residual
     112.12  122.85  -10.73 1.34e+00 5.57e-01 6.41e+01
  angle pdb=" C2  NAG A1304 "
        pdb=" C1  NAG A1304 "
        pdb=" O5  NAG A1304 "
      ideal   model   delta    sigma   weight residual
     109.64  113.85   -4.21 5.38e-01 3.45e+00 6.13e+01
  angle pdb=" C2  NAG C1307 "
        pdb=" C1  NAG C1307 "
        pdb=" O5  NAG C1307 "
      ideal   model   delta    sigma   weight residual
     109.64  113.45   -3.81 5.38e-01 3.45e+00 5.02e+01
  ... (remaining 32723 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 13115
       17.65 -    35.30: 815
       35.30 -    52.95: 189
       52.95 -    70.61: 63
       70.61 -    88.26: 38
  Dihedral angle restraints: 14220
    sinusoidal: 5754
      harmonic: 8466
  Sorted by residual:
  dihedral pdb=" CB  CYS B 662 "
           pdb=" SG  CYS B 662 "
           pdb=" SG  CYS B 671 "
           pdb=" CB  CYS B 671 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.72   80.28     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CB  CYS A1032 "
           pdb=" SG  CYS A1032 "
           pdb=" SG  CYS A1043 "
           pdb=" CB  CYS A1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.59   79.59     1      1.00e+01 1.00e-02 7.86e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   17.11   75.89     1      1.00e+01 1.00e-02 7.26e+01
  ... (remaining 14217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.338: 3868
       0.338 -    0.676: 39
       0.676 -    1.014: 2
       1.014 -    1.353: 2
       1.353 -    1.691: 3
  Chirality restraints: 3914
  Sorted by residual:
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A 331 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.71   -1.69 2.00e-01 2.50e+01 7.15e+01
  chirality pdb=" C1  NAG B1307 "
            pdb=" ND2 ASN B 603 "
            pdb=" C2  NAG B1307 "
            pdb=" O5  NAG B1307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.74   -1.66 2.00e-01 2.50e+01 6.86e+01
  chirality pdb=" C1  NAG L   1 "
            pdb=" ND2 ASN C 717 "
            pdb=" C2  NAG L   1 "
            pdb=" O5  NAG L   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.94   -1.46 2.00e-01 2.50e+01 5.34e+01
  ... (remaining 3911 not shown)

  Planarity restraints: 4191
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C1134 "    0.226 2.00e-02 2.50e+03   3.12e-01 1.21e+03
        pdb=" CG  ASN C1134 "   -0.133 2.00e-02 2.50e+03
        pdb=" OD1 ASN C1134 "   -0.081 2.00e-02 2.50e+03
        pdb=" ND2 ASN C1134 "   -0.459 2.00e-02 2.50e+03
        pdb=" C1  NAG O   1 "    0.447 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 331 "   -0.088 2.00e-02 2.50e+03   2.15e-01 5.77e+02
        pdb=" CG  ASN A 331 "    0.006 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 331 "   -0.068 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 331 "    0.397 2.00e-02 2.50e+03
        pdb=" C1  NAG A1304 "   -0.247 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 616 "    0.184 2.00e-02 2.50e+03   1.86e-01 4.34e+02
        pdb=" CG  ASN C 616 "   -0.080 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 616 "   -0.063 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 616 "   -0.274 2.00e-02 2.50e+03
        pdb=" C1  NAG C1308 "    0.233 2.00e-02 2.50e+03
  ... (remaining 4188 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.08: 7
        2.08 -     2.79: 2524
        2.79 -     3.49: 32772
        3.49 -     4.20: 56504
        4.20 -     4.90: 96716
  Nonbonded interactions: 188523
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 125 "
            pdb=" OG  SER C 172 "
     model   vdw
     1.376 2.440
  nonbonded pdb=" ND2 ASN C1134 "
            pdb=" N2  NAG O   1 "
     model   vdw
     1.829 2.560
  nonbonded pdb=" CE1 PHE C 559 "
            pdb=" CB  GLN C 563 "
     model   vdw
     1.923 3.740
  nonbonded pdb=" ND2 ASN A 125 "
            pdb=" O   SER A 172 "
     model   vdw
     1.997 2.520
  nonbonded pdb=" N   CYS B 617 "
            pdb=" OE1 GLN B 644 "
     model   vdw
     2.028 2.520
  ... (remaining 188518 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 54 through 66 or resid 82 through 140 or resi \ 
d 166 through 196 or resid 200 through 211 or resid 215 through 263 or resid 265 \ 
 through 442 or resid 450 through 451 or resid 453 or resid 455 or resid 457 or  \ 
(resid 458 and (name N or name CA or name C or name O or name CB )) or resid 463 \ 
 through 470 or resid 491 through 515 or resid 522 through 827 or resid 856 thro \ 
ugh 1147 or resid 1301 through 1310))
  selection = (chain 'B' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 
 140 or resid 166 through 263 or resid 265 through 442 or resid 450 through 451  \ 
or resid 453 or resid 455 or resid 457 or (resid 458 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 463 through 470 or resid 491 through 501  \ 
or resid 503 through 676 or resid 690 through 827 or resid 856 through 1147 or r \ 
esid 1301 through 1310))
  selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 54 through 66 or resid 82 through 113 or resi \ 
d 116 through 140 or resid 166 through 196 or resid 200 through 211 or resid 215 \ 
 through 442 or resid 448 through 449 or resid 451 through 452 or resid 454 thro \ 
ugh 501 or resid 503 through 515 or resid 522 through 1147 or resid 1301 through \ 
 1310))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     101      5.16       5
     C   14999      2.51       5
     N    3830      2.21       5
     O    4632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             5.660
  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:             0.010
  Extract box with map and model:          25.240
  Check model and map are aligned:         0.340
  Process input model:                     63.020
  Find NCS groups from input model:        2.050
  Set up NCS constraints:                  0.210
  Set refine NCS operators:                0.000
  Set scattering table:                    0.240
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   99.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
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      :  0.015   0.071  24062  Z= 0.973
  Angle     :  1.939  12.515  32728  Z= 1.309
  Chirality :  0.130   1.691   3914
  Planarity :  0.013   0.118   4147
  Dihedral  : 13.659  88.257   8643
  Min Nonbonded Distance : 1.376

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  7.95 %
    Favored  : 91.62 %
  Rotamer Outliers :  2.00 %
  Cbeta Deviations :  0.37 %
  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: -2.31 (0.14), residues: 2841
  helix: -2.59 (0.15), residues: 670
  sheet: -0.24 (0.22), residues: 465
  loop : -1.48 (0.14), residues: 1706

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  540 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 489
  time to evaluate  : 3.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 51
  outliers final: 13
  residues processed: 531
  average time/residue: 0.3909
  time to fit residues: 316.8976
Evaluate side-chains
  251 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 238
  time to evaluate  : 3.111 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.2779
  time to fit residues: 10.1408
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 244 optimal weight:    0.7980
   chunk 219 optimal weight:    4.9990
   chunk 121 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 117 optimal weight:    0.0670
   chunk 227 optimal weight:    8.9990
   chunk 87 optimal weight:    0.8980
   chunk 138 optimal weight:    8.9990
   chunk 169 optimal weight:    0.6980
   chunk 263 optimal weight:    0.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 493 GLN
A 580 GLN
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 764 ASN
** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1048 HIS
C 207 HIS
C 314 GLN
C 784 GLN
C 901 GLN
C 955 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.084  24062  Z= 0.218
  Angle     :  0.693   9.151  32728  Z= 0.377
  Chirality :  0.049   0.553   3914
  Planarity :  0.005   0.039   4147
  Dihedral  :  6.173  23.366   3448
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.63 %
    Favored  : 96.23 %
  Rotamer Outliers :  1.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.14), residues: 2841
  helix: -0.42 (0.19), residues: 687
  sheet: -0.02 (0.19), residues: 612
  loop : -1.17 (0.14), residues: 1542

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 274
  time to evaluate  : 2.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 45
  outliers final: 20
  residues processed: 308
  average time/residue: 0.3955
  time to fit residues: 198.0251
Evaluate side-chains
  215 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 2.952 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.2521
  time to fit residues: 12.9772
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 219 optimal weight:   10.0000
   chunk 179 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 263 optimal weight:    4.9990
   chunk 285 optimal weight:    3.9990
   chunk 234 optimal weight:    5.9990
   chunk 261 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 211 optimal weight:    9.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1002 GLN
** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 764 ASN
B1002 GLN
C  49 HIS
C1005 GLN
C1048 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.076  24062  Z= 0.394
  Angle     :  0.712  14.640  32728  Z= 0.376
  Chirality :  0.050   0.428   3914
  Planarity :  0.005   0.053   4147
  Dihedral  :  5.883  21.462   3448
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.70 %
    Favored  : 94.16 %
  Rotamer Outliers :  2.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.15), residues: 2841
  helix: -0.47 (0.19), residues: 693
  sheet:  0.03 (0.19), residues: 619
  loop : -1.15 (0.15), residues: 1529

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 212
  time to evaluate  : 2.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 61
  outliers final: 43
  residues processed: 255
  average time/residue: 0.3719
  time to fit residues: 152.8448
Evaluate side-chains
  213 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 170
  time to evaluate  : 2.852 
Switching outliers to nearest non-outliers
  outliers start: 43
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2255
  time to fit residues: 21.8229
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 260 optimal weight:    0.9980
   chunk 198 optimal weight:    0.0770
   chunk 136 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 125 optimal weight:    7.9990
   chunk 177 optimal weight:    2.9990
   chunk 264 optimal weight:    4.9990
   chunk 280 optimal weight:    0.9980
   chunk 138 optimal weight:    5.9990
   chunk 250 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 314 GLN
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1106 GLN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN
B 764 ASN
B 872 GLN
** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.066  24062  Z= 0.196
  Angle     :  0.582   9.355  32728  Z= 0.306
  Chirality :  0.045   0.355   3914
  Planarity :  0.004   0.047   4147
  Dihedral  :  5.442  22.308   3448
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.87 %
    Favored  : 95.99 %
  Rotamer Outliers :  1.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.15), residues: 2841
  helix:  0.14 (0.20), residues: 695
  sheet:  0.08 (0.19), residues: 611
  loop : -1.05 (0.15), residues: 1535

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 204
  time to evaluate  : 2.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 39
  outliers final: 16
  residues processed: 235
  average time/residue: 0.3403
  time to fit residues: 128.9705
Evaluate side-chains
  191 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 2.926 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.2316
  time to fit residues: 10.5735
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 233 optimal weight:   10.0000
   chunk 159 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0770
   chunk 208 optimal weight:   20.0000
   chunk 115 optimal weight:    0.9980
   chunk 239 optimal weight:    3.9990
   chunk 193 optimal weight:    0.0980
   chunk 0 optimal weight:   20.0000
   chunk 143 optimal weight:    0.5980
   chunk 251 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 755 GLN
A1048 HIS
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 764 ASN
B1119 ASN
** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039  24062  Z= 0.157
  Angle     :  0.547   9.030  32728  Z= 0.285
  Chirality :  0.044   0.295   3914
  Planarity :  0.004   0.044   4147
  Dihedral  :  5.113  25.430   3448
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.12 %
    Favored  : 95.74 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.15), residues: 2841
  helix:  0.55 (0.20), residues: 699
  sheet:  0.11 (0.19), residues: 636
  loop : -1.02 (0.15), residues: 1506

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 220
  time to evaluate  : 2.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 11
  residues processed: 233
  average time/residue: 0.3471
  time to fit residues: 130.9754
Evaluate side-chains
  192 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 2.662 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.2388
  time to fit residues: 8.8779
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 252 optimal weight:    0.0570
   chunk 55 optimal weight:    5.9990
   chunk 164 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 280 optimal weight:    5.9990
   chunk 232 optimal weight:    5.9990
   chunk 129 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.7904

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1119 ASN
** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 957 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033  24062  Z= 0.166
  Angle     :  0.539   8.017  32728  Z= 0.279
  Chirality :  0.043   0.272   3914
  Planarity :  0.004   0.042   4147
  Dihedral  :  4.952  24.791   3448
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.56 %
    Favored  : 96.30 %
  Rotamer Outliers :  0.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.15), residues: 2841
  helix:  0.71 (0.20), residues: 698
  sheet:  0.13 (0.19), residues: 642
  loop : -1.03 (0.15), residues: 1501

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 2.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 10
  residues processed: 211
  average time/residue: 0.3434
  time to fit residues: 120.1251
Evaluate side-chains
  187 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 2.857 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.2591
  time to fit residues: 8.4834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 270 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 159 optimal weight:    2.9990
   chunk 204 optimal weight:   20.0000
   chunk 158 optimal weight:    0.7980
   chunk 236 optimal weight:   10.0000
   chunk 156 optimal weight:    0.3980
   chunk 279 optimal weight:    0.7980
   chunk 174 optimal weight:    1.9990
   chunk 170 optimal weight:    1.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
A 460 ASN
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1106 GLN
B1113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031  24062  Z= 0.175
  Angle     :  0.541  10.633  32728  Z= 0.280
  Chirality :  0.044   0.607   3914
  Planarity :  0.004   0.042   4147
  Dihedral  :  4.884  22.999   3448
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.01 %
    Favored  : 95.85 %
  Rotamer Outliers :  0.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.15), residues: 2841
  helix:  0.76 (0.20), residues: 695
  sheet:  0.21 (0.19), residues: 651
  loop : -1.02 (0.15), residues: 1495

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 2.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 17
  residues processed: 202
  average time/residue: 0.3546
  time to fit residues: 117.6835
Evaluate side-chains
  193 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 2.644 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.2293
  time to fit residues: 11.0318
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 172 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 166 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 177 optimal weight:    2.9990
   chunk 190 optimal weight:    2.9990
   chunk 138 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 219 optimal weight:    7.9990
   chunk 254 optimal weight:    5.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.044  24062  Z= 0.241
  Angle     :  0.563  10.905  32728  Z= 0.292
  Chirality :  0.044   0.255   3914
  Planarity :  0.004   0.044   4147
  Dihedral  :  4.931  22.410   3448
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.54 %
    Favored  : 95.35 %
  Rotamer Outliers :  0.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.15), residues: 2841
  helix:  0.59 (0.20), residues: 695
  sheet:  0.13 (0.19), residues: 666
  loop : -1.05 (0.15), residues: 1480

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 2.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 12
  residues processed: 198
  average time/residue: 0.3623
  time to fit residues: 117.1942
Evaluate side-chains
  184 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 2.684 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.2424
  time to fit residues: 8.9041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 267 optimal weight:    0.6980
   chunk 244 optimal weight:    5.9990
   chunk 260 optimal weight:    2.9990
   chunk 156 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 204 optimal weight:    0.2980
   chunk 79 optimal weight:    0.0050
   chunk 235 optimal weight:    6.9990
   chunk 246 optimal weight:    0.4980
   chunk 259 optimal weight:    0.1980
   chunk 171 optimal weight:    3.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 784 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.079  24062  Z= 0.145
  Angle     :  0.525  10.273  32728  Z= 0.270
  Chirality :  0.043   0.220   3914
  Planarity :  0.004   0.043   4147
  Dihedral  :  4.731  23.201   3448
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.63 %
    Favored  : 96.27 %
  Rotamer Outliers :  0.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.15), residues: 2841
  helix:  0.92 (0.20), residues: 690
  sheet:  0.17 (0.19), residues: 660
  loop : -0.96 (0.16), residues: 1491

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 199
  time to evaluate  : 2.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 206
  average time/residue: 0.3640
  time to fit residues: 123.9228
Evaluate side-chains
  176 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 170
  time to evaluate  : 2.676 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.2411
  time to fit residues: 6.3176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 275 optimal weight:    4.9990
   chunk 168 optimal weight:    5.9990
   chunk 130 optimal weight:   30.0000
   chunk 191 optimal weight:    5.9990
   chunk 288 optimal weight:    0.5980
   chunk 265 optimal weight:    3.9990
   chunk 230 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 177 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   chunk 182 optimal weight:    0.5980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN
** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 ASN
C 613 GLN
C 965 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.081  24062  Z= 0.286
  Angle     :  0.593  10.514  32728  Z= 0.307
  Chirality :  0.045   0.327   3914
  Planarity :  0.004   0.047   4147
  Dihedral  :  4.913  24.111   3448
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.68 %
    Favored  : 95.21 %
  Rotamer Outliers :  0.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.15), residues: 2841
  helix:  0.57 (0.20), residues: 686
  sheet:  0.14 (0.19), residues: 660
  loop : -1.09 (0.15), residues: 1495

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

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

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5682 Ramachandran restraints generated.
    2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 177
  time to evaluate  : 2.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 180
  average time/residue: 0.3608
  time to fit residues: 106.6907
Evaluate side-chains
  174 residues out of total 2553 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 170
  time to evaluate  : 2.637 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.2690
  time to fit residues: 6.0655
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 290
   random chunks:
   chunk 245 optimal weight:    0.0270
   chunk 70 optimal weight:    0.9990
   chunk 212 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 230 optimal weight:    9.9990
   chunk 96 optimal weight:   10.0000
   chunk 236 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 202 optimal weight:    7.9990
   overall best weight:    0.6442

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
C 804 GLN
C 935 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.132690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.098350 restraints weight = 51177.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.097245 restraints weight = 38437.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.098166 restraints weight = 33696.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.078  24062  Z= 0.163
  Angle     :  0.534  10.184  32728  Z= 0.276
  Chirality :  0.043   0.274   3914
  Planarity :  0.004   0.045   4147
  Dihedral  :  4.757  22.969   3448
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.70 %
    Favored  : 96.20 %
  Rotamer Outliers :  0.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.15), residues: 2841
  helix:  0.87 (0.20), residues: 684
  sheet:  0.12 (0.19), residues: 648
  loop : -0.99 (0.15), residues: 1509

===============================================================================
Job complete
usr+sys time: 4406.85 seconds
wall clock time: 82 minutes 30.65 seconds (4950.65 seconds total)