Starting phenix.real_space_refine
on Thu Feb 22 00:33:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkh_13472/02_2024/7pkh_13472_trim_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca     20      9.91       5
     P      10      5.49       5
     S      40      5.16       5
     C   10630      2.51       5
     N    2620      2.21       5
     O    3140      1.98       5
     H   15960      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "J PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU  108": "OE1" <-> "OE2"
    Residue "J GLU  130": "OE1" <-> "OE2"
    Residue "J ASP  140": "OD1" <-> "OD2"
    Residue "J GLU  147": "OE1" <-> "OE2"
    Residue "J ASP  155": "OD1" <-> "OD2"
    Residue "J ASP  163": "OD1" <-> "OD2"
    Residue "J PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU  193": "OE1" <-> "OE2"
    Residue "J PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F ASP   70": "OD1" <-> "OD2"
    Residue "F GLU   85": "OE1" <-> "OE2"
    Residue "F ASP  140": "OD1" <-> "OD2"
    Residue "F ASP  163": "OD1" <-> "OD2"
    Residue "F ASP  169": "OD1" <-> "OD2"
    Residue "F GLU  197": "OE1" <-> "OE2"
    Residue "F PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU   81": "OE1" <-> "OE2"
    Residue "G GLU   85": "OE1" <-> "OE2"
    Residue "G ASP  112": "OD1" <-> "OD2"
    Residue "G TYR  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU  147": "OE1" <-> "OE2"
    Residue "G GLU  170": "OE1" <-> "OE2"
    Residue "G PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU  193": "OE1" <-> "OE2"
    Residue "G PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP    3": "OD1" <-> "OD2"
    Residue "H PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU   14": "OE1" <-> "OE2"
    Residue "H PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU   62": "OE1" <-> "OE2"
    Residue "H PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP   70": "OD1" <-> "OD2"
    Residue "H GLU   81": "OE1" <-> "OE2"
    Residue "H TYR  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP  140": "OD1" <-> "OD2"
    Residue "H ASP  169": "OD1" <-> "OD2"
    Residue "H GLU  170": "OE1" <-> "OE2"
    Residue "H TYR  175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU  197": "OE1" <-> "OE2"
    Residue "H PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP   16": "OD1" <-> "OD2"
    Residue "I GLU   42": "OE1" <-> "OE2"
    Residue "I PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I TYR  125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP  163": "OD1" <-> "OD2"
    Residue "I GLU  170": "OE1" <-> "OE2"
    Residue "I TYR  175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU  193": "OE1" <-> "OE2"
    Residue "E PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU   14": "OE1" <-> "OE2"
    Residue "E ASP   16": "OD1" <-> "OD2"
    Residue "E TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU   42": "OE1" <-> "OE2"
    Residue "E PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E ASP   70": "OD1" <-> "OD2"
    Residue "E GLU  130": "OE1" <-> "OE2"
    Residue "E ASP  140": "OD1" <-> "OD2"
    Residue "E PHE  142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU  147": "OE1" <-> "OE2"
    Residue "E GLU  170": "OE1" <-> "OE2"
    Residue "E PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU  193": "OE1" <-> "OE2"
    Residue "E PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP   16": "OD1" <-> "OD2"
    Residue "D TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  140": "OD1" <-> "OD2"
    Residue "D ASP  163": "OD1" <-> "OD2"
    Residue "D ASP  169": "OD1" <-> "OD2"
    Residue "D GLU  170": "OE1" <-> "OE2"
    Residue "D PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  197": "OE1" <-> "OE2"
    Residue "D PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU   81": "OE1" <-> "OE2"
    Residue "C GLU  108": "OE1" <-> "OE2"
    Residue "C GLU  147": "OE1" <-> "OE2"
    Residue "C ASP  163": "OD1" <-> "OD2"
    Residue "C GLU  170": "OE1" <-> "OE2"
    Residue "C TYR  175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP    3": "OD1" <-> "OD2"
    Residue "B PHE   11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP   16": "OD1" <-> "OD2"
    Residue "B TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  147": "OE1" <-> "OE2"
    Residue "B ASP  163": "OD1" <-> "OD2"
    Residue "B GLU  170": "OE1" <-> "OE2"
    Residue "B TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP    3": "OD1" <-> "OD2"
    Residue "A GLU   14": "OE1" <-> "OE2"
    Residue "A ASP   16": "OD1" <-> "OD2"
    Residue "A TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   70": "OD1" <-> "OD2"
    Residue "A GLU   81": "OE1" <-> "OE2"
    Residue "A ASP  140": "OD1" <-> "OD2"
    Residue "A PHE  142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  170": "OE1" <-> "OE2"
    Residue "A PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  193": "OE1" <-> "OE2"
    Residue "A PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 32420
  Number of models: 1
  Model: ""
    Number of chains: 30
    Chain: "J"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "F"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "G"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "H"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "I"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "E"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "C"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "A"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "J"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "F"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "H"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "I"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 13
          Unusual residues: {' CA': 2, ' PC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "J"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "F"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "G"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "I"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 14.63, per 1000 atoms: 0.45
  Number of scatterers: 32420
  At special positions: 0
  Unit cell: (140.448, 126.236, 110.352, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca     20     19.99
     S      40     16.00
     P      10     15.00
     O    3140      8.00
     N    2620      7.00
     C   10630      6.00
     H   15960      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS J  36 " - pdb=" SG  CYS J  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  36 " - pdb=" SG  CYS F  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  36 " - pdb=" SG  CYS G  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  36 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  36 " - pdb=" SG  CYS I  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  97 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 26.64
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3780

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      35 helices and 30 sheets defined
      7.9% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 5.01
  Creating SS restraints...
    Processing helix  chain 'J' and resid 43 through 45
      No H-bonds generated for 'chain 'J' and resid 43 through 45'
    Processing helix  chain 'J' and resid 148 through 150
      No H-bonds generated for 'chain 'J' and resid 148 through 150'
    Processing helix  chain 'J' and resid 168 through 176
    Processing helix  chain 'F' and resid 43 through 45
      No H-bonds generated for 'chain 'F' and resid 43 through 45'
    Processing helix  chain 'F' and resid 148 through 150
      No H-bonds generated for 'chain 'F' and resid 148 through 150'
    Processing helix  chain 'F' and resid 168 through 176
    Processing helix  chain 'F' and resid 187 through 189
      No H-bonds generated for 'chain 'F' and resid 187 through 189'
    Processing helix  chain 'G' and resid 43 through 45
      No H-bonds generated for 'chain 'G' and resid 43 through 45'
    Processing helix  chain 'G' and resid 148 through 150
      No H-bonds generated for 'chain 'G' and resid 148 through 150'
    Processing helix  chain 'G' and resid 168 through 176
    Processing helix  chain 'H' and resid 43 through 45
      No H-bonds generated for 'chain 'H' and resid 43 through 45'
    Processing helix  chain 'H' and resid 148 through 150
      No H-bonds generated for 'chain 'H' and resid 148 through 150'
    Processing helix  chain 'H' and resid 168 through 176
    Processing helix  chain 'I' and resid 43 through 45
      No H-bonds generated for 'chain 'I' and resid 43 through 45'
    Processing helix  chain 'I' and resid 148 through 150
      No H-bonds generated for 'chain 'I' and resid 148 through 150'
    Processing helix  chain 'I' and resid 168 through 175
    Processing helix  chain 'I' and resid 187 through 189
      No H-bonds generated for 'chain 'I' and resid 187 through 189'
    Processing helix  chain 'E' and resid 43 through 45
      No H-bonds generated for 'chain 'E' and resid 43 through 45'
    Processing helix  chain 'E' and resid 148 through 150
      No H-bonds generated for 'chain 'E' and resid 148 through 150'
    Processing helix  chain 'E' and resid 168 through 176
    Processing helix  chain 'E' and resid 187 through 189
      No H-bonds generated for 'chain 'E' and resid 187 through 189'
    Processing helix  chain 'D' and resid 43 through 45
      No H-bonds generated for 'chain 'D' and resid 43 through 45'
    Processing helix  chain 'D' and resid 148 through 150
      No H-bonds generated for 'chain 'D' and resid 148 through 150'
    Processing helix  chain 'D' and resid 168 through 175
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 148 through 150
      No H-bonds generated for 'chain 'C' and resid 148 through 150'
    Processing helix  chain 'C' and resid 168 through 176
    Processing helix  chain 'C' and resid 187 through 189
      No H-bonds generated for 'chain 'C' and resid 187 through 189'
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 148 through 150
      No H-bonds generated for 'chain 'B' and resid 148 through 150'
    Processing helix  chain 'B' and resid 168 through 176
    Processing helix  chain 'B' and resid 187 through 189
      No H-bonds generated for 'chain 'B' and resid 187 through 189'
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 148 through 150
      No H-bonds generated for 'chain 'A' and resid 148 through 150'
    Processing helix  chain 'A' and resid 168 through 176
    Processing sheet with id=  A, first strand: chain 'J' and resid 199 through 202
    Processing sheet with id=  B, first strand: chain 'J' and resid 192 through 195
      removed outlier: 4.027A  pdb=" N   ILE J 133 " --> pdb=" O   LEU J  22 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE J  65 " --> pdb=" O   ILE J  51 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   SER J  53 " --> pdb=" O   ILE J  63 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE J  63 " --> pdb=" O   SER J  53 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR J  73 " --> pdb=" O   PHE J  84 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'J' and resid 34 through 36
    Processing sheet with id=  D, first strand: chain 'F' and resid 199 through 202
    Processing sheet with id=  E, first strand: chain 'F' and resid 192 through 195
      removed outlier: 4.133A  pdb=" N   ILE F 133 " --> pdb=" O   LEU F  22 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE F  65 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  63 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE F  63 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'F' and resid 34 through 36
    Processing sheet with id=  G, first strand: chain 'G' and resid 199 through 202
    Processing sheet with id=  H, first strand: chain 'G' and resid 192 through 195
      removed outlier: 3.923A  pdb=" N   ILE G 133 " --> pdb=" O   LEU G  22 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE G  65 " --> pdb=" O   ILE G  51 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   SER G  53 " --> pdb=" O   ILE G  63 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ILE G  63 " --> pdb=" O   SER G  53 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'G' and resid 34 through 36
    Processing sheet with id=  J, first strand: chain 'H' and resid 199 through 202
    Processing sheet with id=  K, first strand: chain 'H' and resid 192 through 195
      removed outlier: 4.006A  pdb=" N   ILE H 133 " --> pdb=" O   LEU H  22 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ILE H  65 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  63 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE H  63 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'H' and resid 34 through 36
    Processing sheet with id=  M, first strand: chain 'I' and resid 199 through 202
    Processing sheet with id=  N, first strand: chain 'I' and resid 192 through 195
      removed outlier: 3.934A  pdb=" N   ILE I 133 " --> pdb=" O   LEU I  22 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ILE I  65 " --> pdb=" O   ILE I  51 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  63 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ILE I  63 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR I  73 " --> pdb=" O   PHE I  84 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'I' and resid 34 through 36
    Processing sheet with id=  P, first strand: chain 'E' and resid 199 through 202
    Processing sheet with id=  Q, first strand: chain 'E' and resid 192 through 195
      removed outlier: 3.993A  pdb=" N   ILE E 133 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE E  65 " --> pdb=" O   ILE E  51 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   SER E  53 " --> pdb=" O   ILE E  63 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE E  63 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'E' and resid 34 through 36
    Processing sheet with id=  S, first strand: chain 'D' and resid 199 through 202
    Processing sheet with id=  T, first strand: chain 'D' and resid 192 through 195
      removed outlier: 4.112A  pdb=" N   ILE D 133 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ILE D  65 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  63 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE D  63 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'D' and resid 34 through 36
    Processing sheet with id=  V, first strand: chain 'C' and resid 199 through 202
    Processing sheet with id=  W, first strand: chain 'C' and resid 192 through 195
      removed outlier: 3.951A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ILE C  65 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   SER C  53 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE C  63 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'C' and resid 34 through 36
    Processing sheet with id=  Y, first strand: chain 'B' and resid 199 through 202
    Processing sheet with id=  Z, first strand: chain 'B' and resid 192 through 195
      removed outlier: 3.640A  pdb=" N   ILE B 133 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ILE B  65 " --> pdb=" O   ILE B  51 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   SER B  53 " --> pdb=" O   ILE B  63 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE B  63 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B  73 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'B' and resid 34 through 36
    Processing sheet with id= AB, first strand: chain 'A' and resid 199 through 202
    Processing sheet with id= AC, first strand: chain 'A' and resid 192 through 195
      removed outlier: 4.041A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE A  65 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   SER A  53 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE A  63 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'A' and resid 34 through 36

    585 hydrogen bonds defined for protein.
    1464 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: 12.89

  Time building geometry restraints manager: 27.31 seconds

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

  Histogram of bond lengths:
        0.83 -     1.05: 15960
        1.05 -     1.26: 2670
        1.26 -     1.48: 7237
        1.48 -     1.69: 6913
        1.69 -     1.91: 60
  Bond restraints: 32840
  Sorted by residual:
  bond pdb=" O4   PC D 303 "
       pdb=" P1   PC D 303 "
    ideal  model  delta    sigma   weight residual
    1.510  1.609 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" O4   PC G 303 "
       pdb=" P1   PC G 303 "
    ideal  model  delta    sigma   weight residual
    1.510  1.607 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" O4   PC J 303 "
       pdb=" P1   PC J 303 "
    ideal  model  delta    sigma   weight residual
    1.510  1.607 -0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" O4   PC F 303 "
       pdb=" P1   PC F 303 "
    ideal  model  delta    sigma   weight residual
    1.510  1.605 -0.095 2.00e-02 2.50e+03 2.27e+01
  bond pdb=" O1   PC J 303 "
       pdb=" P1   PC J 303 "
    ideal  model  delta    sigma   weight residual
    1.510  1.604 -0.094 2.00e-02 2.50e+03 2.21e+01
  ... (remaining 32835 not shown)

  Histogram of bond angle deviations from ideal:
       77.75 -    89.04: 72
       89.04 -   100.33: 5
      100.33 -   111.62: 36179
      111.62 -   122.91: 18606
      122.91 -   134.20: 4398
  Bond angle restraints: 59260
  Sorted by residual:
  angle pdb=" CG2 THR J  17 "
        pdb=" CB  THR J  17 "
        pdb=" HB  THR J  17 "
      ideal   model   delta    sigma   weight residual
     108.00   77.75   30.25 3.00e+00 1.11e-01 1.02e+02
  angle pdb=" CG2 THR A  46 "
        pdb=" CB  THR A  46 "
        pdb=" HB  THR A  46 "
      ideal   model   delta    sigma   weight residual
     108.00   79.66   28.34 3.00e+00 1.11e-01 8.92e+01
  angle pdb=" CA  THR J  17 "
        pdb=" CB  THR J  17 "
        pdb=" HB  THR J  17 "
      ideal   model   delta    sigma   weight residual
     109.00   81.03   27.97 3.00e+00 1.11e-01 8.69e+01
  angle pdb=" CG2 THR J  46 "
        pdb=" CB  THR J  46 "
        pdb=" HB  THR J  46 "
      ideal   model   delta    sigma   weight residual
     108.00   80.08   27.92 3.00e+00 1.11e-01 8.66e+01
  angle pdb=" CG2 THR A 173 "
        pdb=" CB  THR A 173 "
        pdb=" HB  THR A 173 "
      ideal   model   delta    sigma   weight residual
     108.00   80.12   27.88 3.00e+00 1.11e-01 8.64e+01
  ... (remaining 59255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 14085
       17.67 -    35.35: 965
       35.35 -    53.02: 305
       53.02 -    70.69: 218
       70.69 -    88.36: 27
  Dihedral angle restraints: 15600
    sinusoidal: 8230
      harmonic: 7370
  Sorted by residual:
  dihedral pdb=" CB  CYS B  36 "
           pdb=" SG  CYS B  36 "
           pdb=" SG  CYS B  97 "
           pdb=" CB  CYS B  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.74   54.26     1      1.00e+01 1.00e-02 3.99e+01
  dihedral pdb=" CA  ARG H  58 "
           pdb=" C   ARG H  58 "
           pdb=" N   GLN H  59 "
           pdb=" CA  GLN H  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.70  -28.30     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  GLU D  62 "
           pdb=" C   GLU D  62 "
           pdb=" N   ILE D  63 "
           pdb=" CA  ILE D  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.18   27.82     0      5.00e+00 4.00e-02 3.10e+01
  ... (remaining 15597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.367: 2446
       0.367 -    0.733: 0
       0.733 -    1.100: 1
       1.100 -    1.466: 12
       1.466 -    1.833: 11
  Chirality restraints: 2470
  Sorted by residual:
  chirality pdb=" CG  LEU A  83 "
            pdb=" CB  LEU A  83 "
            pdb=" CD1 LEU A  83 "
            pdb=" CD2 LEU A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.76   -1.83 2.00e-01 2.50e+01 8.40e+01
  chirality pdb=" CG  LEU J  83 "
            pdb=" CB  LEU J  83 "
            pdb=" CD1 LEU J  83 "
            pdb=" CD2 LEU J  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.80   -1.79 2.00e-01 2.50e+01 7.99e+01
  chirality pdb=" CG  LEU F  83 "
            pdb=" CB  LEU F  83 "
            pdb=" CD1 LEU F  83 "
            pdb=" CD2 LEU F  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.85   -1.74 2.00e-01 2.50e+01 7.53e+01
  ... (remaining 2467 not shown)

  Planarity restraints: 4840
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  58 "   -0.058 9.50e-02 1.11e+02   3.87e-02 2.57e+01
        pdb=" NE  ARG G  58 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  58 "   -0.041 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  58 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  58 "    0.067 2.00e-02 2.50e+03
        pdb="HH11 ARG G  58 "   -0.009 2.00e-02 2.50e+03
        pdb="HH12 ARG G  58 "    0.028 2.00e-02 2.50e+03
        pdb="HH21 ARG G  58 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG G  58 "   -0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN I 183 "   -0.033 2.00e-02 2.50e+03   4.09e-02 2.50e+01
        pdb=" CG  ASN I 183 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN I 183 "    0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN I 183 "    0.066 2.00e-02 2.50e+03
        pdb="HD21 ASN I 183 "    0.002 2.00e-02 2.50e+03
        pdb="HD22 ASN I 183 "   -0.063 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  38 "   -0.009 2.00e-02 2.50e+03   3.11e-02 2.41e+01
        pdb=" CG  HIS G  38 "    0.005 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  38 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  38 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  38 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  38 "   -0.020 2.00e-02 2.50e+03
        pdb=" HD1 HIS G  38 "    0.055 2.00e-02 2.50e+03
        pdb=" HD2 HIS G  38 "    0.040 2.00e-02 2.50e+03
        pdb=" HE1 HIS G  38 "    0.018 2.00e-02 2.50e+03
        pdb=" HE2 HIS G  38 "    0.015 2.00e-02 2.50e+03
  ... (remaining 4837 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 806
        2.08 -     2.71: 53752
        2.71 -     3.34: 94257
        3.34 -     3.97: 130753
        3.97 -     4.60: 202707
  Nonbonded interactions: 482275
  Sorted by model distance:
  nonbonded pdb="HE21 GLN H 139 "
            pdb=" O   PHE H 142 "
     model   vdw
     1.448 1.850
  nonbonded pdb=" H   SER B 167 "
            pdb=" OE1 GLU B 170 "
     model   vdw
     1.504 1.850
  nonbonded pdb=" HG1 THR C  41 "
            pdb=" O   VAL C 153 "
     model   vdw
     1.507 1.850
  nonbonded pdb=" HG1 THR D  41 "
            pdb=" O   VAL D 153 "
     model   vdw
     1.511 1.850
  nonbonded pdb=" HG  SER B  74 "
            pdb=" OE2 GLU B  81 "
     model   vdw
     1.514 1.850
  ... (remaining 482270 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.910
  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:             0.470
  Extract box with map and model:          11.780
  Check model and map are aligned:         0.470
  Set scattering table:                    0.300
  Process input model:                     105.000
  Find NCS groups from input model:        1.810
  Set up NCS constraints:                  0.230
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  138.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
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      :  0.009   0.115  16880  Z= 0.589
  Angle     :  0.992  19.206  22960  Z= 0.528
  Chirality :  0.155   1.833   2470
  Planarity :  0.006   0.074   2900
  Dihedral  : 13.272  88.365   6010
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -0.72 (0.18), residues: 2040
  helix: -1.30 (0.38), residues: 100
  sheet: -0.04 (0.16), residues: 910
  loop : -0.72 (0.19), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.006   TRP F  67 
 HIS   0.021   0.006   HIS G  38 
 PHE   0.022   0.003   PHE H  66 
 TYR   0.031   0.005   TYR F  54 
 ARG   0.069   0.010   ARG G 188 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 2.969 
Fit side-chains
   revert: symmetry clash
REVERT: D  145 ASN cc_start: 0.8573 (m110) cc_final: 0.8165 (m110)
REVERT: D  172 ASN cc_start: 0.8116 (t0) cc_final: 0.7768 (t0)
REVERT: C  194 VAL cc_start: 0.9091 (t) cc_final: 0.8801 (p)
REVERT: A  169 ASP cc_start: 0.8182 (m-30) cc_final: 0.7927 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 3.1884
  time to fit residues: 686.7364
Evaluate side-chains
  144 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 2.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 168 optimal weight:    0.9980
   chunk 151 optimal weight:    0.0980
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 156 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 181 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
J 172 ASN
G 145 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  16880  Z= 0.263
  Angle     :  0.763  15.911  22960  Z= 0.391
  Chirality :  0.157   1.796   2470
  Planarity :  0.004   0.055   2900
  Dihedral  :  6.359  58.533   2230
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.50 %
    Favored  : 93.67 %
  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: -0.20 (0.18), residues: 2040
  helix:  1.62 (0.44), residues: 100
  sheet:  0.14 (0.16), residues: 910
  loop : -0.49 (0.19), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 110 
 HIS   0.007   0.002   HIS G  38 
 PHE   0.014   0.001   PHE J  52 
 TYR   0.016   0.001   TYR D  54 
 ARG   0.006   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 2.674 
Fit side-chains
   revert: symmetry clash
REVERT: J   18 SER cc_start: 0.8765 (m) cc_final: 0.8284 (p)
REVERT: J  197 GLU cc_start: 0.6992 (tp30) cc_final: 0.6646 (pp20)
REVERT: G  126 THR cc_start: 0.8517 (p) cc_final: 0.8314 (m)
REVERT: I  188 ARG cc_start: 0.7857 (mpt-90) cc_final: 0.7629 (mmt-90)
REVERT: D  145 ASN cc_start: 0.8525 (m110) cc_final: 0.8119 (m110)
REVERT: D  163 ASP cc_start: 0.7585 (p0) cc_final: 0.7371 (p0)
REVERT: D  172 ASN cc_start: 0.8045 (t0) cc_final: 0.7678 (t0)
REVERT: C   80 SER cc_start: 0.8640 (m) cc_final: 0.8369 (t)
REVERT: C   88 GLU cc_start: 0.7267 (pp20) cc_final: 0.6881 (pm20)
  outliers start: 15
  outliers final: 5
  residues processed: 167
  average time/residue: 2.9826
  time to fit residues: 553.3416
Evaluate side-chains
  146 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 2.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain H residue   18 SER
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain A residue   76 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 100 optimal weight:    0.0070
   chunk 56 optimal weight:    1.9990
   chunk 151 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 181 optimal weight:    1.9990
   chunk 196 optimal weight:    0.9990
   chunk 162 optimal weight:    0.6980
   chunk 180 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 145 optimal weight:    2.9990
   overall best weight:    0.9002

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  16880  Z= 0.225
  Angle     :  0.717  15.664  22960  Z= 0.365
  Chirality :  0.155   1.796   2470
  Planarity :  0.003   0.053   2900
  Dihedral  :  5.779  59.170   2230
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.11 %
    Favored  : 92.00 %
  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: -0.04 (0.18), residues: 2040
  helix:  1.98 (0.45), residues: 110
  sheet:  0.25 (0.16), residues: 890
  loop : -0.43 (0.19), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 110 
 HIS   0.005   0.001   HIS G  38 
 PHE   0.014   0.001   PHE D 180 
 TYR   0.015   0.001   TYR B  54 
 ARG   0.011   0.001   ARG J   6 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 2.872 
Fit side-chains
REVERT: J   16 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7612 (p0)
REVERT: I  155 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (m-30)
REVERT: D  145 ASN cc_start: 0.8514 (m110) cc_final: 0.8152 (m110)
REVERT: D  163 ASP cc_start: 0.7536 (p0) cc_final: 0.7315 (p0)
REVERT: D  172 ASN cc_start: 0.8121 (t0) cc_final: 0.7430 (t0)
REVERT: C   80 SER cc_start: 0.8590 (m) cc_final: 0.8306 (t)
REVERT: C   88 GLU cc_start: 0.7251 (pp20) cc_final: 0.6851 (pm20)
REVERT: C  155 ASP cc_start: 0.8429 (m-30) cc_final: 0.8207 (m-30)
REVERT: A   13 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7678 (mtmm)
  outliers start: 16
  outliers final: 4
  residues processed: 155
  average time/residue: 2.8393
  time to fit residues: 489.6959
Evaluate side-chains
  142 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 2.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain G residue  155 ASP
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 179 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 182 optimal weight:    3.9990
   chunk 193 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 173 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
J 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  16880  Z= 0.301
  Angle     :  0.728  15.773  22960  Z= 0.370
  Chirality :  0.156   1.769   2470
  Planarity :  0.004   0.077   2900
  Dihedral  :  5.902  69.325   2230
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.89 %
    Favored  : 91.28 %
  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: -0.24 (0.18), residues: 2040
  helix:  1.96 (0.46), residues: 110
  sheet:  0.11 (0.16), residues: 910
  loop : -0.58 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I 162 
 HIS   0.006   0.002   HIS G  38 
 PHE   0.015   0.001   PHE D 180 
 TYR   0.017   0.002   TYR B  54 
 ARG   0.012   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 2.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   88 GLU cc_start: 0.6787 (pm20) cc_final: 0.6585 (pm20)
REVERT: G  138 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7476 (tm-30)
REVERT: I  155 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7992 (m-30)
REVERT: E  169 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7602 (m-30)
REVERT: D  145 ASN cc_start: 0.8514 (m110) cc_final: 0.8167 (m110)
REVERT: D  172 ASN cc_start: 0.8170 (t0) cc_final: 0.7706 (t0)
REVERT: C   80 SER cc_start: 0.8574 (m) cc_final: 0.8267 (t)
REVERT: C   88 GLU cc_start: 0.7261 (pp20) cc_final: 0.6850 (pm20)
REVERT: A  163 ASP cc_start: 0.8219 (p0) cc_final: 0.8012 (p0)
  outliers start: 15
  outliers final: 8
  residues processed: 143
  average time/residue: 3.1136
  time to fit residues: 491.5042
Evaluate side-chains
  141 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 2.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain G residue   57 LYS
Chi-restraints excluded: chain G residue  155 ASP
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 161 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0570
   chunk 143 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 164 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 173 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  16880  Z= 0.248
  Angle     :  0.705  15.741  22960  Z= 0.357
  Chirality :  0.156   1.761   2470
  Planarity :  0.004   0.073   2900
  Dihedral  :  5.780  79.016   2230
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.44 %
    Favored  : 90.39 %
  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: -0.21 (0.18), residues: 2040
  helix:  2.15 (0.46), residues: 110
  sheet:  0.12 (0.16), residues: 910
  loop : -0.58 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 162 
 HIS   0.005   0.001   HIS G  38 
 PHE   0.014   0.001   PHE D 180 
 TYR   0.014   0.001   TYR B  54 
 ARG   0.013   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 2.756 
Fit side-chains
   revert: symmetry clash
REVERT: J   16 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7658 (p0)
REVERT: G   89 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7611 (p)
REVERT: I  155 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7993 (m-30)
REVERT: D  145 ASN cc_start: 0.8500 (m110) cc_final: 0.8201 (m110)
REVERT: D  172 ASN cc_start: 0.8125 (t0) cc_final: 0.7730 (t0)
REVERT: C   88 GLU cc_start: 0.7241 (pp20) cc_final: 0.6833 (pm20)
  outliers start: 21
  outliers final: 13
  residues processed: 161
  average time/residue: 3.0212
  time to fit residues: 538.6334
Evaluate side-chains
  147 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 2.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain G residue   57 LYS
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  155 ASP
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 174 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 193 optimal weight:    2.9990
   chunk 160 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  16880  Z= 0.345
  Angle     :  0.731  15.783  22960  Z= 0.373
  Chirality :  0.156   1.775   2470
  Planarity :  0.004   0.084   2900
  Dihedral  :  6.099  86.063   2230
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.28 %
    Favored  : 89.17 %
  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: -0.39 (0.18), residues: 2040
  helix:  1.86 (0.46), residues: 110
  sheet:  0.05 (0.16), residues: 910
  loop : -0.73 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I 162 
 HIS   0.006   0.001   HIS G  38 
 PHE   0.013   0.001   PHE D 180 
 TYR   0.017   0.002   TYR E  54 
 ARG   0.016   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 2.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   89 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7587 (p)
REVERT: H    6 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7678 (mtp85)
REVERT: I  155 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8049 (m-30)
REVERT: E  169 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7609 (m-30)
REVERT: D  145 ASN cc_start: 0.8470 (m110) cc_final: 0.8197 (m110)
REVERT: D  172 ASN cc_start: 0.8169 (t0) cc_final: 0.7773 (t0)
REVERT: C   88 GLU cc_start: 0.7285 (pp20) cc_final: 0.6861 (pm20)
  outliers start: 28
  outliers final: 19
  residues processed: 152
  average time/residue: 3.1038
  time to fit residues: 522.4841
Evaluate side-chains
  147 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 2.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  155 ASP
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain D residue    1 GLN
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 186 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 141 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 162 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 192 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   chunk 88 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  16880  Z= 0.195
  Angle     :  0.694  15.713  22960  Z= 0.351
  Chirality :  0.155   1.743   2470
  Planarity :  0.004   0.088   2900
  Dihedral  :  5.744  82.497   2230
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.28 %
    Favored  : 88.67 %
  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: -0.18 (0.18), residues: 2040
  helix:  2.22 (0.46), residues: 110
  sheet:  0.20 (0.17), residues: 890
  loop : -0.62 (0.19), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 162 
 HIS   0.004   0.001   HIS G  38 
 PHE   0.012   0.001   PHE D 180 
 TYR   0.011   0.001   TYR B  54 
 ARG   0.016   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 2.738 
Fit side-chains
REVERT: J   16 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7654 (p0)
REVERT: G   89 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7556 (p)
REVERT: H    6 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7687 (mtp85)
REVERT: I   58 ARG cc_start: 0.6448 (pmm150) cc_final: 0.6231 (pmt170)
REVERT: I  155 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7954 (m-30)
REVERT: D    1 GLN cc_start: 0.6643 (mm110) cc_final: 0.6425 (mp10)
REVERT: D  145 ASN cc_start: 0.8529 (m110) cc_final: 0.8249 (m110)
REVERT: D  172 ASN cc_start: 0.8129 (t0) cc_final: 0.7743 (t0)
REVERT: C   88 GLU cc_start: 0.7193 (pp20) cc_final: 0.6796 (pm20)
REVERT: B    7 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8412 (mttt)
  outliers start: 19
  outliers final: 12
  residues processed: 148
  average time/residue: 3.0620
  time to fit residues: 502.1562
Evaluate side-chains
  140 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 3.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 151 optimal weight:    2.9990
   chunk 175 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  16880  Z= 0.278
  Angle     :  0.711  15.819  22960  Z= 0.361
  Chirality :  0.156   1.757   2470
  Planarity :  0.004   0.099   2900
  Dihedral  :  5.782  75.327   2230
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.61 %
    Favored  : 87.89 %
  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 (0.18), residues: 2040
  helix:  2.09 (0.46), residues: 110
  sheet:  0.05 (0.16), residues: 910
  loop : -0.70 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I 162 
 HIS   0.006   0.001   HIS G  38 
 PHE   0.011   0.001   PHE D 180 
 TYR   0.014   0.001   TYR E  54 
 ARG   0.017   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 3.077 
Fit side-chains
REVERT: J   16 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7694 (p0)
REVERT: G   89 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7568 (p)
REVERT: H    6 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7693 (mtp85)
REVERT: I  155 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8001 (m-30)
REVERT: D    1 GLN cc_start: 0.6745 (mm110) cc_final: 0.6462 (mp10)
REVERT: D  145 ASN cc_start: 0.8510 (m110) cc_final: 0.8230 (m110)
REVERT: D  172 ASN cc_start: 0.8168 (t0) cc_final: 0.7784 (t0)
REVERT: D  191 LYS cc_start: 0.7948 (mmmt) cc_final: 0.7659 (tmtm)
  outliers start: 27
  outliers final: 15
  residues processed: 149
  average time/residue: 2.8195
  time to fit residues: 470.1914
Evaluate side-chains
  142 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 2.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain G residue   89 VAL
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  181 SER
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain I residue  155 ASP
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 184 optimal weight:    0.0370
   chunk 168 optimal weight:    0.9990
   chunk 179 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 141 optimal weight:    0.0670
   chunk 55 optimal weight:    1.9990
   chunk 162 optimal weight:    0.7980
   chunk 169 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 189 optimal weight:    0.5980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  16880  Z= 0.171
  Angle     :  0.681  15.726  22960  Z= 0.343
  Chirality :  0.155   1.741   2470
  Planarity :  0.004   0.088   2900
  Dihedral  :  5.385  69.636   2230
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.33 %
    Favored  : 87.89 %
  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: -0.10 (0.18), residues: 2040
  helix:  2.43 (0.47), residues: 110
  sheet:  0.22 (0.17), residues: 890
  loop : -0.54 (0.19), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 162 
 HIS   0.004   0.001   HIS G  38 
 PHE   0.010   0.001   PHE A  39 
 TYR   0.009   0.001   TYR J  54 
 ARG   0.013   0.001   ARG J  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 2.709 
Fit side-chains
REVERT: H    6 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7707 (mtp85)
REVERT: I  114 LYS cc_start: 0.8490 (mmpt) cc_final: 0.8281 (mmpt)
REVERT: D    1 GLN cc_start: 0.6709 (mm110) cc_final: 0.6424 (mp10)
REVERT: D  145 ASN cc_start: 0.8561 (m110) cc_final: 0.8258 (m110)
REVERT: D  172 ASN cc_start: 0.8126 (t0) cc_final: 0.7770 (t0)
REVERT: D  191 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7651 (tmtm)
REVERT: B    7 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8406 (mttt)
  outliers start: 14
  outliers final: 10
  residues processed: 144
  average time/residue: 2.9884
  time to fit residues: 477.8038
Evaluate side-chains
  136 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 2.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue   89 VAL
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 199 optimal weight:    0.9990
   chunk 183 optimal weight:    0.5980
   chunk 158 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 169 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  16880  Z= 0.203
  Angle     :  0.689  15.850  22960  Z= 0.347
  Chirality :  0.155   1.734   2470
  Planarity :  0.004   0.075   2900
  Dihedral  :  5.319  61.972   2230
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.61 %
    Favored  : 87.61 %
  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:  0.02 (0.18), residues: 2040
  helix:  2.45 (0.47), residues: 110
  sheet:  0.55 (0.17), residues: 830
  loop : -0.65 (0.18), residues: 1100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 162 
 HIS   0.005   0.001   HIS G  38 
 PHE   0.009   0.001   PHE E  52 
 TYR   0.011   0.001   TYR A  54 
 ARG   0.013   0.001   ARG E  58 

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

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

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4080 Ramachandran restraints generated.
    2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 2.798 
Fit side-chains
REVERT: H    6 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7684 (mtp85)
REVERT: I  114 LYS cc_start: 0.8494 (mmpt) cc_final: 0.8286 (mmpt)
REVERT: D    1 GLN cc_start: 0.6646 (mm110) cc_final: 0.6384 (mp10)
REVERT: D  145 ASN cc_start: 0.8542 (m110) cc_final: 0.8237 (m110)
REVERT: D  172 ASN cc_start: 0.8146 (t0) cc_final: 0.7790 (t0)
REVERT: D  191 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7624 (tmtm)
REVERT: B    7 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8413 (mttt)
  outliers start: 14
  outliers final: 11
  residues processed: 139
  average time/residue: 3.0120
  time to fit residues: 465.0915
Evaluate side-chains
  137 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 2.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue   98 THR
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain E residue   80 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  191 LYS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  169 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 146 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9980
   chunk 158 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 163 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 139 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H 150 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.090733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.073317 restraints weight = 73232.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 1.99
r_work: 0.2668 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  16880  Z= 0.182
  Angle     :  0.681  15.805  22960  Z= 0.343
  Chirality :  0.155   1.739   2470
  Planarity :  0.004   0.067   2900
  Dihedral  :  5.142  50.781   2230
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.56 %
    Favored  : 87.61 %
  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:  0.08 (0.18), residues: 2040
  helix:  2.56 (0.47), residues: 110
  sheet:  0.58 (0.17), residues: 830
  loop : -0.60 (0.18), residues: 1100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 162 
 HIS   0.004   0.001   HIS G  38 
 PHE   0.012   0.001   PHE D 180 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.013   0.001   ARG E  58 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10000.87 seconds
wall clock time: 177 minutes 30.85 seconds (10650.85 seconds total)