Starting phenix.real_space_refine
on Thu Dec  7 23:01:19 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.map

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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/12_2023/8tj2_41298.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=   0.007 sd=   0.150
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     126      5.16       5
     C   17406      2.51       5
     N    4824      2.21       5
     O    5436      1.98       5
     H   26460      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP   55": "OD1" <-> "OD2"
    Residue "C GLU   63": "OE1" <-> "OE2"
    Residue "C ASP   92": "OD1" <-> "OD2"
    Residue "C ASP  106": "OD1" <-> "OD2"
    Residue "C ASP  118": "OD1" <-> "OD2"
    Residue "C ASP  146": "OD1" <-> "OD2"
    Residue "C ASP  168": "OD1" <-> "OD2"
    Residue "D PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU   35": "OE1" <-> "OE2"
    Residue "D PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP   55": "OD1" <-> "OD2"
    Residue "D ASP   59": "OD1" <-> "OD2"
    Residue "D GLU   63": "OE1" <-> "OE2"
    Residue "D GLU   86": "OE1" <-> "OE2"
    Residue "D ASP  106": "OD1" <-> "OD2"
    Residue "D ASP  118": "OD1" <-> "OD2"
    Residue "E PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E ASP   55": "OD1" <-> "OD2"
    Residue "E GLU   63": "OE1" <-> "OE2"
    Residue "E ASP  146": "OD1" <-> "OD2"
    Residue "E ASP  168": "OD1" <-> "OD2"
    Residue "F TYR   44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F GLU   53": "OE1" <-> "OE2"
    Residue "F ASP   55": "OD1" <-> "OD2"
    Residue "F ASP   59": "OD1" <-> "OD2"
    Residue "F GLU   63": "OE1" <-> "OE2"
    Residue "F ASP   92": "OD1" <-> "OD2"
    Residue "F ASP  106": "OD1" <-> "OD2"
    Residue "F ASP  117": "OD1" <-> "OD2"
    Residue "F ASP  118": "OD1" <-> "OD2"
    Residue "F ASP  146": "OD1" <-> "OD2"
    Residue "G GLU   53": "OE1" <-> "OE2"
    Residue "G ASP   55": "OD1" <-> "OD2"
    Residue "G GLU   63": "OE1" <-> "OE2"
    Residue "G GLU   86": "OE1" <-> "OE2"
    Residue "G ASP  106": "OD1" <-> "OD2"
    Residue "G ASP  146": "OD1" <-> "OD2"
    Residue "G ASP  167": "OD1" <-> "OD2"
    Residue "G GLU  175": "OE1" <-> "OE2"
    Residue "H PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP   55": "OD1" <-> "OD2"
    Residue "H GLU   63": "OE1" <-> "OE2"
    Residue "H GLU   86": "OE1" <-> "OE2"
    Residue "H ASP  106": "OD1" <-> "OD2"
    Residue "H ASP  146": "OD1" <-> "OD2"
    Residue "H GLU  175": "OE1" <-> "OE2"
    Residue "I PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP   59": "OD1" <-> "OD2"
    Residue "I ASP  118": "OD1" <-> "OD2"
    Residue "I ASP  146": "OD1" <-> "OD2"
    Residue "I ASP  167": "OD1" <-> "OD2"
    Residue "I ASP  168": "OD1" <-> "OD2"
    Residue "I GLU  175": "OE1" <-> "OE2"
    Residue "I ASP  200": "OD1" <-> "OD2"
    Residue "J PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J TYR   44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU   53": "OE1" <-> "OE2"
    Residue "J ASP   59": "OD1" <-> "OD2"
    Residue "J GLU   63": "OE1" <-> "OE2"
    Residue "J ASP  106": "OD1" <-> "OD2"
    Residue "J ASP  167": "OD1" <-> "OD2"
    Residue "J GLU  175": "OE1" <-> "OE2"
    Residue "K GLU   53": "OE1" <-> "OE2"
    Residue "K ASP   55": "OD1" <-> "OD2"
    Residue "K ASP   59": "OD1" <-> "OD2"
    Residue "K GLU   86": "OE1" <-> "OE2"
    Residue "K ASP  106": "OD1" <-> "OD2"
    Residue "K ASP  118": "OD1" <-> "OD2"
    Residue "K GLU  175": "OE1" <-> "OE2"
    Residue "A PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   53": "OE1" <-> "OE2"
    Residue "A GLU   63": "OE1" <-> "OE2"
    Residue "A GLU   86": "OE1" <-> "OE2"
    Residue "A ASP  106": "OD1" <-> "OD2"
    Residue "A ASP  117": "OD1" <-> "OD2"
    Residue "A ASP  146": "OD1" <-> "OD2"
    Residue "A ASP  167": "OD1" <-> "OD2"
    Residue "L PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L TYR   44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L GLU   53": "OE1" <-> "OE2"
    Residue "L ASP   55": "OD1" <-> "OD2"
    Residue "L GLU   63": "OE1" <-> "OE2"
    Residue "L GLU   86": "OE1" <-> "OE2"
    Residue "L ASP   92": "OD1" <-> "OD2"
    Residue "L ASP  168": "OD1" <-> "OD2"
    Residue "L GLU  175": "OE1" <-> "OE2"
    Residue "M GLU   53": "OE1" <-> "OE2"
    Residue "M ASP   55": "OD1" <-> "OD2"
    Residue "M ASP   59": "OD1" <-> "OD2"
    Residue "M GLU   63": "OE1" <-> "OE2"
    Residue "M GLU   86": "OE1" <-> "OE2"
    Residue "M ASP  106": "OD1" <-> "OD2"
    Residue "M ASP  118": "OD1" <-> "OD2"
    Residue "M ASP  167": "OD1" <-> "OD2"
    Residue "M GLU  175": "OE1" <-> "OE2"
    Residue "N PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N GLU   53": "OE1" <-> "OE2"
    Residue "N ASP   55": "OD1" <-> "OD2"
    Residue "N ASP   59": "OD1" <-> "OD2"
    Residue "N GLU   63": "OE1" <-> "OE2"
    Residue "N ASP  106": "OD1" <-> "OD2"
    Residue "N ASP  118": "OD1" <-> "OD2"
    Residue "N ASP  146": "OD1" <-> "OD2"
    Residue "N ASP  168": "OD1" <-> "OD2"
    Residue "O PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O GLU   53": "OE1" <-> "OE2"
    Residue "O ASP   92": "OD1" <-> "OD2"
    Residue "O ASP  168": "OD1" <-> "OD2"
    Residue "P PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P TYR   44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P GLU   53": "OE1" <-> "OE2"
    Residue "P ASP   55": "OD1" <-> "OD2"
    Residue "P ASP   59": "OD1" <-> "OD2"
    Residue "P GLU   63": "OE1" <-> "OE2"
    Residue "P GLU   86": "OE1" <-> "OE2"
    Residue "P ASP  146": "OD1" <-> "OD2"
    Residue "P ASP  200": "OD1" <-> "OD2"
    Residue "Q PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q GLU   53": "OE1" <-> "OE2"
    Residue "Q ASP   55": "OD1" <-> "OD2"
    Residue "Q ASP   59": "OD1" <-> "OD2"
    Residue "Q ASP  106": "OD1" <-> "OD2"
    Residue "Q ASP  118": "OD1" <-> "OD2"
    Residue "Q ASP  146": "OD1" <-> "OD2"
    Residue "Q ASP  167": "OD1" <-> "OD2"
    Residue "R ASP   59": "OD1" <-> "OD2"
    Residue "R GLU   63": "OE1" <-> "OE2"
    Residue "R GLU   86": "OE1" <-> "OE2"
    Residue "R ASP  118": "OD1" <-> "OD2"
    Residue "R ASP  168": "OD1" <-> "OD2"
    Residue "R GLU  175": "OE1" <-> "OE2"
    Residue "S PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S GLU   63": "OE1" <-> "OE2"
    Residue "S ASP   92": "OD1" <-> "OD2"
    Residue "S ASP  167": "OD1" <-> "OD2"
    Residue "S GLU  175": "OE1" <-> "OE2"
    Residue "S ASP  200": "OD1" <-> "OD2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 54252
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "C"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "D"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "E"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "G"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "H"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "I"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "J"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "K"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "A"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "L"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "M"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "N"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "O"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "P"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "Q"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "R"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
    Chain: "S"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3014
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 195}
  Time building chain proxies: 18.60, per 1000 atoms: 0.34
  Number of scatterers: 54252
  At special positions: 0
  Unit cell: (84.24, 84.24, 272.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     126     16.00
     O    5436      8.00
     N    4824      7.00
     C   17406      6.00
     H   26460      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  85 " - pdb=" SG  CYS C 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 183 " - pdb=" SG  CYS C 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  85 " - pdb=" SG  CYS D 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 183 " - pdb=" SG  CYS D 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  85 " - pdb=" SG  CYS E 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 183 " - pdb=" SG  CYS E 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  85 " - pdb=" SG  CYS F 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 183 " - pdb=" SG  CYS F 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  85 " - pdb=" SG  CYS G 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 183 " - pdb=" SG  CYS G 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  85 " - pdb=" SG  CYS H 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 183 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  85 " - pdb=" SG  CYS I 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 183 " - pdb=" SG  CYS I 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  85 " - pdb=" SG  CYS J 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 183 " - pdb=" SG  CYS J 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  85 " - pdb=" SG  CYS K 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 183 " - pdb=" SG  CYS K 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  85 " - pdb=" SG  CYS L 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 183 " - pdb=" SG  CYS L 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  85 " - pdb=" SG  CYS M 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 183 " - pdb=" SG  CYS M 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  85 " - pdb=" SG  CYS N 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 183 " - pdb=" SG  CYS N 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  85 " - pdb=" SG  CYS O 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 183 " - pdb=" SG  CYS O 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  85 " - pdb=" SG  CYS P 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 183 " - pdb=" SG  CYS P 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  85 " - pdb=" SG  CYS Q 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q 183 " - pdb=" SG  CYS Q 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 183 " - pdb=" SG  CYS R 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  85 " - pdb=" SG  CYS S 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 183 " - pdb=" SG  CYS S 203 " 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: 32.73
  Conformation dependent library (CDL) restraints added in 4.9 seconds
  

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6804

  Finding SS restraints...
    Secondary structure from input PDB file:
      90 helices and 39 sheets defined
      29.3% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.29
  Creating SS restraints...
    Processing helix  chain 'C' and resid 2 through 18
      removed outlier: 3.534A  pdb=" N   ALA C  18 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 33
    Processing helix  chain 'C' and resid 33 through 55
      removed outlier: 3.769A  pdb=" N   LYS C  37 " --> pdb=" O   GLN C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 65
      removed outlier: 3.685A  pdb=" N   ILE C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 115
    Processing helix  chain 'D' and resid 2 through 18
      removed outlier: 3.519A  pdb=" N   ALA D  18 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 33
    Processing helix  chain 'D' and resid 33 through 55
      removed outlier: 3.720A  pdb=" N   LYS D  37 " --> pdb=" O   GLN D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 65
      removed outlier: 3.589A  pdb=" N   ILE D  64 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 115
    Processing helix  chain 'E' and resid 2 through 18
      removed outlier: 3.570A  pdb=" N   ALA E  18 " --> pdb=" O   GLY E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 33
    Processing helix  chain 'E' and resid 33 through 55
      removed outlier: 3.767A  pdb=" N   LYS E  37 " --> pdb=" O   GLN E  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 65
      removed outlier: 3.642A  pdb=" N   ILE E  64 " --> pdb=" O   PHE E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 115
      removed outlier: 3.548A  pdb=" N   ALA E 115 " --> pdb=" O   ALA E 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 18
      removed outlier: 3.535A  pdb=" N   ALA F  18 " --> pdb=" O   GLY F  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 33
    Processing helix  chain 'F' and resid 33 through 55
      removed outlier: 3.766A  pdb=" N   LYS F  37 " --> pdb=" O   GLN F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 60 through 65
      removed outlier: 3.519A  pdb=" N   ILE F  64 " --> pdb=" O   PHE F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 115
    Processing helix  chain 'G' and resid 2 through 18
      removed outlier: 3.567A  pdb=" N   ALA G  18 " --> pdb=" O   GLY G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 24 through 33
    Processing helix  chain 'G' and resid 33 through 55
      removed outlier: 3.807A  pdb=" N   LYS G  37 " --> pdb=" O   GLN G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 60 through 65
      removed outlier: 3.547A  pdb=" N   ILE G  64 " --> pdb=" O   PHE G  60 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 111 through 115
    Processing helix  chain 'H' and resid 2 through 18
    Processing helix  chain 'H' and resid 24 through 33
    Processing helix  chain 'H' and resid 33 through 55
      removed outlier: 3.784A  pdb=" N   LYS H  37 " --> pdb=" O   GLN H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 65
      removed outlier: 3.654A  pdb=" N   ILE H  64 " --> pdb=" O   PHE H  60 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 111 through 115
    Processing helix  chain 'I' and resid 2 through 18
      removed outlier: 3.502A  pdb=" N   ALA I  18 " --> pdb=" O   GLY I  14 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 23 through 33
      removed outlier: 4.220A  pdb=" N   PHE I  27 " --> pdb=" O   ASN I  23 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 33 through 55
      removed outlier: 3.795A  pdb=" N   LYS I  37 " --> pdb=" O   GLN I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 60 through 65
      removed outlier: 3.590A  pdb=" N   ILE I  64 " --> pdb=" O   PHE I  60 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 111 through 115
    Processing helix  chain 'J' and resid 2 through 18
      removed outlier: 3.511A  pdb=" N   ALA J  18 " --> pdb=" O   GLY J  14 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 24 through 33
    Processing helix  chain 'J' and resid 33 through 55
      removed outlier: 3.784A  pdb=" N   LYS J  37 " --> pdb=" O   GLN J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 60 through 65
    Processing helix  chain 'J' and resid 111 through 115
    Processing helix  chain 'K' and resid 2 through 18
    Processing helix  chain 'K' and resid 24 through 33
    Processing helix  chain 'K' and resid 33 through 55
      removed outlier: 3.773A  pdb=" N   LYS K  37 " --> pdb=" O   GLN K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 60 through 65
    Processing helix  chain 'K' and resid 111 through 115
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 3.535A  pdb=" N   ALA A  18 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 33
    Processing helix  chain 'A' and resid 33 through 55
      removed outlier: 3.788A  pdb=" N   LYS A  37 " --> pdb=" O   GLN A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 65
      removed outlier: 3.674A  pdb=" N   ILE A  64 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
      removed outlier: 3.560A  pdb=" N   ALA A 115 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 18
    Processing helix  chain 'L' and resid 24 through 33
    Processing helix  chain 'L' and resid 33 through 55
      removed outlier: 3.796A  pdb=" N   LYS L  37 " --> pdb=" O   GLN L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 60 through 65
      removed outlier: 3.599A  pdb=" N   ILE L  64 " --> pdb=" O   PHE L  60 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 111 through 115
    Processing helix  chain 'M' and resid 2 through 18
      removed outlier: 3.533A  pdb=" N   ALA M  18 " --> pdb=" O   GLY M  14 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 24 through 33
    Processing helix  chain 'M' and resid 33 through 55
      removed outlier: 3.796A  pdb=" N   LYS M  37 " --> pdb=" O   GLN M  33 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 60 through 65
    Processing helix  chain 'M' and resid 111 through 115
    Processing helix  chain 'N' and resid 2 through 18
      removed outlier: 3.524A  pdb=" N   ALA N  18 " --> pdb=" O   GLY N  14 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 24 through 33
    Processing helix  chain 'N' and resid 33 through 55
      removed outlier: 3.715A  pdb=" N   LYS N  37 " --> pdb=" O   GLN N  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 60 through 65
      removed outlier: 3.556A  pdb=" N   ILE N  64 " --> pdb=" O   PHE N  60 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 111 through 115
    Processing helix  chain 'O' and resid 2 through 17
    Processing helix  chain 'O' and resid 24 through 33
    Processing helix  chain 'O' and resid 33 through 55
      removed outlier: 3.805A  pdb=" N   LYS O  37 " --> pdb=" O   GLN O  33 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 60 through 65
      removed outlier: 3.528A  pdb=" N   ILE O  64 " --> pdb=" O   PHE O  60 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 111 through 115
    Processing helix  chain 'P' and resid 2 through 18
      removed outlier: 3.616A  pdb=" N   ALA P  18 " --> pdb=" O   GLY P  14 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 23 through 33
      removed outlier: 4.232A  pdb=" N   PHE P  27 " --> pdb=" O   ASN P  23 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 33 through 55
      removed outlier: 3.776A  pdb=" N   LYS P  37 " --> pdb=" O   GLN P  33 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 60 through 65
      removed outlier: 3.721A  pdb=" N   ILE P  64 " --> pdb=" O   PHE P  60 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 111 through 115
    Processing helix  chain 'Q' and resid 2 through 18
    Processing helix  chain 'Q' and resid 24 through 33
    Processing helix  chain 'Q' and resid 33 through 55
      removed outlier: 3.777A  pdb=" N   LYS Q  37 " --> pdb=" O   GLN Q  33 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 60 through 65
      removed outlier: 3.591A  pdb=" N   ILE Q  64 " --> pdb=" O   PHE Q  60 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 111 through 115
    Processing helix  chain 'R' and resid 2 through 17
    Processing helix  chain 'R' and resid 24 through 33
    Processing helix  chain 'R' and resid 33 through 55
      removed outlier: 3.761A  pdb=" N   LYS R  37 " --> pdb=" O   GLN R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 65
      removed outlier: 3.566A  pdb=" N   ILE R  64 " --> pdb=" O   PHE R  60 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 115
      removed outlier: 3.525A  pdb=" N   ALA R 115 " --> pdb=" O   ALA R 112 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 18
      removed outlier: 3.571A  pdb=" N   ALA S  18 " --> pdb=" O   GLY S  14 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 24 through 33
    Processing helix  chain 'S' and resid 33 through 55
      removed outlier: 3.784A  pdb=" N   LYS S  37 " --> pdb=" O   GLN S  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 60 through 65
      removed outlier: 3.637A  pdb=" N   ILE S  64 " --> pdb=" O   PHE S  60 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 111 through 115
    Processing sheet with id=AA1, first strand: chain 'C' and resid 102 through 103
      removed outlier: 7.004A  pdb=" N   VAL C 170 " --> pdb=" O   ASN C 196 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ASN C 196 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 126 through 128
      removed outlier: 3.841A  pdb=" N   GLY C 187 " --> pdb=" O   GLY C 178 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 102 through 103
      removed outlier: 6.378A  pdb=" N   ASP D 168 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 126 through 128
    Processing sheet with id=AA5, first strand: chain 'E' and resid 102 through 103
    Processing sheet with id=AA6, first strand: chain 'E' and resid 102 through 103
      removed outlier: 3.517A  pdb=" N   ARG E 198 " --> pdb=" O   ASP E 168 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   VAL E 170 " --> pdb=" O   ASN E 196 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   ASN E 196 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 128
      removed outlier: 3.881A  pdb=" N   GLY E 187 " --> pdb=" O   GLY E 178 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 102 through 103
      removed outlier: 6.390A  pdb=" N   ASP F 168 " --> pdb=" O   THR F 197 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 126 through 128
      removed outlier: 3.881A  pdb=" N   GLY F 187 " --> pdb=" O   GLY F 178 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 102 through 103
      removed outlier: 6.378A  pdb=" N   ASP G 168 " --> pdb=" O   THR G 197 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 126 through 128
      removed outlier: 3.798A  pdb=" N   GLY G 187 " --> pdb=" O   GLY G 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 102 through 103
      removed outlier: 6.410A  pdb=" N   ASP H 168 " --> pdb=" O   THR H 197 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 126 through 128
    Processing sheet with id=AB5, first strand: chain 'I' and resid 102 through 103
      removed outlier: 6.332A  pdb=" N   ASP I 168 " --> pdb=" O   THR I 197 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 128
      removed outlier: 3.902A  pdb=" N   GLY I 187 " --> pdb=" O   GLY I 178 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103
    Processing sheet with id=AB8, first strand: chain 'J' and resid 102 through 103
      removed outlier: 6.438A  pdb=" N   ASP J 168 " --> pdb=" O   THR J 197 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 126 through 128
      removed outlier: 3.794A  pdb=" N   GLY J 187 " --> pdb=" O   GLY J 178 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'K' and resid 102 through 103
      removed outlier: 6.429A  pdb=" N   ASP K 168 " --> pdb=" O   THR K 197 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'K' and resid 126 through 128
      removed outlier: 3.909A  pdb=" N   GLY K 187 " --> pdb=" O   GLY K 178 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 102 through 103
      removed outlier: 6.386A  pdb=" N   ASP A 168 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AC5, first strand: chain 'L' and resid 102 through 103
      removed outlier: 6.411A  pdb=" N   ASP L 168 " --> pdb=" O   THR L 197 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 126 through 128
      removed outlier: 3.806A  pdb=" N   GLY L 187 " --> pdb=" O   GLY L 178 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103
      removed outlier: 6.400A  pdb=" N   ASP M 168 " --> pdb=" O   THR M 197 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 126 through 128
      removed outlier: 3.777A  pdb=" N   GLY M 187 " --> pdb=" O   GLY M 178 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'N' and resid 102 through 103
      removed outlier: 7.022A  pdb=" N   VAL N 170 " --> pdb=" O   ASN N 196 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   ASN N 196 " --> pdb=" O   VAL N 170 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'N' and resid 126 through 128
      removed outlier: 3.868A  pdb=" N   GLY N 187 " --> pdb=" O   GLY N 178 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'O' and resid 102 through 103
      removed outlier: 7.054A  pdb=" N   VAL O 170 " --> pdb=" O   ASN O 196 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ASN O 196 " --> pdb=" O   VAL O 170 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'O' and resid 126 through 128
      removed outlier: 3.965A  pdb=" N   GLY O 187 " --> pdb=" O   GLY O 178 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'P' and resid 102 through 103
      removed outlier: 6.402A  pdb=" N   ASP P 168 " --> pdb=" O   THR P 197 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'P' and resid 126 through 128
      removed outlier: 3.878A  pdb=" N   GLY P 187 " --> pdb=" O   GLY P 178 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'Q' and resid 102 through 103
      removed outlier: 6.420A  pdb=" N   ASP Q 168 " --> pdb=" O   THR Q 197 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'Q' and resid 126 through 128
      removed outlier: 3.830A  pdb=" N   GLY Q 187 " --> pdb=" O   GLY Q 178 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'R' and resid 102 through 103
    Processing sheet with id=AD9, first strand: chain 'R' and resid 102 through 103
      removed outlier: 6.400A  pdb=" N   ASP R 168 " --> pdb=" O   THR R 197 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'R' and resid 126 through 128
      removed outlier: 3.870A  pdb=" N   GLY R 187 " --> pdb=" O   GLY R 178 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'S' and resid 102 through 103
      removed outlier: 6.357A  pdb=" N   ASP S 168 " --> pdb=" O   THR S 197 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'S' and resid 126 through 128
      removed outlier: 3.983A  pdb=" N   GLY S 187 " --> pdb=" O   GLY S 178 " (cutoff:3.500A)

    1082 hydrogen bonds defined for protein.
    2988 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: 16.55

  Time building geometry restraints manager: 34.57 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 26424
        1.03 -     1.23: 460
        1.23 -     1.42: 11870
        1.42 -     1.62: 15966
        1.62 -     1.81: 144
  Bond restraints: 54864
  Sorted by residual:
  bond pdb=" CB  PRO J 148 "
       pdb=" CG  PRO J 148 "
    ideal  model  delta    sigma   weight residual
    1.492  1.606 -0.114 5.00e-02 4.00e+02 5.21e+00
  bond pdb=" CB  PRO E 148 "
       pdb=" CG  PRO E 148 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.18e+00
  bond pdb=" CB  ASN D 199 "
       pdb=" CG  ASN D 199 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 2.50e-02 1.60e+03 1.94e+00
  bond pdb=" CB  ASN A 199 "
       pdb=" CG  ASN A 199 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 2.50e-02 1.60e+03 1.91e+00
  bond pdb=" CB  ASN H 199 "
       pdb=" CG  ASN H 199 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.79e+00
  ... (remaining 54859 not shown)

  Histogram of bond angle deviations from ideal:
       64.33 -    79.25: 36
       79.25 -    94.16: 0
       94.16 -   109.07: 27880
      109.07 -   123.98: 67421
      123.98 -   138.90: 3321
  Bond angle restraints: 98658
  Sorted by residual:
  angle pdb=" C   SER F 184 "
        pdb=" N   GLU F 185 "
        pdb=" H   GLU F 185 "
      ideal   model   delta    sigma   weight residual
     124.11   73.72   50.39 3.00e+00 1.11e-01 2.82e+02
  angle pdb=" C   SER I 184 "
        pdb=" N   GLU I 185 "
        pdb=" H   GLU I 185 "
      ideal   model   delta    sigma   weight residual
     124.11   74.02   50.10 3.00e+00 1.11e-01 2.79e+02
  angle pdb=" C   SER G 184 "
        pdb=" N   GLU G 185 "
        pdb=" H   GLU G 185 "
      ideal   model   delta    sigma   weight residual
     124.11   74.02   50.09 3.00e+00 1.11e-01 2.79e+02
  angle pdb=" C   SER A 184 "
        pdb=" N   GLU A 185 "
        pdb=" H   GLU A 185 "
      ideal   model   delta    sigma   weight residual
     124.11   74.03   50.08 3.00e+00 1.11e-01 2.79e+02
  angle pdb=" C   SER S 184 "
        pdb=" N   GLU S 185 "
        pdb=" H   GLU S 185 "
      ideal   model   delta    sigma   weight residual
     124.11   74.06   50.06 3.00e+00 1.11e-01 2.78e+02
  ... (remaining 98653 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 23390
       17.05 -    34.10: 1639
       34.10 -    51.14: 464
       51.14 -    68.19: 96
       68.19 -    85.24: 7
  Dihedral angle restraints: 25596
    sinusoidal: 13140
      harmonic: 12456
  Sorted by residual:
  dihedral pdb=" CB  CYS C 183 "
           pdb=" SG  CYS C 183 "
           pdb=" SG  CYS C 203 "
           pdb=" CB  CYS C 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.48  -41.48     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CB  CYS A 183 "
           pdb=" SG  CYS A 183 "
           pdb=" SG  CYS A 203 "
           pdb=" CB  CYS A 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.37  -41.37     1      1.00e+01 1.00e-02 2.40e+01
  dihedral pdb=" CB  CYS S 183 "
           pdb=" SG  CYS S 183 "
           pdb=" SG  CYS S 203 "
           pdb=" CB  CYS S 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.12  -41.12     1      1.00e+01 1.00e-02 2.37e+01
  ... (remaining 25593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 2042
       0.028 -    0.057: 1345
       0.057 -    0.085: 510
       0.085 -    0.113: 219
       0.113 -    0.142: 78
  Chirality restraints: 4194
  Sorted by residual:
  chirality pdb=" CA  ILE H 116 "
            pdb=" N   ILE H 116 "
            pdb=" C   ILE H 116 "
            pdb=" CB  ILE H 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ILE G 116 "
            pdb=" N   ILE G 116 "
            pdb=" C   ILE G 116 "
            pdb=" CB  ILE G 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE C  21 "
            pdb=" N   ILE C  21 "
            pdb=" C   ILE C  21 "
            pdb=" CB  ILE C  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 4191 not shown)

  Planarity restraints: 8820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS J 147 "    0.123 5.00e-02 4.00e+02   1.79e-01 5.12e+01
        pdb=" N   PRO J 148 "   -0.309 5.00e-02 4.00e+02
        pdb=" CA  PRO J 148 "    0.095 5.00e-02 4.00e+02
        pdb=" CD  PRO J 148 "    0.091 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS M 147 "    0.108 5.00e-02 4.00e+02   1.62e-01 4.20e+01
        pdb=" N   PRO M 148 "   -0.280 5.00e-02 4.00e+02
        pdb=" CA  PRO M 148 "    0.086 5.00e-02 4.00e+02
        pdb=" CD  PRO M 148 "    0.086 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E 147 "   -0.107 5.00e-02 4.00e+02   1.60e-01 4.11e+01
        pdb=" N   PRO E 148 "    0.277 5.00e-02 4.00e+02
        pdb=" CA  PRO E 148 "   -0.085 5.00e-02 4.00e+02
        pdb=" CD  PRO E 148 "   -0.084 5.00e-02 4.00e+02
  ... (remaining 8817 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 1019
        2.09 -     2.72: 91414
        2.72 -     3.35: 152453
        3.35 -     3.97: 203749
        3.97 -     4.60: 327931
  Nonbonded interactions: 776566
  Sorted by model distance:
  nonbonded pdb=" H   GLU F 185 "
            pdb=" HA  GLU F 185 "
     model   vdw
     1.468 1.816
  nonbonded pdb=" H   GLU A 185 "
            pdb=" HA  GLU A 185 "
     model   vdw
     1.476 1.816
  nonbonded pdb=" H   GLU G 185 "
            pdb=" HA  GLU G 185 "
     model   vdw
     1.479 1.816
  nonbonded pdb=" H   GLU N 185 "
            pdb=" HA  GLU N 185 "
     model   vdw
     1.481 1.816
  nonbonded pdb=" H   GLU O 185 "
            pdb=" HA  GLU O 185 "
     model   vdw
     1.485 1.816
  ... (remaining 776561 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
}

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:             0.700
  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:             0.650
  Extract box with map and model:          5.590
  Check model and map are aligned:         0.610
  Set scattering table:                    0.390
  Process input model:                     129.370
  Find NCS groups from input model:        2.180
  Set up NCS constraints:                  0.270
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  148.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.114  28404  Z= 0.383
  Angle     :  0.791  16.827  38682  Z= 0.454
  Chirality :  0.045   0.142   4194
  Planarity :  0.006   0.179   5310
  Dihedral  : 13.711  85.242   9972
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.81 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.12), residues: 3708
  helix:  1.10 (0.17), residues: 882
  sheet: -0.10 (0.20), residues: 594
  loop : -1.87 (0.10), residues: 2232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP E 134 
   PHE   0.021   0.002   PHE N 153 
   TYR   0.016   0.002   TYR P  44 
   ARG   0.006   0.001   ARG K 198 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 415
  time to evaluate  : 3.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 47
  outliers final: 35
  residues processed: 457
  average time/residue: 1.8396
  time to fit residues: 1037.3292
Evaluate side-chains
  405 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 370
  time to evaluate  : 3.286 
Switching outliers to nearest non-outliers
  outliers start: 35
  outliers final: 35
  residues processed: 1
  average time/residue: 0.6005
  time to fit residues: 4.8377
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 303 optimal weight:    3.9990
   chunk 272 optimal weight:    3.9990
   chunk 151 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 184 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 282 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 171 optimal weight:    3.9990
   chunk 210 optimal weight:    3.9990
   chunk 326 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
D 179 GLN
H 151 ASN
H 179 GLN
K 179 GLN
M 179 GLN
N 179 GLN
O 129 GLN
Q 129 GLN
R 179 GLN
S 179 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.0818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  28404  Z= 0.406
  Angle     :  0.704  20.741  38682  Z= 0.390
  Chirality :  0.046   0.149   4194
  Planarity :  0.005   0.109   5310
  Dihedral  :  5.121  19.588   4014
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.53 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.12), residues: 3708
  helix:  1.05 (0.18), residues: 882
  sheet: -0.13 (0.18), residues: 774
  loop : -2.03 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP C 169 
   PHE   0.013   0.002   PHE H 153 
   TYR   0.010   0.002   TYR C  44 
   ARG   0.004   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  485 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 103
    poor density    : 382
  time to evaluate  : 3.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 103
  outliers final: 60
  residues processed: 461
  average time/residue: 1.9751
  time to fit residues: 1123.2167
Evaluate side-chains
  434 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 374
  time to evaluate  : 3.225 
Switching outliers to nearest non-outliers
  outliers start: 60
  outliers final: 49
  residues processed: 12
  average time/residue: 1.0666
  time to fit residues: 22.1034
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 181 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 272 optimal weight:    3.9990
   chunk 222 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 327 optimal weight:    4.9990
   chunk 353 optimal weight:    0.8980
   chunk 291 optimal weight:    0.9990
   chunk 324 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 262 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
F 129 GLN
G 179 GLN
H  39 ASN
H 151 ASN
H 179 GLN
I  39 ASN
I 129 GLN
J 179 GLN
K 179 GLN
L  39 ASN
M 179 GLN
P 179 GLN
Q  39 ASN
R  39 ASN
R 151 ASN
R 179 GLN
S  39 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  28404  Z= 0.210
  Angle     :  0.631  21.355  38682  Z= 0.346
  Chirality :  0.043   0.142   4194
  Planarity :  0.004   0.084   5310
  Dihedral  :  4.698  19.880   4014
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.49 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.13), residues: 3708
  helix:  1.41 (0.18), residues: 882
  sheet: -0.13 (0.19), residues: 774
  loop : -1.91 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP N 169 
   PHE   0.012   0.001   PHE F   1 
   TYR   0.008   0.001   TYR C  44 
   ARG   0.005   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  502 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 418
  time to evaluate  : 3.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 84
  outliers final: 58
  residues processed: 495
  average time/residue: 1.8966
  time to fit residues: 1153.1372
Evaluate side-chains
  454 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 396
  time to evaluate  : 3.286 
Switching outliers to nearest non-outliers
  outliers start: 58
  outliers final: 56
  residues processed: 4
  average time/residue: 0.4921
  time to fit residues: 7.5327
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 323 optimal weight:    4.9990
   chunk 246 optimal weight:    4.9990
   chunk 169 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 156 optimal weight:    3.9990
   chunk 219 optimal weight:    4.9990
   chunk 328 optimal weight:    6.9990
   chunk 347 optimal weight:    5.9990
   chunk 171 optimal weight:    3.9990
   chunk 311 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN
D 179 GLN
F 129 GLN
G 179 GLN
H 151 ASN
H 179 GLN
J 179 GLN
K 179 GLN
M 179 GLN
N 179 GLN
R 151 ASN
R 179 GLN
S 179 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  28404  Z= 0.485
  Angle     :  0.722  20.839  38682  Z= 0.401
  Chirality :  0.047   0.153   4194
  Planarity :  0.005   0.081   5310
  Dihedral  :  5.198  21.497   4014
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.99 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.13), residues: 3708
  helix:  0.98 (0.17), residues: 882
  sheet:  0.18 (0.19), residues: 720
  loop : -2.19 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.002   TRP C 134 
   PHE   0.014   0.002   PHE H 153 
   TYR   0.013   0.003   TYR F  44 
   ARG   0.004   0.000   ARG F  88 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  500 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 110
    poor density    : 390
  time to evaluate  : 3.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 110
  outliers final: 78
  residues processed: 475
  average time/residue: 2.0786
  time to fit residues: 1204.3113
Evaluate side-chains
  449 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 371
  time to evaluate  : 3.271 
Switching outliers to nearest non-outliers
  outliers start: 78
  outliers final: 64
  residues processed: 15
  average time/residue: 1.0558
  time to fit residues: 26.4412
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 289 optimal weight:    6.9990
   chunk 197 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 259 optimal weight:    3.9990
   chunk 143 optimal weight:    4.9990
   chunk 296 optimal weight:    0.6980
   chunk 240 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 177 optimal weight:    1.9990
   chunk 312 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
G  39 ASN
G 179 GLN
H 151 ASN
H 179 GLN
J 151 ASN
J 179 GLN
K  39 ASN
K 151 ASN
K 179 GLN
A  39 ASN
M  39 ASN
M 179 GLN
O  39 ASN
P 129 GLN
P 179 GLN
R 151 ASN
R 179 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  28404  Z= 0.272
  Angle     :  0.646  21.345  38682  Z= 0.356
  Chirality :  0.043   0.149   4194
  Planarity :  0.004   0.077   5310
  Dihedral  :  4.921  22.104   4014
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.03 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.13), residues: 3708
  helix:  1.28 (0.18), residues: 882
  sheet:  0.14 (0.19), residues: 720
  loop : -2.13 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP N 169 
   PHE   0.012   0.001   PHE H 153 
   TYR   0.009   0.001   TYR C  44 
   ARG   0.005   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  485 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 401
  time to evaluate  : 3.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 84
  outliers final: 70
  residues processed: 477
  average time/residue: 1.9226
  time to fit residues: 1121.1376
Evaluate side-chains
  470 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 400
  time to evaluate  : 3.200 
Switching outliers to nearest non-outliers
  outliers start: 70
  outliers final: 66
  residues processed: 6
  average time/residue: 0.5411
  time to fit residues: 9.5728
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 313 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 204 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 348 optimal weight:    7.9990
   chunk 289 optimal weight:    8.9990
   chunk 161 optimal weight:    5.9990
   chunk 28 optimal weight:    0.4980
   chunk 115 optimal weight:    0.8980
   chunk 182 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
C  39 ASN
C 179 GLN
E  39 ASN
F  39 ASN
G 179 GLN
H 129 GLN
H 151 ASN
J  39 ASN
J 151 ASN
J 179 GLN
K 151 ASN
K 179 GLN
M 179 GLN
N  39 ASN
N 179 GLN
R 151 ASN
R 179 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  28404  Z= 0.223
  Angle     :  0.625  21.530  38682  Z= 0.343
  Chirality :  0.043   0.147   4194
  Planarity :  0.004   0.070   5310
  Dihedral  :  4.655  20.818   4014
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.31 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.13), residues: 3708
  helix:  1.50 (0.18), residues: 882
  sheet: -0.29 (0.19), residues: 774
  loop : -1.99 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP N 169 
   PHE   0.010   0.001   PHE H 153 
   TYR   0.013   0.001   TYR F  44 
   ARG   0.003   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  504 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 413
  time to evaluate  : 3.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 91
  outliers final: 71
  residues processed: 492
  average time/residue: 1.9706
  time to fit residues: 1189.2255
Evaluate side-chains
  469 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 398
  time to evaluate  : 3.204 
Switching outliers to nearest non-outliers
  outliers start: 71
  outliers final: 68
  residues processed: 5
  average time/residue: 0.5517
  time to fit residues: 8.7164
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 335 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 198 optimal weight:    0.0870
   chunk 254 optimal weight:    4.9990
   chunk 197 optimal weight:    0.8980
   chunk 293 optimal weight:    3.9990
   chunk 194 optimal weight:    0.9990
   chunk 346 optimal weight:    0.7980
   chunk 217 optimal weight:    3.9990
   chunk 211 optimal weight:    0.9980
   chunk 160 optimal weight:    4.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN
D  39 ASN
D 151 ASN
H 151 ASN
H 179 GLN
I 135 ASN
J 151 ASN
J 179 GLN
K 151 ASN
K 179 GLN
A 129 GLN
M 179 GLN
P  39 ASN
P 179 GLN
R 151 ASN
R 179 GLN
S 151 ASN
S 179 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  28404  Z= 0.152
  Angle     :  0.598  21.727  38682  Z= 0.328
  Chirality :  0.042   0.143   4194
  Planarity :  0.004   0.066   5310
  Dihedral  :  4.316  19.683   4014
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.60 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.85 (0.13), residues: 3708
  helix:  1.81 (0.18), residues: 882
  sheet: -0.28 (0.19), residues: 774
  loop : -1.85 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP N 169 
   PHE   0.013   0.001   PHE P   1 
   TYR   0.007   0.001   TYR K  44 
   ARG   0.003   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  499 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 416
  time to evaluate  : 4.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 83
  outliers final: 67
  residues processed: 494
  average time/residue: 1.9431
  time to fit residues: 1188.2932
Evaluate side-chains
  457 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 390
  time to evaluate  : 3.255 
Switching outliers to nearest non-outliers
  outliers start: 67
  outliers final: 65
  residues processed: 4
  average time/residue: 0.5953
  time to fit residues: 8.2092
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 214 optimal weight:    4.9990
   chunk 138 optimal weight:    4.9990
   chunk 207 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 220 optimal weight:    2.9990
   chunk 236 optimal weight:    5.9990
   chunk 171 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 272 optimal weight:    0.9980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
G 179 GLN
H 151 ASN
I 135 ASN
J 179 GLN
K 179 GLN
M 179 GLN
N 179 GLN
R 151 ASN
R 179 GLN
S 151 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  28404  Z= 0.330
  Angle     :  0.649  21.208  38682  Z= 0.359
  Chirality :  0.044   0.149   4194
  Planarity :  0.004   0.065   5310
  Dihedral  :  4.629  20.470   4014
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.63 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.97 (0.13), residues: 3708
  helix:  1.54 (0.18), residues: 882
  sheet:  0.11 (0.19), residues: 720
  loop : -2.01 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP C 134 
   PHE   0.011   0.001   PHE O 153 
   TYR   0.011   0.002   TYR C  44 
   ARG   0.003   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  482 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 394
  time to evaluate  : 3.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 88
  outliers final: 69
  residues processed: 467
  average time/residue: 1.9804
  time to fit residues: 1123.7305
Evaluate side-chains
  454 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 385
  time to evaluate  : 3.175 
Switching outliers to nearest non-outliers
  outliers start: 69
  outliers final: 64
  residues processed: 6
  average time/residue: 0.5487
  time to fit residues: 9.5543
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 315 optimal weight:    3.9990
   chunk 332 optimal weight:    0.9980
   chunk 303 optimal weight:    3.9990
   chunk 323 optimal weight:    4.9990
   chunk 194 optimal weight:    0.5980
   chunk 140 optimal weight:    5.9990
   chunk 253 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 292 optimal weight:    3.9990
   chunk 305 optimal weight:    0.9990
   chunk 322 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN
D 151 ASN
H 151 ASN
H 179 GLN
I 135 ASN
J 151 ASN
J 179 GLN
K 151 ASN
M 179 GLN
N 151 ASN
P 179 GLN
R 151 ASN
R 179 GLN
S 179 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  28404  Z= 0.188
  Angle     :  0.612  21.584  38682  Z= 0.336
  Chirality :  0.042   0.144   4194
  Planarity :  0.004   0.065   5310
  Dihedral  :  4.428  20.896   4014
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.95 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.92 (0.13), residues: 3708
  helix:  1.75 (0.18), residues: 882
  sheet: -0.36 (0.19), residues: 774
  loop : -1.88 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP N 169 
   PHE   0.008   0.001   PHE H 153 
   TYR   0.008   0.001   TYR C  44 
   ARG   0.003   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  468 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 394
  time to evaluate  : 3.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 74
  outliers final: 68
  residues processed: 464
  average time/residue: 2.0173
  time to fit residues: 1144.4240
Evaluate side-chains
  454 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 386
  time to evaluate  : 3.227 
Switching outliers to nearest non-outliers
  outliers start: 68
  outliers final: 65
  residues processed: 4
  average time/residue: 0.5773
  time to fit residues: 7.8834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 212 optimal weight:    0.8980
   chunk 341 optimal weight:    5.9990
   chunk 208 optimal weight:    3.9990
   chunk 162 optimal weight:    0.8980
   chunk 237 optimal weight:    0.7980
   chunk 358 optimal weight:    0.7980
   chunk 330 optimal weight:    4.9990
   chunk 285 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 220 optimal weight:    0.9990
   chunk 175 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN
D 151 ASN
G 179 GLN
H 151 ASN
** I  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 135 ASN
J 151 ASN
J 179 GLN
K 151 ASN
K 179 GLN
A 151 ASN
M 179 GLN
N 151 ASN
N 179 GLN
R 151 ASN
R 179 GLN
S 151 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  28404  Z= 0.161
  Angle     :  0.600  21.671  38682  Z= 0.328
  Chirality :  0.042   0.143   4194
  Planarity :  0.004   0.064   5310
  Dihedral  :  4.205  23.824   4014
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.66 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.78 (0.13), residues: 3708
  helix:  1.95 (0.18), residues: 882
  sheet: -0.32 (0.19), residues: 774
  loop : -1.82 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP C 169 
   PHE   0.007   0.001   PHE H 153 
   TYR   0.008   0.001   TYR K  44 
   ARG   0.004   0.000   ARG S  56 

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

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

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7416 Ramachandran restraints generated.
    3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 379
  time to evaluate  : 3.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 69
  outliers final: 66
  residues processed: 445
  average time/residue: 1.9620
  time to fit residues: 1064.0870
Evaluate side-chains
  443 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 377
  time to evaluate  : 3.183 
Switching outliers to nearest non-outliers
  outliers start: 66
  outliers final: 65
  residues processed: 2
  average time/residue: 0.5646
  time to fit residues: 5.7534
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 226 optimal weight:    0.6980
   chunk 304 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 263 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 286 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 293 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN
D 151 ASN
H 151 ASN
H 179 GLN
** I  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 135 ASN
J 179 GLN
A 151 ASN
M 179 GLN
P 179 GLN
R 151 ASN
R 179 GLN
S 151 ASN
S 179 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.135296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122319 restraints weight = 84825.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.30
r_work: 0.3283 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  28404  Z= 0.166
  Angle     :  0.596  21.649  38682  Z= 0.326
  Chirality :  0.042   0.143   4194
  Planarity :  0.004   0.063   5310
  Dihedral  :  4.113  19.526   4014
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.49 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.73 (0.13), residues: 3708
  helix:  2.04 (0.18), residues: 882
  sheet: -0.32 (0.19), residues: 774
  loop : -1.78 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP N 169 
   PHE   0.007   0.001   PHE H 153 
   TYR   0.008   0.001   TYR K  44 
   ARG   0.003   0.000   ARG S  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16223.96 seconds
wall clock time: 279 minutes 1.30 seconds (16741.30 seconds total)