Starting phenix.real_space_refine
on Fri Apr  5 20:54:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/04_2024/8tj2_41298.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/04_2024/8tj2_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_41298/04_2024/8tj2_41298.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/04_2024/8tj2_41298.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/04_2024/8tj2_41298.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tj2_41298/04_2024/8tj2_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-dev-5288/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: 17.90, per 1000 atoms: 0.33
  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: 30.57
  Conformation dependent library (CDL) restraints added in 4.6 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: 3.00
  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: 17.58

  Time building geometry restraints manager: 32.59 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: 23682
       17.05 -    34.10: 1847
       34.10 -    51.14: 741
       51.14 -    68.19: 165
       68.19 -    85.24: 7
  Dihedral angle restraints: 26442
    sinusoidal: 13986
      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 26439 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:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.660
  Extract box with map and model:          5.400
  Check model and map are aligned:         0.600
  Set scattering table:                    0.390
  Process input model:                     127.360
  Find NCS groups from input model:        2.330
  Set up NCS constraints:                  0.300
  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:9.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  147.840
-------------------------------------------------------------------------------
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  : 3.050 
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
REVERT: C  135 ASN cc_start: 0.7948 (t0) cc_final: 0.7743 (m-40)
REVERT: M   92 ASP cc_start: 0.8133 (m-30) cc_final: 0.7855 (m-30)
  outliers start: 47
  outliers final: 35
  residues processed: 457
  average time/residue: 1.8070
  time to fit residues: 1013.4818
Evaluate side-chains
  406 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 371
  time to evaluate  : 3.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue  104 SER
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue  104 SER
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue  104 SER
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   79 SER
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue  104 SER
Chi-restraints excluded: chain N residue  104 SER
Chi-restraints excluded: chain O residue  104 SER
Chi-restraints excluded: chain P residue  104 SER
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   21 ILE
Chi-restraints excluded: chain Q residue   79 SER
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  104 SER
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:    3.9990
   chunk 184 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 282 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 171 optimal weight:    3.9990
   chunk 210 optimal weight:    3.9990
   chunk 326 optimal weight:    2.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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: 0.8316
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  28404  Z= 0.428
  Angle     :  0.712  20.653  38682  Z= 0.395
  Chirality :  0.046   0.152   4194
  Planarity :  0.006   0.112   5310
  Dihedral  :  5.995  57.905   4064
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.81 %
    Favored  : 81.87 %
  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: -1.32 (0.12), residues: 3708
  helix:  1.03 (0.17), residues: 882
  sheet:  0.05 (0.20), residues: 594
  loop : -2.07 (0.10), residues: 2232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP N 169 
 PHE   0.012   0.002   PHE R 153 
 TYR   0.010   0.002   TYR C  44 
 ARG   0.005   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
  470 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 93
    poor density    : 377
  time to evaluate  : 3.672 
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: C  167 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (p0)
REVERT: E  102 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7753 (p)
REVERT: K   49 SER cc_start: 0.9020 (t) cc_final: 0.8753 (m)
REVERT: A   49 SER cc_start: 0.8944 (t) cc_final: 0.8702 (m)
REVERT: A  102 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7417 (p)
REVERT: L  102 CYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7863 (p)
REVERT: M   92 ASP cc_start: 0.8199 (m-30) cc_final: 0.7960 (m-30)
REVERT: O  102 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7668 (p)
REVERT: P  109 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8204 (ptm160)
REVERT: S  102 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7627 (p)
REVERT: S  143 THR cc_start: 0.8961 (p) cc_final: 0.8710 (p)
  outliers start: 93
  outliers final: 55
  residues processed: 450
  average time/residue: 2.0258
  time to fit residues: 1116.8097
Evaluate side-chains
  434 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 372
  time to evaluate  : 3.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  109 ARG
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain E residue   13 ILE
Chi-restraints excluded: chain E residue  102 CYS
Chi-restraints excluded: chain E residue  104 SER
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue  104 SER
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   92 ASP
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue   92 ASP
Chi-restraints excluded: chain I residue  104 SER
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain J residue  102 CYS
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  109 ARG
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue  104 SER
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   59 ASP
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  102 CYS
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  102 CYS
Chi-restraints excluded: chain M residue  104 SER
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  104 SER
Chi-restraints excluded: chain O residue   54 LYS
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  104 SER
Chi-restraints excluded: chain O residue  109 ARG
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue   92 ASP
Chi-restraints excluded: chain P residue  104 SER
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue   79 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   92 ASP
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain S residue   92 ASP
Chi-restraints excluded: chain S residue  102 CYS
Chi-restraints excluded: chain S residue  104 SER
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:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 327 optimal weight:    3.9990
   chunk 353 optimal weight:    2.9990
   chunk 291 optimal weight:    0.8980
   chunk 324 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   chunk 262 optimal weight:    0.3980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
E  28 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
Q  39 ASN
R  39 ASN
R 151 ASN
R 179 GLN
S  39 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  28404  Z= 0.174
  Angle     :  0.620  21.451  38682  Z= 0.340
  Chirality :  0.042   0.142   4194
  Planarity :  0.004   0.085   5310
  Dihedral  :  5.173  57.541   4055
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.38 %
    Favored  : 82.34 %
  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: -0.95 (0.13), residues: 3708
  helix:  1.47 (0.18), residues: 882
  sheet: -0.13 (0.18), residues: 774
  loop : -1.88 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N 169 
 PHE   0.011   0.001   PHE R 153 
 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
  488 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 424
  time to evaluate  : 3.075 
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: D  102 CYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7722 (p)
REVERT: E  102 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7422 (p)
REVERT: E  167 ASP cc_start: 0.8461 (p0) cc_final: 0.8204 (p0)
REVERT: F   48 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.7615 (mptp)
REVERT: F  167 ASP cc_start: 0.8660 (p0) cc_final: 0.8345 (p0)
REVERT: G   86 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7541 (tt0)
REVERT: H  102 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7862 (p)
REVERT: I  102 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7816 (p)
REVERT: J  167 ASP cc_start: 0.8627 (p0) cc_final: 0.7999 (p0)
REVERT: J  175 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8097 (mm-30)
REVERT: K  167 ASP cc_start: 0.8702 (p0) cc_final: 0.8246 (p0)
REVERT: L  167 ASP cc_start: 0.8611 (p0) cc_final: 0.8408 (p0)
REVERT: M   92 ASP cc_start: 0.8187 (m-30) cc_final: 0.7961 (m-30)
REVERT: M  167 ASP cc_start: 0.8673 (p0) cc_final: 0.8216 (p0)
REVERT: N  167 ASP cc_start: 0.8371 (p0) cc_final: 0.8115 (p0)
REVERT: O   54 LYS cc_start: 0.8772 (mttp) cc_final: 0.8542 (mmtm)
REVERT: O  102 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7541 (p)
REVERT: P   55 ASP cc_start: 0.7949 (m-30) cc_final: 0.7685 (m-30)
REVERT: P  109 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8065 (ptm160)
REVERT: Q  167 ASP cc_start: 0.8561 (p0) cc_final: 0.8278 (p0)
REVERT: R  102 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7713 (p)
REVERT: R  167 ASP cc_start: 0.8600 (p0) cc_final: 0.8398 (p0)
REVERT: S  102 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7494 (p)
REVERT: S  106 ASP cc_start: 0.8895 (t0) cc_final: 0.8693 (t0)
REVERT: S  143 THR cc_start: 0.8935 (p) cc_final: 0.8675 (p)
REVERT: S  167 ASP cc_start: 0.8608 (p0) cc_final: 0.8352 (p0)
  outliers start: 64
  outliers final: 30
  residues processed: 480
  average time/residue: 1.8885
  time to fit residues: 1104.5844
Evaluate side-chains
  442 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 402
  time to evaluate  : 3.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain E residue  102 CYS
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   48 LYS
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue  102 CYS
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  143 THR
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue  102 CYS
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
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:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 156 optimal weight:    5.9990
   chunk 219 optimal weight:    4.9990
   chunk 328 optimal weight:    6.9990
   chunk 347 optimal weight:    3.9990
   chunk 171 optimal weight:    2.9990
   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
J 179 GLN
K 179 GLN
M 179 GLN
N 179 GLN
P 179 GLN
R 179 GLN
S 179 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  28404  Z= 0.492
  Angle     :  0.727  20.870  38682  Z= 0.405
  Chirality :  0.047   0.154   4194
  Planarity :  0.005   0.080   5310
  Dihedral  :  5.468  58.751   4038
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.28 %
    Favored  : 81.05 %
  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: -1.46 (0.12), residues: 3708
  helix:  0.91 (0.17), residues: 882
  sheet: -0.06 (0.21), residues: 594
  loop : -2.16 (0.10), residues: 2232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 134 
 PHE   0.014   0.002   PHE F   1 
 TYR   0.014   0.003   TYR F  76 
 ARG   0.005   0.001   ARG S  56 

*********************** 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
  487 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 103
    poor density    : 384
  time to evaluate  : 3.096 
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
   revert: symmetry clash
REVERT: D  102 CYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7795 (p)
REVERT: E  102 CYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7709 (p)
REVERT: H  102 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8047 (p)
REVERT: I  102 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (p)
REVERT: K   49 SER cc_start: 0.9036 (t) cc_final: 0.8788 (m)
REVERT: A   49 SER cc_start: 0.8970 (t) cc_final: 0.8725 (m)
REVERT: L  167 ASP cc_start: 0.8939 (p0) cc_final: 0.8683 (p0)
REVERT: N  167 ASP cc_start: 0.8781 (p0) cc_final: 0.8517 (p0)
REVERT: O  102 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7614 (p)
REVERT: O  109 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8196 (ptm160)
REVERT: O  167 ASP cc_start: 0.8709 (p0) cc_final: 0.8466 (p0)
REVERT: P   59 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (t0)
REVERT: P  109 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8401 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8271 (t70) cc_final: 0.8035 (t70)
REVERT: S  102 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7574 (p)
  outliers start: 103
  outliers final: 59
  residues processed: 463
  average time/residue: 1.9879
  time to fit residues: 1112.9046
Evaluate side-chains
  439 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 371
  time to evaluate  : 3.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain E residue  102 CYS
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   49 SER
Chi-restraints excluded: chain F residue   92 ASP
Chi-restraints excluded: chain F residue  109 ARG
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   78 VAL
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue   92 ASP
Chi-restraints excluded: chain H residue  102 CYS
Chi-restraints excluded: chain H residue  109 ARG
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  109 ARG
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain J residue  180 VAL
Chi-restraints excluded: chain K residue   13 ILE
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   59 ASP
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  102 CYS
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue   13 ILE
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  109 ARG
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain N residue  168 ASP
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   49 SER
Chi-restraints excluded: chain O residue   54 LYS
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  109 ARG
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   21 ILE
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   92 ASP
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain R residue  167 ASP
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 289 optimal weight:    7.9990
   chunk 197 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 259 optimal weight:    0.9990
   chunk 143 optimal weight:    4.9990
   chunk 296 optimal weight:    3.9990
   chunk 240 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 177 optimal weight:    2.9990
   chunk 312 optimal weight:    0.0870
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.2166

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

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

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  28404  Z= 0.269
  Angle     :  0.642  21.389  38682  Z= 0.354
  Chirality :  0.043   0.148   4194
  Planarity :  0.004   0.077   5310
  Dihedral  :  5.152  58.573   4038
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.35 %
    Favored  : 81.02 %
  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: -1.15 (0.13), residues: 3708
  helix:  1.26 (0.18), residues: 882
  sheet:  0.15 (0.19), residues: 720
  loop : -2.13 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N 169 
 PHE   0.011   0.001   PHE H 153 
 TYR   0.009   0.001   TYR C  44 
 ARG   0.004   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
  477 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 403
  time to evaluate  : 3.070 
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: D  102 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7703 (p)
REVERT: E  102 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7470 (p)
REVERT: E  167 ASP cc_start: 0.8626 (p0) cc_final: 0.8413 (p0)
REVERT: F   48 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7604 (mptp)
REVERT: F  167 ASP cc_start: 0.8712 (p0) cc_final: 0.8362 (p0)
REVERT: G   86 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7690 (tt0)
REVERT: H  106 ASP cc_start: 0.8824 (t70) cc_final: 0.8592 (t70)
REVERT: H  167 ASP cc_start: 0.8718 (p0) cc_final: 0.8354 (p0)
REVERT: I  102 CYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7826 (p)
REVERT: K   49 SER cc_start: 0.8977 (t) cc_final: 0.8746 (m)
REVERT: K  167 ASP cc_start: 0.8849 (p0) cc_final: 0.8279 (p0)
REVERT: L  167 ASP cc_start: 0.8725 (p0) cc_final: 0.8520 (p0)
REVERT: M   86 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7344 (tt0)
REVERT: O  102 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7341 (p)
REVERT: O  109 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8046 (ptm160)
REVERT: P   55 ASP cc_start: 0.8014 (m-30) cc_final: 0.7744 (m-30)
REVERT: P   59 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7899 (t0)
REVERT: P  109 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8285 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8245 (t70) cc_final: 0.7978 (t70)
REVERT: Q  167 ASP cc_start: 0.8691 (p0) cc_final: 0.8378 (p0)
REVERT: R  167 ASP cc_start: 0.8720 (p0) cc_final: 0.8517 (p0)
REVERT: S  102 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7509 (p)
REVERT: S  106 ASP cc_start: 0.8956 (t0) cc_final: 0.8623 (t70)
  outliers start: 74
  outliers final: 43
  residues processed: 466
  average time/residue: 1.9191
  time to fit residues: 1084.7824
Evaluate side-chains
  443 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 389
  time to evaluate  : 3.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain E residue  102 CYS
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   48 LYS
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   78 VAL
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  109 ARG
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue   54 LYS
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue   86 GLU
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue  109 ARG
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  109 ARG
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue   92 ASP
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 313 optimal weight:    0.7980
   chunk 68 optimal weight:    7.9990
   chunk 204 optimal weight:    4.9990
   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:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 182 optimal weight:    5.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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
D 179 GLN
H 151 ASN
H 179 GLN
J 151 ASN
J 179 GLN
K  39 ASN
K 151 ASN
K 179 GLN
M 179 GLN
N 179 GLN
P 129 GLN
P 179 GLN
R 151 ASN
R 179 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  28404  Z= 0.347
  Angle     :  0.664  21.343  38682  Z= 0.367
  Chirality :  0.045   0.150   4194
  Planarity :  0.005   0.071   5310
  Dihedral  :  5.212  58.897   4038
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.13 %
    Favored  : 80.56 %
  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 (0.13), residues: 3708
  helix:  1.20 (0.18), residues: 882
  sheet:  0.11 (0.19), residues: 720
  loop : -2.16 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP N 169 
 PHE   0.012   0.001   PHE H 153 
 TYR   0.011   0.002   TYR M  44 
 ARG   0.003   0.000   ARG F  88 

*********************** 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
  491 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 93
    poor density    : 398
  time to evaluate  : 3.085 
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: C   54 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8469 (mptm)
REVERT: D  102 CYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7704 (p)
REVERT: D  141 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8588 (pt0)
REVERT: D  167 ASP cc_start: 0.8896 (p0) cc_final: 0.8557 (p0)
REVERT: E  102 CYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7507 (p)
REVERT: E  167 ASP cc_start: 0.8759 (p0) cc_final: 0.8529 (p0)
REVERT: F   48 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7608 (mptp)
REVERT: G   86 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7773 (tt0)
REVERT: H  167 ASP cc_start: 0.8775 (p0) cc_final: 0.8402 (p0)
REVERT: I  102 CYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7867 (p)
REVERT: J  167 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (p0)
REVERT: K   49 SER cc_start: 0.8982 (t) cc_final: 0.8740 (m)
REVERT: K  167 ASP cc_start: 0.8916 (p0) cc_final: 0.8397 (p0)
REVERT: L  167 ASP cc_start: 0.8778 (p0) cc_final: 0.8469 (p0)
REVERT: N  167 ASP cc_start: 0.8589 (p0) cc_final: 0.8338 (p0)
REVERT: O  102 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7458 (p)
REVERT: O  109 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8122 (ptm160)
REVERT: O  167 ASP cc_start: 0.8462 (p0) cc_final: 0.8198 (p0)
REVERT: P   55 ASP cc_start: 0.8025 (m-30) cc_final: 0.7765 (m-30)
REVERT: P   59 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7957 (t0)
REVERT: P  109 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8350 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8218 (t70) cc_final: 0.7961 (t70)
REVERT: S  102 CYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7489 (p)
REVERT: S  106 ASP cc_start: 0.8987 (t0) cc_final: 0.8628 (t70)
  outliers start: 93
  outliers final: 58
  residues processed: 468
  average time/residue: 2.0095
  time to fit residues: 1138.9154
Evaluate side-chains
  458 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 387
  time to evaluate  : 3.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  141 GLN
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain E residue  102 CYS
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   48 LYS
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   78 VAL
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue   92 ASP
Chi-restraints excluded: chain H residue  109 ARG
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain I residue   92 ASP
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain J residue   49 SER
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain J residue  167 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  102 CYS
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue   72 ASN
Chi-restraints excluded: chain N residue  109 ARG
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  109 ARG
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue   92 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   21 ILE
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   54 LYS
Chi-restraints excluded: chain R residue   72 ASN
Chi-restraints excluded: chain R residue   92 ASP
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue   92 ASP
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 335 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 198 optimal weight:    0.0270
   chunk 254 optimal weight:    4.9990
   chunk 197 optimal weight:    0.8980
   chunk 293 optimal weight:    4.9990
   chunk 194 optimal weight:    2.9990
   chunk 346 optimal weight:    2.9990
   chunk 217 optimal weight:    4.9990
   chunk 211 optimal weight:    0.5980
   chunk 160 optimal weight:    5.9990
   overall best weight:    1.5042

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

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

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  28404  Z= 0.205
  Angle     :  0.620  21.586  38682  Z= 0.341
  Chirality :  0.042   0.146   4194
  Planarity :  0.004   0.069   5310
  Dihedral  :  4.942  58.723   4038
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.52 %
    Favored  : 80.77 %
  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: -1.03 (0.13), residues: 3708
  helix:  1.49 (0.18), residues: 882
  sheet:  0.09 (0.19), residues: 720
  loop : -2.05 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP N 169 
 PHE   0.009   0.001   PHE H 153 
 TYR   0.008   0.001   TYR C  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
  489 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 413
  time to evaluate  : 3.036 
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: C   54 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8471 (mptm)
REVERT: D  102 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7644 (p)
REVERT: D  167 ASP cc_start: 0.8689 (p0) cc_final: 0.8141 (p0)
REVERT: F   48 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7591 (mptp)
REVERT: F  167 ASP cc_start: 0.8576 (p0) cc_final: 0.8201 (p0)
REVERT: F  200 ASP cc_start: 0.7316 (t0) cc_final: 0.6956 (t0)
REVERT: G   86 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7690 (tt0)
REVERT: H  167 ASP cc_start: 0.8596 (p0) cc_final: 0.8230 (p0)
REVERT: I  102 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7775 (p)
REVERT: I  167 ASP cc_start: 0.8406 (p0) cc_final: 0.8053 (p0)
REVERT: J   53 GLU cc_start: 0.7504 (tt0) cc_final: 0.7159 (tt0)
REVERT: K   49 SER cc_start: 0.8962 (t) cc_final: 0.8713 (m)
REVERT: K  167 ASP cc_start: 0.8716 (p0) cc_final: 0.8324 (p0)
REVERT: M  167 ASP cc_start: 0.8716 (p0) cc_final: 0.8220 (p0)
REVERT: O  102 CYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7193 (p)
REVERT: O  109 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8080 (ptm160)
REVERT: P   55 ASP cc_start: 0.8000 (m-30) cc_final: 0.7743 (m-30)
REVERT: P   59 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7895 (t0)
REVERT: P  109 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8203 (ptm160)
REVERT: Q  167 ASP cc_start: 0.8621 (p0) cc_final: 0.8360 (p0)
REVERT: S   63 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8186 (mt-10)
REVERT: S  102 CYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7446 (p)
REVERT: S  106 ASP cc_start: 0.8947 (t0) cc_final: 0.8586 (t70)
  outliers start: 76
  outliers final: 49
  residues processed: 477
  average time/residue: 2.0602
  time to fit residues: 1210.4862
Evaluate side-chains
  457 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 398
  time to evaluate  : 3.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue  109 ARG
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   48 LYS
Chi-restraints excluded: chain F residue   92 ASP
Chi-restraints excluded: chain F residue  109 ARG
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   78 VAL
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  147 CYS
Chi-restraints excluded: chain H residue   72 ASN
Chi-restraints excluded: chain H residue   79 SER
Chi-restraints excluded: chain H residue  109 ARG
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain H residue  147 CYS
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  147 CYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue   79 SER
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue   13 ILE
Chi-restraints excluded: chain N residue   72 ASN
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  109 ARG
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   54 LYS
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 214 optimal weight:    0.0370
   chunk 138 optimal weight:    6.9990
   chunk 207 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 220 optimal weight:    5.9990
   chunk 236 optimal weight:    2.9990
   chunk 171 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 272 optimal weight:    0.4980
   overall best weight:    0.9860

-------------------------------------------------------------------------------
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
D 179 GLN
H 151 ASN
I 135 ASN
J 151 ASN
J 179 GLN
K 151 ASN
K 179 GLN
A 129 GLN
M 179 GLN
N 179 GLN
P  39 ASN
P 179 GLN
R 151 ASN
S 151 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  28404  Z= 0.170
  Angle     :  0.602  21.707  38682  Z= 0.330
  Chirality :  0.042   0.143   4194
  Planarity :  0.004   0.066   5310
  Dihedral  :  4.615  58.014   4038
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.09 %
    Favored  : 80.52 %
  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: -0.91 (0.13), residues: 3708
  helix:  1.75 (0.18), residues: 882
  sheet: -0.35 (0.19), residues: 774
  loop : -1.87 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP O 169 
 PHE   0.010   0.001   PHE P   1 
 TYR   0.008   0.001   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
  480 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 413
  time to evaluate  : 3.108 
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: C   54 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8475 (mptm)
REVERT: D  102 CYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7559 (p)
REVERT: D  177 SER cc_start: 0.9082 (p) cc_final: 0.8788 (t)
REVERT: F  200 ASP cc_start: 0.7235 (t0) cc_final: 0.6748 (t0)
REVERT: G   86 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: I  102 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7709 (p)
REVERT: K  136 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8610 (p)
REVERT: O   63 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: O  102 CYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7147 (p)
REVERT: O  167 ASP cc_start: 0.7970 (p0) cc_final: 0.7751 (p0)
REVERT: P   55 ASP cc_start: 0.8004 (m-30) cc_final: 0.7759 (m-30)
REVERT: P   59 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7860 (t0)
REVERT: P  109 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8128 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8220 (t70) cc_final: 0.7994 (t70)
REVERT: Q  167 ASP cc_start: 0.8534 (p0) cc_final: 0.8269 (p0)
REVERT: R  167 ASP cc_start: 0.8413 (p0) cc_final: 0.8178 (p0)
REVERT: S   63 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: S  102 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7518 (p)
REVERT: S  106 ASP cc_start: 0.8937 (t0) cc_final: 0.8557 (t70)
REVERT: S  157 ARG cc_start: 0.8641 (ttt90) cc_final: 0.8385 (ttt180)
REVERT: S  167 ASP cc_start: 0.8475 (p0) cc_final: 0.8214 (p0)
  outliers start: 67
  outliers final: 48
  residues processed: 473
  average time/residue: 1.9375
  time to fit residues: 1113.0926
Evaluate side-chains
  451 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 394
  time to evaluate  : 3.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue   92 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain H residue   72 ASN
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain H residue  147 CYS
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain I residue  147 CYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  136 THR
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain K residue  147 CYS
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain O residue  150 CYS
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue  104 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain R residue  109 ARG
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 315 optimal weight:    2.9990
   chunk 332 optimal weight:    0.0980
   chunk 303 optimal weight:    3.9990
   chunk 323 optimal weight:    4.9990
   chunk 194 optimal weight:    0.6980
   chunk 140 optimal weight:    5.9990
   chunk 253 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 292 optimal weight:    0.8980
   chunk 305 optimal weight:    0.6980
   chunk 322 optimal weight:    1.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  28404  Z= 0.160
  Angle     :  0.597  21.663  38682  Z= 0.327
  Chirality :  0.042   0.142   4194
  Planarity :  0.004   0.065   5310
  Dihedral  :  4.472  57.539   4038
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.84 %
    Favored  : 80.09 %
  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: -0.80 (0.13), residues: 3708
  helix:  1.91 (0.18), residues: 882
  sheet: -0.32 (0.19), residues: 774
  loop : -1.81 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 169 
 PHE   0.010   0.001   PHE L   1 
 TYR   0.009   0.001   TYR F  44 
 ARG   0.004   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
  462 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 404
  time to evaluate  : 3.103 
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: C   54 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (mptm)
REVERT: D  102 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7543 (p)
REVERT: D  177 SER cc_start: 0.9044 (p) cc_final: 0.8799 (t)
REVERT: E   63 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8113 (mt-10)
REVERT: E  167 ASP cc_start: 0.8389 (p0) cc_final: 0.8085 (p0)
REVERT: F   95 VAL cc_start: 0.9130 (m) cc_final: 0.8874 (t)
REVERT: F  167 ASP cc_start: 0.8592 (p0) cc_final: 0.8118 (p0)
REVERT: G   86 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7687 (tt0)
REVERT: H  106 ASP cc_start: 0.8835 (t70) cc_final: 0.8580 (t70)
REVERT: H  175 GLU cc_start: 0.8785 (mp0) cc_final: 0.8535 (mp0)
REVERT: I  102 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (p)
REVERT: K  136 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8584 (p)
REVERT: K  167 ASP cc_start: 0.8657 (p0) cc_final: 0.8202 (p0)
REVERT: O   63 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: O  102 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7158 (p)
REVERT: O  167 ASP cc_start: 0.7876 (p0) cc_final: 0.7675 (p0)
REVERT: P   55 ASP cc_start: 0.7993 (m-30) cc_final: 0.7744 (m-30)
REVERT: P   59 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7711 (t0)
REVERT: P  109 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8025 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8200 (t70) cc_final: 0.7978 (t70)
REVERT: Q  167 ASP cc_start: 0.8443 (p0) cc_final: 0.8178 (p0)
REVERT: S   63 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: S  102 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7456 (p)
REVERT: S  106 ASP cc_start: 0.8873 (t0) cc_final: 0.8667 (t70)
REVERT: S  157 ARG cc_start: 0.8639 (ttt90) cc_final: 0.8377 (ttt180)
  outliers start: 58
  outliers final: 40
  residues processed: 455
  average time/residue: 1.9341
  time to fit residues: 1071.1374
Evaluate side-chains
  440 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 391
  time to evaluate  : 3.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  147 CYS
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain H residue  147 CYS
Chi-restraints excluded: chain I residue  102 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain I residue  147 CYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  136 THR
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain K residue  147 CYS
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain O residue  150 CYS
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   54 LYS
Chi-restraints excluded: chain R residue   72 ASN
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
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:    4.9990
   chunk 208 optimal weight:    6.9990
   chunk 162 optimal weight:    0.6980
   chunk 237 optimal weight:    3.9990
   chunk 358 optimal weight:    7.9990
   chunk 330 optimal weight:    0.9990
   chunk 285 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 220 optimal weight:    0.8980
   chunk 175 optimal weight:    3.9990
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  28404  Z= 0.190
  Angle     :  0.601  21.664  38682  Z= 0.330
  Chirality :  0.042   0.143   4194
  Planarity :  0.004   0.064   5310
  Dihedral  :  4.450  57.255   4036
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.91 %
    Favored  : 79.95 %
  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: -0.80 (0.13), residues: 3708
  helix:  1.92 (0.18), residues: 882
  sheet: -0.33 (0.19), residues: 774
  loop : -1.82 (0.11), residues: 2052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP O 169 
 PHE   0.008   0.001   PHE H 153 
 TYR   0.008   0.001   TYR C  44 
 ARG   0.003   0.000   ARG N  70 

********************** 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
  450 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 390
  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: C   54 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8444 (mptm)
REVERT: D  102 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7508 (p)
REVERT: D  167 ASP cc_start: 0.8633 (p0) cc_final: 0.7984 (p0)
REVERT: D  177 SER cc_start: 0.9066 (p) cc_final: 0.8830 (t)
REVERT: E  167 ASP cc_start: 0.8433 (p0) cc_final: 0.8171 (p0)
REVERT: F   95 VAL cc_start: 0.9113 (m) cc_final: 0.8873 (t)
REVERT: F  167 ASP cc_start: 0.8618 (p0) cc_final: 0.8294 (p0)
REVERT: G   86 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7725 (tt0)
REVERT: G  167 ASP cc_start: 0.8720 (p0) cc_final: 0.8422 (p0)
REVERT: H  106 ASP cc_start: 0.8844 (t70) cc_final: 0.8570 (t70)
REVERT: H  167 ASP cc_start: 0.8561 (p0) cc_final: 0.8199 (p0)
REVERT: H  175 GLU cc_start: 0.8785 (mp0) cc_final: 0.8542 (mp0)
REVERT: K  136 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (p)
REVERT: K  167 ASP cc_start: 0.8734 (p0) cc_final: 0.8104 (p0)
REVERT: L   59 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7587 (t0)
REVERT: M   86 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: M  167 ASP cc_start: 0.8667 (p0) cc_final: 0.8125 (p0)
REVERT: O   63 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: O  102 CYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7314 (p)
REVERT: P   55 ASP cc_start: 0.7967 (m-30) cc_final: 0.7708 (m-30)
REVERT: P   59 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7811 (t0)
REVERT: P  109 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8091 (ptm160)
REVERT: Q  118 ASP cc_start: 0.8195 (t70) cc_final: 0.7994 (t70)
REVERT: Q  167 ASP cc_start: 0.8533 (p0) cc_final: 0.8262 (p0)
REVERT: R  167 ASP cc_start: 0.8485 (p0) cc_final: 0.8251 (p0)
REVERT: S   63 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8146 (mt-10)
REVERT: S  102 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7437 (p)
REVERT: S  106 ASP cc_start: 0.8908 (t0) cc_final: 0.8697 (t70)
REVERT: S  157 ARG cc_start: 0.8661 (ttt90) cc_final: 0.8397 (ttt180)
REVERT: S  167 ASP cc_start: 0.8450 (p0) cc_final: 0.8193 (p0)
  outliers start: 60
  outliers final: 43
  residues processed: 446
  average time/residue: 1.9140
  time to fit residues: 1036.9717
Evaluate side-chains
  438 residues out of total 2808 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 386
  time to evaluate  : 3.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LYS
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain D residue  102 CYS
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain D residue  109 ARG
Chi-restraints excluded: chain E residue  146 ASP
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue  146 ASP
Chi-restraints excluded: chain G residue   78 VAL
Chi-restraints excluded: chain G residue   86 GLU
Chi-restraints excluded: chain G residue  104 SER
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  147 CYS
Chi-restraints excluded: chain H residue  146 ASP
Chi-restraints excluded: chain H residue  147 CYS
Chi-restraints excluded: chain I residue  146 ASP
Chi-restraints excluded: chain I residue  147 CYS
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain J residue  146 ASP
Chi-restraints excluded: chain K residue   54 LYS
Chi-restraints excluded: chain K residue  136 THR
Chi-restraints excluded: chain K residue  146 ASP
Chi-restraints excluded: chain K residue  147 CYS
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   59 ASP
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain L residue  146 ASP
Chi-restraints excluded: chain M residue    2 THR
Chi-restraints excluded: chain M residue  146 ASP
Chi-restraints excluded: chain N residue  146 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue   21 ILE
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain O residue  102 CYS
Chi-restraints excluded: chain O residue  146 ASP
Chi-restraints excluded: chain O residue  150 CYS
Chi-restraints excluded: chain P residue   59 ASP
Chi-restraints excluded: chain P residue  109 ARG
Chi-restraints excluded: chain P residue  146 ASP
Chi-restraints excluded: chain Q residue   13 ILE
Chi-restraints excluded: chain Q residue   52 SER
Chi-restraints excluded: chain Q residue  109 ARG
Chi-restraints excluded: chain Q residue  146 ASP
Chi-restraints excluded: chain R residue   72 ASN
Chi-restraints excluded: chain R residue  104 SER
Chi-restraints excluded: chain S residue   21 ILE
Chi-restraints excluded: chain S residue  102 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 360
   random chunks:
   chunk 226 optimal weight:    3.9990
   chunk 304 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 263 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 286 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 293 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 135 ASN
J 179 GLN
K 179 GLN
A 151 ASN
M 179 GLN
N 179 GLN
P 179 GLN
R 151 ASN
R 179 GLN
S 179 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.132947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.119855 restraints weight = 84936.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.31
r_work: 0.3247 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  28404  Z= 0.235
  Angle     :  0.615  21.262  38682  Z= 0.338
  Chirality :  0.042   0.145   4194
  Planarity :  0.004   0.064   5310
  Dihedral  :  4.591  57.346   4036
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.88 %
    Favored  : 80.02 %
  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: -0.81 (0.13), residues: 3708
  helix:  1.83 (0.18), residues: 882
  sheet:  0.09 (0.19), residues: 720
  loop : -1.93 (0.11), residues: 2106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP O 169 
 PHE   0.009   0.001   PHE L   1 
 TYR   0.009   0.001   TYR C  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: 16033.74 seconds
wall clock time: 274 minutes 33.92 seconds (16473.92 seconds total)