Starting phenix.real_space_refine
on Sat Apr  6 17:32:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/04_2024/8ote_17176.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5544      2.51       5
     N    1384      2.21       5
     O    1696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  180": "NH1" <-> "NH2"
    Residue "A TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  205": "OE1" <-> "OE2"
    Residue "A GLU  206": "OE1" <-> "OE2"
    Residue "A TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  246": "OE1" <-> "OE2"
    Residue "A ARG  247": "NH1" <-> "NH2"
    Residue "B TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  180": "NH1" <-> "NH2"
    Residue "B TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  205": "OE1" <-> "OE2"
    Residue "B GLU  206": "OE1" <-> "OE2"
    Residue "B TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  246": "OE1" <-> "OE2"
    Residue "B ARG  247": "NH1" <-> "NH2"
    Residue "C TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  180": "NH1" <-> "NH2"
    Residue "C TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  205": "OE1" <-> "OE2"
    Residue "C GLU  206": "OE1" <-> "OE2"
    Residue "C TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  246": "OE1" <-> "OE2"
    Residue "C ARG  247": "NH1" <-> "NH2"
    Residue "D TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  180": "NH1" <-> "NH2"
    Residue "D TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  205": "OE1" <-> "OE2"
    Residue "D GLU  206": "OE1" <-> "OE2"
    Residue "D TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  246": "OE1" <-> "OE2"
    Residue "D ARG  247": "NH1" <-> "NH2"
    Residue "E TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  180": "NH1" <-> "NH2"
    Residue "E TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  205": "OE1" <-> "OE2"
    Residue "E GLU  206": "OE1" <-> "OE2"
    Residue "E TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E GLU  246": "OE1" <-> "OE2"
    Residue "E ARG  247": "NH1" <-> "NH2"
    Residue "F TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  180": "NH1" <-> "NH2"
    Residue "F TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  205": "OE1" <-> "OE2"
    Residue "F GLU  206": "OE1" <-> "OE2"
    Residue "F TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU  246": "OE1" <-> "OE2"
    Residue "F ARG  247": "NH1" <-> "NH2"
    Residue "G TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  180": "NH1" <-> "NH2"
    Residue "G TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  205": "OE1" <-> "OE2"
    Residue "G GLU  206": "OE1" <-> "OE2"
    Residue "G TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  246": "OE1" <-> "OE2"
    Residue "G ARG  247": "NH1" <-> "NH2"
    Residue "H TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  171": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG  180": "NH1" <-> "NH2"
    Residue "H TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU  205": "OE1" <-> "OE2"
    Residue "H GLU  206": "OE1" <-> "OE2"
    Residue "H TYR  209": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE  213": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU  246": "OE1" <-> "OE2"
    Residue "H ARG  247": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 8680
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "E"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "F"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "G"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "H"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Time building chain proxies: 4.84, per 1000 atoms: 0.56
  Number of scatterers: 8680
  At special positions: 0
  Unit cell: (191.992, 144.2, 36.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1696      8.00
     N    1384      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 214 " - pdb=" SG  CYS E 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 214 " - pdb=" SG  CYS F 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 214 " - pdb=" SG  CYS G 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 214 " - pdb=" SG  CYS H 253 " distance=2.04

  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: 3.28
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 23 sheets defined
      0.0% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 121 through 126
      removed outlier: 6.905A  pdb=" N   ASP A 122 " --> pdb=" O   ILE E 121 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE A 121 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   LYS C 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL A 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ILE C 126 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TYR A 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ILE C 121 " --> pdb=" O   ASP G 122 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   LYS G 124 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL C 123 " --> pdb=" O   LYS G 124 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ILE G 126 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TYR C 125 " --> pdb=" O   ILE G 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 129 through 130
      removed outlier: 6.680A  pdb=" N   LYS A 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS C 129 " --> pdb=" O   SER G 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 144 through 148
      removed outlier: 6.797A  pdb=" N   ILE E 146 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR A 147 " --> pdb=" O   ILE E 146 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN E 148 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   LEU A 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   THR C 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.434A  pdb=" N   ILE A 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   LEU C 144 " --> pdb=" O   ASN G 145 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   THR G 147 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 9.434A  pdb=" N   ILE C 146 " --> pdb=" O   THR G 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 155 through 157
      removed outlier: 6.668A  pdb=" N   ASN A 156 " --> pdb=" O   TYR E 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 165
      removed outlier: 6.409A  pdb=" N   GLU A 163 " --> pdb=" O   ASN E 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 168 through 175
      removed outlier: 6.894A  pdb=" N   VAL A 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   SER C 172 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   PHE A 171 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   THR C 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LYS A 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL C 169 " --> pdb=" O   GLN G 170 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   SER G 172 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   PHE C 171 " --> pdb=" O   SER G 172 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   THR G 174 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LYS C 173 " --> pdb=" O   THR G 174 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 180 through 181
      removed outlier: 6.644A  pdb=" N   ARG A 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG C 180 " --> pdb=" O   LEU G 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 184 through 187
      removed outlier: 6.876A  pdb=" N   ILE A 184 " --> pdb=" O   SER E 185 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ILE E 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   ILE A 186 " --> pdb=" O   ILE E 187 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 201 through 206
      removed outlier: 6.795A  pdb=" N   THR A 201 " --> pdb=" O   VAL E 202 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ALA E 204 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE A 203 " --> pdb=" O   ALA E 204 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   GLU E 206 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU A 205 " --> pdb=" O   GLU E 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 230
      removed outlier: 6.165A  pdb=" N   VAL A 225 " --> pdb=" O   LEU E 226 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   MET E 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   MET A 227 " --> pdb=" O   MET E 228 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   VAL E 230 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   GLN A 229 " --> pdb=" O   VAL E 230 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL A 230 " --> pdb=" O   GLN C 229 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL C 230 " --> pdb=" O   GLN G 229 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 237
      removed outlier: 6.439A  pdb=" N   THR A 235 " --> pdb=" O   TYR E 236 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 246 through 247
      removed outlier: 6.278A  pdb=" N   GLU A 246 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLU C 246 " --> pdb=" O   ARG G 247 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 121 through 126
      removed outlier: 6.902A  pdb=" N   ASP B 122 " --> pdb=" O   ILE F 121 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE B 121 " --> pdb=" O   ASP D 122 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   LYS D 124 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL B 123 " --> pdb=" O   LYS D 124 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ILE D 126 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR B 125 " --> pdb=" O   ILE D 126 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE D 121 " --> pdb=" O   ASP H 122 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   LYS H 124 " --> pdb=" O   ILE D 121 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL D 123 " --> pdb=" O   LYS H 124 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ILE H 126 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR D 125 " --> pdb=" O   ILE H 126 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 130
      removed outlier: 6.678A  pdb=" N   LYS B 129 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LYS D 129 " --> pdb=" O   SER H 130 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 148
      removed outlier: 6.128A  pdb=" N   THR B 147 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   THR D 147 " --> pdb=" O   ASN H 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 155 through 157
      removed outlier: 6.663A  pdb=" N   ASN B 156 " --> pdb=" O   TYR F 157 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 165
      removed outlier: 6.418A  pdb=" N   GLU B 163 " --> pdb=" O   ASN F 164 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 175
      removed outlier: 6.931A  pdb=" N   VAL B 169 " --> pdb=" O   GLN D 170 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   SER D 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   PHE B 171 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   THR D 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LYS B 173 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL D 169 " --> pdb=" O   GLN H 170 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   SER H 172 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   PHE D 171 " --> pdb=" O   SER H 172 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   THR H 174 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS D 173 " --> pdb=" O   THR H 174 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 180 through 181
      removed outlier: 6.650A  pdb=" N   ARG B 180 " --> pdb=" O   LEU D 181 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ARG D 180 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 184 through 187
      removed outlier: 6.903A  pdb=" N   ILE B 184 " --> pdb=" O   SER F 185 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   ILE F 187 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE B 186 " --> pdb=" O   ILE F 187 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 204
      removed outlier: 6.792A  pdb=" N   THR B 201 " --> pdb=" O   VAL F 202 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   ALA F 204 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ILE B 203 " --> pdb=" O   ALA F 204 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 224 through 230
      removed outlier: 6.161A  pdb=" N   VAL B 225 " --> pdb=" O   LEU F 226 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   MET F 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   MET B 227 " --> pdb=" O   MET F 228 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL F 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   GLN B 229 " --> pdb=" O   VAL F 230 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B 230 " --> pdb=" O   GLN D 229 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL D 230 " --> pdb=" O   GLN H 229 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 247
      removed outlier: 6.274A  pdb=" N   GLU B 246 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLU D 246 " --> pdb=" O   ARG H 247 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    294 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: 2.15

  Time building geometry restraints manager: 3.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1852
        1.34 -     1.46: 2574
        1.46 -     1.58: 4302
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 8824
  Sorted by residual:
  bond pdb=" CA  SER A 130 "
       pdb=" CB  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 1.02e+01
  bond pdb=" CA  SER G 130 "
       pdb=" CB  SER G 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 1.01e+01
  bond pdb=" CA  SER E 130 "
       pdb=" CB  SER E 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 9.96e+00
  bond pdb=" CA  SER C 130 "
       pdb=" CB  SER C 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.055 1.76e-02 3.23e+03 9.89e+00
  bond pdb=" CA  SER H 130 "
       pdb=" CB  SER H 130 "
    ideal  model  delta    sigma   weight residual
    1.533  1.476  0.057 1.82e-02 3.02e+03 9.66e+00
  ... (remaining 8819 not shown)

  Histogram of bond angle deviations from ideal:
       98.96 -   105.51: 140
      105.51 -   112.06: 3368
      112.06 -   118.61: 3735
      118.61 -   125.15: 4653
      125.15 -   131.70: 96
  Bond angle restraints: 11992
  Sorted by residual:
  angle pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
        pdb=" C   GLU C 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.20   -8.06 1.52e+00 4.33e-01 2.81e+01
  angle pdb=" N   GLU G 246 "
        pdb=" CA  GLU G 246 "
        pdb=" C   GLU G 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.19   -8.05 1.52e+00 4.33e-01 2.81e+01
  angle pdb=" N   GLU A 246 "
        pdb=" CA  GLU A 246 "
        pdb=" C   GLU A 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.19   -8.05 1.52e+00 4.33e-01 2.80e+01
  angle pdb=" N   GLU E 246 "
        pdb=" CA  GLU E 246 "
        pdb=" C   GLU E 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.18   -8.04 1.52e+00 4.33e-01 2.80e+01
  angle pdb=" CA  ASP F 252 "
        pdb=" CB  ASP F 252 "
        pdb=" CG  ASP F 252 "
      ideal   model   delta    sigma   weight residual
     112.60  117.87   -5.27 1.00e+00 1.00e+00 2.78e+01
  ... (remaining 11987 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.48: 4285
       14.48 -    28.95: 683
       28.95 -    43.42: 196
       43.42 -    57.90: 116
       57.90 -    72.37: 40
  Dihedral angle restraints: 5320
    sinusoidal: 2072
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CA  ALA G 131 "
           pdb=" C   ALA G 131 "
           pdb=" N   TYR G 132 "
           pdb=" CA  TYR G 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.61   30.39     0      5.00e+00 4.00e-02 3.69e+01
  dihedral pdb=" CA  ALA H 131 "
           pdb=" C   ALA H 131 "
           pdb=" N   TYR H 132 "
           pdb=" CA  TYR H 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.65   30.35     0      5.00e+00 4.00e-02 3.68e+01
  dihedral pdb=" CA  ALA A 131 "
           pdb=" C   ALA A 131 "
           pdb=" N   TYR A 132 "
           pdb=" CA  TYR A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.65   30.35     0      5.00e+00 4.00e-02 3.68e+01
  ... (remaining 5317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 508
       0.056 -    0.112: 557
       0.112 -    0.169: 244
       0.169 -    0.225: 96
       0.225 -    0.281: 35
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  THR D 153 "
            pdb=" N   THR D 153 "
            pdb=" C   THR D 153 "
            pdb=" CB  THR D 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  THR B 153 "
            pdb=" N   THR B 153 "
            pdb=" C   THR B 153 "
            pdb=" CB  THR B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  THR H 153 "
            pdb=" N   THR H 153 "
            pdb=" C   THR H 153 "
            pdb=" CB  THR H 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 180 "    0.257 9.50e-02 1.11e+02   1.15e-01 9.10e+00
        pdb=" NE  ARG C 180 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 180 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 180 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 180 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 180 "   -0.256 9.50e-02 1.11e+02   1.15e-01 9.07e+00
        pdb=" NE  ARG D 180 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 180 "    0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 180 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 180 "    0.257 9.50e-02 1.11e+02   1.15e-01 9.06e+00
        pdb=" NE  ARG A 180 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 180 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 180 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 180 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2959
        2.88 -     3.39: 8779
        3.39 -     3.89: 14955
        3.89 -     4.40: 16737
        4.40 -     4.90: 32031
  Nonbonded interactions: 75461
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 138 "
            pdb=" OG1 THR A 141 "
     model   vdw
     2.378 2.440
  nonbonded pdb=" O   GLN C 138 "
            pdb=" OG1 THR C 141 "
     model   vdw
     2.378 2.440
  nonbonded pdb=" O   GLN E 138 "
            pdb=" OG1 THR E 141 "
     model   vdw
     2.378 2.440
  nonbonded pdb=" O   GLN G 138 "
            pdb=" OG1 THR G 141 "
     model   vdw
     2.378 2.440
  nonbonded pdb=" O   GLN H 138 "
            pdb=" OG1 THR H 141 "
     model   vdw
     2.378 2.440
  ... (remaining 75456 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          13.440
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     26.940
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.060
  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:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.059   8824  Z= 0.581
  Angle     :  1.701   8.060  11992  Z= 1.088
  Chirality :  0.101   0.281   1440
  Planarity :  0.013   0.116   1488
  Dihedral  : 18.705  72.373   3216
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 10.32 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.77 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.76 %

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: -4.51 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.005   HIS G 239 
 PHE   0.011   0.004   PHE C 237 
 TYR   0.046   0.008   TYR C 143 
 ARG   0.017   0.005   ARG D 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 171
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (ptmt)
REVERT: A  157 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.5896 (m-80)
REVERT: A  193 LYS cc_start: 0.8767 (tttt) cc_final: 0.8556 (ttmt)
REVERT: A  246 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8706 (pt0)
REVERT: B  157 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5883 (m-80)
REVERT: B  193 LYS cc_start: 0.8772 (tttt) cc_final: 0.8571 (ttmt)
REVERT: B  246 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8720 (pt0)
REVERT: C  129 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8190 (ptmt)
REVERT: C  138 GLN cc_start: 0.8378 (mt0) cc_final: 0.8070 (tt0)
REVERT: C  157 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5502 (m-80)
REVERT: C  246 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8627 (pt0)
REVERT: D  129 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8204 (ptmt)
REVERT: D  157 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5479 (m-80)
REVERT: D  246 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (pt0)
REVERT: E  129 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7939 (pttp)
REVERT: E  246 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (pt0)
REVERT: F  129 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7912 (pttp)
REVERT: F  246 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8443 (pt0)
REVERT: G  124 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8241 (mtpp)
REVERT: G  129 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8057 (ptmt)
REVERT: G  157 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6451 (m-80)
REVERT: G  210 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7750 (ttm)
REVERT: H  124 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8250 (mtpp)
REVERT: H  129 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7981 (ptmt)
REVERT: H  157 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6440 (m-80)
  outliers start: 64
  outliers final: 32
  residues processed: 211
  average time/residue: 0.2381
  time to fit residues: 66.4261
Evaluate side-chains
  195 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 141
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  157 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  157 TYR
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  246 GLU
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  157 TYR
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  157 TYR
Chi-restraints excluded: chain F residue  201 THR
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  157 TYR
Chi-restraints excluded: chain G residue  201 THR
Chi-restraints excluded: chain G residue  210 MET
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  201 THR
Chi-restraints excluded: chain H residue  246 GLU
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0980
   chunk 43 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   overall best weight:    3.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 170 GLN
A 194 GLN
A 242 GLN
A 245 GLN
B 154 ASN
B 170 GLN
B 194 GLN
B 242 GLN
B 245 GLN
C 154 ASN
C 170 GLN
C 242 GLN
D 154 ASN
D 170 GLN
D 242 GLN
E 154 ASN
E 170 GLN
E 242 GLN
E 245 GLN
F 154 ASN
F 170 GLN
F 242 GLN
F 245 GLN
G 148 ASN
G 154 ASN
G 170 GLN
G 242 GLN
H 148 ASN
H 154 ASN
H 170 GLN
H 242 GLN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   8824  Z= 0.253
  Angle     :  0.651   3.746  11992  Z= 0.373
  Chirality :  0.054   0.133   1440
  Planarity :  0.003   0.035   1488
  Dihedral  : 11.930  59.485   1317
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 10.81 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 222 
 PHE   0.013   0.003   PHE B 237 
 TYR   0.027   0.003   TYR D 236 
 ARG   0.002   0.001   ARG G 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 158
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7504 (pttp)
REVERT: A  193 LYS cc_start: 0.8740 (tttt) cc_final: 0.8469 (mttt)
REVERT: A  246 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8044 (pt0)
REVERT: B  193 LYS cc_start: 0.8784 (tttt) cc_final: 0.8545 (ttmt)
REVERT: B  206 GLU cc_start: 0.6153 (pt0) cc_final: 0.5574 (tm-30)
REVERT: B  246 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8045 (pt0)
REVERT: C  129 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8119 (ptmt)
REVERT: C  246 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8231 (pt0)
REVERT: D  129 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8155 (ptmt)
REVERT: D  206 GLU cc_start: 0.6304 (pt0) cc_final: 0.5620 (tm-30)
REVERT: D  246 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (pt0)
REVERT: E  129 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7012 (pttp)
REVERT: E  153 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.7047 (p)
REVERT: E  193 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8706 (mtpt)
REVERT: E  246 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (pt0)
REVERT: F  129 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7035 (pttp)
REVERT: F  153 THR cc_start: 0.7353 (OUTLIER) cc_final: 0.7075 (p)
REVERT: F  193 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8656 (mtpt)
REVERT: F  246 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7985 (pt0)
REVERT: G  129 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7675 (ptmt)
REVERT: G  193 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8685 (mttp)
REVERT: H  129 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7656 (ptmt)
  outliers start: 64
  outliers final: 42
  residues processed: 211
  average time/residue: 0.2124
  time to fit residues: 61.2992
Evaluate side-chains
  194 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 137
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  246 GLU
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  153 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  246 GLU
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 GLN
B 148 ASN
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
C 148 ASN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 148 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 148 ASN
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 222 HIS
F 148 ASN
** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   8824  Z= 0.395
  Angle     :  0.733   6.208  11992  Z= 0.420
  Chirality :  0.057   0.138   1440
  Planarity :  0.004   0.034   1488
  Dihedral  : 11.937  63.969   1292
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.65 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  8.43 %
    Allowed  : 14.29 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.18), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 239 
 PHE   0.015   0.003   PHE C 213 
 TYR   0.028   0.004   TYR D 236 
 ARG   0.002   0.000   ARG A 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 154
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7549 (pttp)
REVERT: A  193 LYS cc_start: 0.8800 (tttt) cc_final: 0.8555 (ttmt)
REVERT: B  193 LYS cc_start: 0.8780 (tttt) cc_final: 0.8537 (ttmt)
REVERT: C  129 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7557 (pttp)
REVERT: C  157 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.5984 (m-80)
REVERT: D  129 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7567 (pttp)
REVERT: D  157 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5906 (m-80)
REVERT: E  193 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8719 (mtpt)
REVERT: E  210 MET cc_start: 0.8568 (ttt) cc_final: 0.8360 (ttm)
REVERT: F  193 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8709 (mtpt)
REVERT: G  129 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7592 (ptmt)
REVERT: G  157 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6166 (m-80)
REVERT: G  192 MET cc_start: 0.8274 (mtt) cc_final: 0.8056 (ttm)
REVERT: G  193 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8826 (mtmt)
REVERT: G  236 TYR cc_start: 0.8887 (t80) cc_final: 0.8642 (t80)
REVERT: H  129 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7580 (ptmt)
REVERT: H  157 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6194 (m-80)
  outliers start: 85
  outliers final: 61
  residues processed: 223
  average time/residue: 0.1994
  time to fit residues: 61.6053
Evaluate side-chains
  208 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 138
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  157 TYR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  157 TYR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  157 TYR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  246 GLU
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 71 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 194 GLN
B 156 ASN
C 156 ASN
D 156 ASN
D 229 GLN
E 156 ASN
F 156 ASN
G 156 ASN
H 156 ASN
** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8824  Z= 0.266
  Angle     :  0.649   5.512  11992  Z= 0.367
  Chirality :  0.053   0.140   1440
  Planarity :  0.003   0.026   1488
  Dihedral  :  9.403  58.332   1274
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 17.26 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 239 
 PHE   0.018   0.002   PHE D 213 
 TYR   0.026   0.003   TYR D 236 
 ARG   0.001   0.000   ARG B 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 147
  time to evaluate  : 0.947 
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: A  129 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7556 (pttp)
REVERT: A  193 LYS cc_start: 0.8773 (tttt) cc_final: 0.8528 (ttmt)
REVERT: A  206 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5429 (tm-30)
REVERT: B  193 LYS cc_start: 0.8790 (tttt) cc_final: 0.8558 (ttmt)
REVERT: C  129 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7657 (pttp)
REVERT: D  129 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7626 (pttp)
REVERT: E  193 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8735 (mtpt)
REVERT: F  193 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8782 (mtpt)
REVERT: F  210 MET cc_start: 0.8672 (ttt) cc_final: 0.8359 (ttm)
REVERT: G  192 MET cc_start: 0.8272 (mtt) cc_final: 0.8060 (ttm)
REVERT: G  193 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8816 (mtmt)
REVERT: G  236 TYR cc_start: 0.8792 (t80) cc_final: 0.8565 (t80)
REVERT: H  190 LEU cc_start: 0.9352 (mp) cc_final: 0.9107 (mt)
  outliers start: 67
  outliers final: 54
  residues processed: 207
  average time/residue: 0.1972
  time to fit residues: 56.5317
Evaluate side-chains
  199 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 141
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8824  Z= 0.395
  Angle     :  0.734   5.805  11992  Z= 0.417
  Chirality :  0.056   0.142   1440
  Planarity :  0.004   0.024   1488
  Dihedral  :  8.878  51.067   1236
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 21.13 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.29 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.021   0.003   PHE D 213 
 TYR   0.027   0.004   TYR D 236 
 ARG   0.001   0.000   ARG F 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 146
  time to evaluate  : 1.092 
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: A  129 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7544 (pttp)
REVERT: A  193 LYS cc_start: 0.8812 (tttt) cc_final: 0.8581 (ttmt)
REVERT: E  193 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8710 (mtpt)
REVERT: F  193 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8728 (mtpt)
REVERT: F  210 MET cc_start: 0.8649 (ttt) cc_final: 0.8308 (ttm)
REVERT: G  193 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8811 (mtmt)
REVERT: G  228 MET cc_start: 0.8135 (ttt) cc_final: 0.7792 (ttt)
REVERT: G  236 TYR cc_start: 0.8861 (t80) cc_final: 0.8642 (t80)
REVERT: H  190 LEU cc_start: 0.9396 (mp) cc_final: 0.9148 (mt)
REVERT: H  236 TYR cc_start: 0.8855 (t80) cc_final: 0.8641 (t80)
  outliers start: 72
  outliers final: 62
  residues processed: 204
  average time/residue: 0.1963
  time to fit residues: 55.8678
Evaluate side-chains
  203 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 140
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  190 LEU
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  138 GLN
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 59 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 83 optimal weight:   30.0000
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8824  Z= 0.291
  Angle     :  0.672   6.185  11992  Z= 0.379
  Chirality :  0.054   0.140   1440
  Planarity :  0.003   0.022   1488
  Dihedral  :  8.194  47.319   1236
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 22.32 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.023   0.003   PHE D 213 
 TYR   0.025   0.003   TYR D 236 
 ARG   0.001   0.000   ARG E 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 74
    poor density    : 144
  time to evaluate  : 1.050 
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: A  129 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7509 (pttp)
REVERT: E  193 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8698 (mtpt)
REVERT: F  193 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8664 (mtpt)
REVERT: F  210 MET cc_start: 0.8648 (ttt) cc_final: 0.8319 (ttm)
REVERT: G  157 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6130 (m-80)
REVERT: G  192 MET cc_start: 0.8327 (mtt) cc_final: 0.8099 (ttm)
REVERT: G  193 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8793 (mtmt)
REVERT: G  228 MET cc_start: 0.8072 (ttt) cc_final: 0.7728 (ttt)
REVERT: H  190 LEU cc_start: 0.9373 (mp) cc_final: 0.9130 (mt)
  outliers start: 74
  outliers final: 66
  residues processed: 205
  average time/residue: 0.1964
  time to fit residues: 56.0308
Evaluate side-chains
  206 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 138
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  231 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  157 TYR
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  138 GLN
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    0.4980
   chunk 46 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8824  Z= 0.236
  Angle     :  0.635   6.292  11992  Z= 0.357
  Chirality :  0.052   0.137   1440
  Planarity :  0.003   0.023   1488
  Dihedral  :  7.567  41.801   1235
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 23.41 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 239 
 PHE   0.025   0.002   PHE D 213 
 TYR   0.033   0.003   TYR H 236 
 ARG   0.001   0.000   ARG F 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 70
    poor density    : 139
  time to evaluate  : 1.027 
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: A  129 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7573 (pttp)
REVERT: C  129 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7667 (pttp)
REVERT: D  129 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7665 (pttp)
REVERT: E  193 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8765 (mtpt)
REVERT: F  193 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8693 (mtpt)
REVERT: F  210 MET cc_start: 0.8635 (ttt) cc_final: 0.8311 (ttm)
REVERT: G  192 MET cc_start: 0.8217 (mtt) cc_final: 0.8015 (ttm)
REVERT: G  228 MET cc_start: 0.7992 (ttt) cc_final: 0.7680 (ttt)
  outliers start: 70
  outliers final: 61
  residues processed: 195
  average time/residue: 0.1958
  time to fit residues: 53.3917
Evaluate side-chains
  201 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 137
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  181 LEU
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  181 LEU
Chi-restraints excluded: chain F residue  231 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  138 GLN
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  138 GLN
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 96 optimal weight:   20.0000
   chunk 87 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
G 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8824  Z= 0.189
  Angle     :  0.597   6.687  11992  Z= 0.334
  Chirality :  0.051   0.133   1440
  Planarity :  0.002   0.022   1488
  Dihedral  :  7.048  36.992   1234
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 23.71 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 239 
 PHE   0.028   0.002   PHE D 213 
 TYR   0.027   0.002   TYR H 236 
 ARG   0.001   0.000   ARG A 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 150
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7662 (pttp)
REVERT: B  206 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5987 (mp0)
REVERT: C  124 LYS cc_start: 0.8515 (ptpp) cc_final: 0.8299 (mttm)
REVERT: C  129 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7638 (pttp)
REVERT: D  124 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8310 (mttm)
REVERT: D  129 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (pttp)
REVERT: E  193 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8740 (mtpt)
REVERT: F  210 MET cc_start: 0.8657 (ttt) cc_final: 0.8353 (ttm)
REVERT: G  193 LYS cc_start: 0.8974 (mttp) cc_final: 0.8712 (mttm)
REVERT: G  228 MET cc_start: 0.7853 (ttt) cc_final: 0.7569 (ttt)
REVERT: H  234 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8374 (m)
  outliers start: 67
  outliers final: 50
  residues processed: 206
  average time/residue: 0.1955
  time to fit residues: 55.8574
Evaluate side-chains
  195 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 140
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  231 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  138 GLN
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  138 GLN
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 40 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 84 optimal weight:   20.0000
   chunk 88 optimal weight:    9.9990
   chunk 93 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 60 optimal weight:    0.2980
   overall best weight:    3.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8824  Z= 0.234
  Angle     :  0.626   6.837  11992  Z= 0.349
  Chirality :  0.052   0.134   1440
  Planarity :  0.003   0.021   1488
  Dihedral  :  7.131  36.974   1234
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 23.91 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 239 
 PHE   0.028   0.002   PHE D 213 
 TYR   0.025   0.003   TYR H 236 
 ARG   0.002   0.000   ARG A 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 145
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7645 (pttp)
REVERT: C  124 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8305 (mttm)
REVERT: C  129 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7653 (pttp)
REVERT: D  129 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7650 (pttp)
REVERT: G  193 LYS cc_start: 0.8924 (mttp) cc_final: 0.8641 (mttm)
REVERT: G  228 MET cc_start: 0.8011 (ttt) cc_final: 0.7680 (ttt)
  outliers start: 61
  outliers final: 56
  residues processed: 195
  average time/residue: 0.1997
  time to fit residues: 54.0826
Evaluate side-chains
  201 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 142
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  231 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  138 GLN
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  138 GLN
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 82 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 87 optimal weight:   20.0000
   chunk 25 optimal weight:    4.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
G 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8824  Z= 0.385
  Angle     :  0.737   7.516  11992  Z= 0.412
  Chirality :  0.055   0.139   1440
  Planarity :  0.004   0.023   1488
  Dihedral  :  8.027  40.423   1234
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 23.81 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.20 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G 239 
 PHE   0.028   0.003   PHE D 213 
 TYR   0.026   0.004   TYR H 236 
 ARG   0.002   0.000   ARG H 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 152
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7637 (pttp)
REVERT: F  210 MET cc_start: 0.8718 (ttt) cc_final: 0.8470 (ttm)
REVERT: G  193 LYS cc_start: 0.9011 (mttp) cc_final: 0.8748 (mttm)
REVERT: G  228 MET cc_start: 0.8210 (ttt) cc_final: 0.7888 (ttt)
  outliers start: 64
  outliers final: 55
  residues processed: 203
  average time/residue: 0.1974
  time to fit residues: 55.4861
Evaluate side-chains
  207 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 151
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  231 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  206 GLU
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  231 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  138 GLN
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain H residue  138 GLN
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.124597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.111439 restraints weight = 15513.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.113745 restraints weight = 6889.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.115384 restraints weight = 4020.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8824  Z= 0.239
  Angle     :  0.657   7.997  11992  Z= 0.363
  Chirality :  0.052   0.138   1440
  Planarity :  0.003   0.021   1488
  Dihedral  :  7.290  36.929   1226
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 24.40 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 239 
 PHE   0.031   0.003   PHE D 213 
 TYR   0.025   0.003   TYR H 236 
 ARG   0.001   0.000   ARG F 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2131.10 seconds
wall clock time: 39 minutes 54.65 seconds (2394.65 seconds total)