Starting phenix.real_space_refine
on Tue Feb 11 19:33:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvf_14176/02_2025/7qvf_14176.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4164      2.51       5
     N    1038      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6516
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "E"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "F"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Time building chain proxies: 6.30, per 1000 atoms: 0.97
  Number of scatterers: 6516
  At special positions: 0
  Unit cell: (175.95, 204.7, 36.8, 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      42     16.00
     O    1272      8.00
     N    1038      7.00
     C    4164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.05
    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=2.05
    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=2.05
    Simple disulfide: pdb=" SG  CYS F 214 " - pdb=" SG  CYS F 253 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 1.53
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 34 sheets defined
      0.0% alpha, 60.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126
      removed outlier: 6.737A  pdb=" N   ASP A 122 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP B 122 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.823A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 139
      removed outlier: 6.647A  pdb=" N   GLN A 138 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   VAL B 137 " --> pdb=" O   GLN C 138 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 144
    Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 153
    Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160
    Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 176
      removed outlier: 6.867A  pdb=" N   ASN A 164 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE B 165 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR A 166 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ASN B 164 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE C 165 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   THR B 166 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.447A  pdb=" N   ILE A 184 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE B 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE A 186 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE B 184 " --> pdb=" O   THR C 185 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   ILE C 187 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE B 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 192 through 193
      removed outlier: 6.589A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 196 through 198
      removed outlier: 6.419A  pdb=" N   TYR A 197 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TYR B 197 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 201 through 206
    Processing sheet with id=AB5, first strand: chain 'A' and resid 209 through 213
    Processing sheet with id=AB6, first strand: chain 'A' and resid 216 through 219
    Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 228
      removed outlier: 5.995A  pdb=" N   ASN A 223 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LEU B 226 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL A 225 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   MET B 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   MET A 227 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 231 through 253
      removed outlier: 5.752A  pdb=" N   THR A 231 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   THR B 234 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   THR A 233 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   TYR B 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   THR A 235 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   GLY B 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE A 237 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   SER B 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   HIS A 239 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   GLN B 242 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLU A 241 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   SER B 244 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE A 243 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   GLU B 246 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A 245 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   TYR B 248 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ARG A 247 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   TYR B 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.750A  pdb=" N   GLN A 249 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASP B 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 9.138A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   THR B 231 " --> pdb=" O   VAL C 232 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   THR C 234 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR B 233 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   TYR C 236 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR B 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   GLY C 238 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   PHE B 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   SER C 240 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   HIS B 239 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   GLN C 242 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLU B 241 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER C 244 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE B 243 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   GLU C 246 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLN B 245 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   TYR C 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ARG B 247 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   TYR C 250 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 8.781A  pdb=" N   GLN B 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP C 252 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 121 through 126
      removed outlier: 6.737A  pdb=" N   ASP D 122 " --> pdb=" O   ILE E 121 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ILE D 121 " --> pdb=" O   ASP F 122 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   LYS F 124 " --> pdb=" O   ILE D 121 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   VAL D 123 " --> pdb=" O   LYS F 124 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ILE F 126 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   TYR D 125 " --> pdb=" O   ILE F 126 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 130
      removed outlier: 6.510A  pdb=" N   LYS D 129 " --> pdb=" O   SER F 130 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134
      removed outlier: 6.893A  pdb=" N   VAL D 133 " --> pdb=" O   SER E 134 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 137 through 139
      removed outlier: 8.555A  pdb=" N   VAL D 137 " --> pdb=" O   GLN E 138 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   GLN F 138 " --> pdb=" O   VAL D 137 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 142 through 144
      removed outlier: 6.148A  pdb=" N   ILE D 142 " --> pdb=" O   TYR F 143 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 147 through 153
      removed outlier: 6.182A  pdb=" N   THR D 147 " --> pdb=" O   ASN F 148 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   LEU F 150 " --> pdb=" O   THR D 147 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   THR D 149 " --> pdb=" O   LEU F 150 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ILE F 152 " --> pdb=" O   THR D 149 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ASN D 151 " --> pdb=" O   ILE F 152 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 156 through 160
      removed outlier: 6.511A  pdb=" N   TYR D 157 " --> pdb=" O   TYR F 158 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   VAL F 160 " --> pdb=" O   TYR D 157 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER D 159 " --> pdb=" O   VAL F 160 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 163 through 176
      removed outlier: 6.897A  pdb=" N   ASN D 164 " --> pdb=" O   GLU E 163 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE E 165 " --> pdb=" O   ASN D 164 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   THR D 166 " --> pdb=" O   ILE E 165 " (cutoff:3.500A)
      removed outlier: 9.401A  pdb=" N   GLU D 163 " --> pdb=" O   ASN F 164 " (cutoff:3.500A)
      removed outlier: 10.227A  pdb=" N   THR F 166 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE D 165 " --> pdb=" O   THR F 166 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   GLN F 168 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA D 167 " --> pdb=" O   GLN F 168 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   GLN F 170 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL D 169 " --> pdb=" O   GLN F 170 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   SER F 172 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   PHE D 171 " --> pdb=" O   SER F 172 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   THR F 174 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LYS D 173 " --> pdb=" O   THR F 174 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ILE F 176 " --> pdb=" O   LYS D 173 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL D 175 " --> pdb=" O   ILE F 176 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 180 through 181
      removed outlier: 6.520A  pdb=" N   ARG D 180 " --> pdb=" O   LEU F 181 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'E' and resid 184 through 187
      removed outlier: 6.521A  pdb=" N   ILE D 184 " --> pdb=" O   THR E 185 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   ILE E 187 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE D 186 " --> pdb=" O   ILE E 187 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 193
      removed outlier: 6.577A  pdb=" N   MET D 192 " --> pdb=" O   LYS E 193 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 196 through 198
      removed outlier: 6.400A  pdb=" N   TYR D 197 " --> pdb=" O   THR E 198 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 201 through 206
      removed outlier: 6.314A  pdb=" N   VAL D 202 " --> pdb=" O   ILE F 203 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   GLU F 205 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ALA D 204 " --> pdb=" O   GLU F 205 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 209 through 213
      removed outlier: 6.394A  pdb=" N   TYR D 209 " --> pdb=" O   MET F 210 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   ASP F 212 " --> pdb=" O   TYR D 209 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   TYR D 211 " --> pdb=" O   ASP F 212 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 216 through 219
      removed outlier: 6.275A  pdb=" N   LEU D 216 " --> pdb=" O   ILE F 217 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   ILE F 219 " --> pdb=" O   LEU D 216 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   SER D 218 " --> pdb=" O   ILE F 219 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'E' and resid 222 through 228
      removed outlier: 6.230A  pdb=" N   ASN D 223 " --> pdb=" O   ILE E 224 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   LEU E 226 " --> pdb=" O   ASN D 223 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL D 225 " --> pdb=" O   LEU E 226 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   MET E 228 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   MET D 227 " --> pdb=" O   MET E 228 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASN F 223 " --> pdb=" O   HIS D 222 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'E' and resid 231 through 253
      removed outlier: 5.687A  pdb=" N   THR D 231 " --> pdb=" O   VAL E 232 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   THR E 234 " --> pdb=" O   THR D 231 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR D 233 " --> pdb=" O   THR E 234 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   TYR E 236 " --> pdb=" O   THR D 233 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR D 235 " --> pdb=" O   TYR E 236 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   GLY E 238 " --> pdb=" O   THR D 235 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   PHE D 237 " --> pdb=" O   GLY E 238 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   SER E 240 " --> pdb=" O   PHE D 237 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   HIS D 239 " --> pdb=" O   SER E 240 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   GLN E 242 " --> pdb=" O   HIS D 239 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLU D 241 " --> pdb=" O   GLN E 242 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER E 244 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE D 243 " --> pdb=" O   SER E 244 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLU E 246 " --> pdb=" O   ILE D 243 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLN D 245 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   TYR E 248 " --> pdb=" O   GLN D 245 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ARG D 247 " --> pdb=" O   TYR E 248 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   TYR E 250 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   GLN D 249 " --> pdb=" O   TYR E 250 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ASP E 252 " --> pdb=" O   GLN D 249 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   VAL D 251 " --> pdb=" O   ASP E 252 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   VAL D 232 " --> pdb=" O   THR F 231 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL F 251 " --> pdb=" O   TYR D 250 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ASP D 252 " --> pdb=" O   VAL F 251 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   CYS F 253 " --> pdb=" O   ASP D 252 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    453 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: 2.01

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1812
        1.33 -     1.45: 1086
        1.45 -     1.57: 3654
        1.57 -     1.69: 0
        1.69 -     1.82: 72
  Bond restraints: 6624
  Sorted by residual:
  bond pdb=" CZ  ARG C 247 "
       pdb=" NH2 ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.42e+00
  bond pdb=" CZ  ARG E 247 "
       pdb=" NH2 ARG E 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.22e+00
  bond pdb=" CZ  ARG D 247 "
       pdb=" NH2 ARG D 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.69e+00
  bond pdb=" CZ  ARG B 247 "
       pdb=" NH2 ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.56e+00
  bond pdb=" CZ  ARG D 180 "
       pdb=" NH2 ARG D 180 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.86e+00
  ... (remaining 6619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 6904
        2.31 -     4.62: 1744
        4.62 -     6.93: 320
        6.93 -     9.25: 34
        9.25 -    11.56: 4
  Bond angle restraints: 9006
  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
     108.55  120.11  -11.56 1.62e+00 3.81e-01 5.09e+01
  angle pdb=" N   GLU E 246 "
        pdb=" CA  GLU E 246 "
        pdb=" C   GLU E 246 "
      ideal   model   delta    sigma   weight residual
     108.55  120.09  -11.54 1.62e+00 3.81e-01 5.08e+01
  angle pdb=" CB  ASN A 183 "
        pdb=" CG  ASN A 183 "
        pdb=" ND2 ASN A 183 "
      ideal   model   delta    sigma   weight residual
     116.40  106.14   10.26 1.50e+00 4.44e-01 4.68e+01
  angle pdb=" CB  ASN F 183 "
        pdb=" CG  ASN F 183 "
        pdb=" ND2 ASN F 183 "
      ideal   model   delta    sigma   weight residual
     116.40  106.15   10.25 1.50e+00 4.44e-01 4.67e+01
  angle pdb=" CA  ASP B 136 "
        pdb=" CB  ASP B 136 "
        pdb=" CG  ASP B 136 "
      ideal   model   delta    sigma   weight residual
     112.60  119.34   -6.74 1.00e+00 1.00e+00 4.54e+01
  ... (remaining 9001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3626
       17.73 -    35.45: 268
       35.45 -    53.18: 54
       53.18 -    70.91: 14
       70.91 -    88.63: 28
  Dihedral angle restraints: 3990
    sinusoidal: 1554
      harmonic: 2436
  Sorted by residual:
  dihedral pdb=" CA  ILE C 152 "
           pdb=" C   ILE C 152 "
           pdb=" N   THR C 153 "
           pdb=" CA  THR C 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.39   28.61     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ILE B 152 "
           pdb=" C   ILE B 152 "
           pdb=" N   THR B 153 "
           pdb=" CA  THR B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.42   28.58     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ILE E 152 "
           pdb=" C   ILE E 152 "
           pdb=" N   THR E 153 "
           pdb=" CA  THR E 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.42   28.58     0      5.00e+00 4.00e-02 3.27e+01
  ... (remaining 3987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 695
       0.108 -    0.216: 314
       0.216 -    0.324: 55
       0.324 -    0.432: 12
       0.432 -    0.540: 10
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  GLN E 138 "
            pdb=" N   GLN E 138 "
            pdb=" C   GLN E 138 "
            pdb=" CB  GLN E 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.29e+00
  chirality pdb=" CA  GLN C 138 "
            pdb=" N   GLN C 138 "
            pdb=" C   GLN C 138 "
            pdb=" CB  GLN C 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.28e+00
  chirality pdb=" CA  GLN D 194 "
            pdb=" N   GLN D 194 "
            pdb=" C   GLN D 194 "
            pdb=" CB  GLN D 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.05e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "   -0.138 2.00e-02 2.50e+03   7.16e-02 1.03e+02
        pdb=" CG  TYR A 143 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "    0.065 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "    0.058 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "    0.026 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 143 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 143 "   -0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 143 "    0.138 2.00e-02 2.50e+03   7.15e-02 1.02e+02
        pdb=" CG  TYR F 143 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 143 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 143 "   -0.058 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 143 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 143 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 143 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR F 143 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 250 "    0.096 2.00e-02 2.50e+03   5.64e-02 6.36e+01
        pdb=" CG  TYR F 250 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 250 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 250 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 250 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 250 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 250 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR F 250 "    0.092 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 3273
        3.00 -     3.47: 5692
        3.47 -     3.95: 10879
        3.95 -     4.42: 11354
        4.42 -     4.90: 21068
  Nonbonded interactions: 52266
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 134 "
            pdb=" OD1 ASP D 136 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" OG  SER B 134 "
            pdb=" OD1 ASP B 136 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" OE2 GLU D 241 "
            pdb=" OG  SER E 120 "
     model   vdw
     2.528 3.040
  nonbonded pdb=" OE2 GLU B 241 "
            pdb=" OG  SER C 120 "
     model   vdw
     2.529 3.040
  nonbonded pdb=" OG  SER D 120 "
            pdb=" OE2 GLU F 241 "
     model   vdw
     2.542 3.040
  ... (remaining 52261 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             6.210
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.220
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
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      :  0.012   0.047   6624  Z= 0.795
  Angle     :  2.103  11.556   9006  Z= 1.357
  Chirality :  0.125   0.540   1086
  Planarity :  0.013   0.095   1116
  Dihedral  : 15.513  88.633   2412
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.76 %
    Favored  : 94.71 %
  Cbeta Deviations :  2.82 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.24), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.18), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.005   HIS B 239 
 PHE   0.032   0.010   PHE F 171 
 TYR   0.138   0.025   TYR A 143 
 ARG   0.002   0.000   ARG D 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 335
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LEU cc_start: 0.8674 (tp) cc_final: 0.8445 (tp)
REVERT: A  168 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7842 (tp40)
REVERT: A  247 ARG cc_start: 0.7785 (tpt90) cc_final: 0.7518 (tpm170)
REVERT: A  250 TYR cc_start: 0.7455 (t80) cc_final: 0.6875 (p90)
REVERT: B  134 SER cc_start: 0.8964 (t) cc_final: 0.8589 (t)
REVERT: B  228 MET cc_start: 0.8416 (ttp) cc_final: 0.7375 (ttm)
REVERT: C  173 LYS cc_start: 0.7530 (tttt) cc_final: 0.7277 (tppt)
REVERT: C  228 MET cc_start: 0.8256 (ttp) cc_final: 0.7422 (ttm)
REVERT: C  245 GLN cc_start: 0.7761 (mt0) cc_final: 0.7125 (mt0)
REVERT: C  247 ARG cc_start: 0.7087 (tpt90) cc_final: 0.6398 (pmt-80)
REVERT: D  245 GLN cc_start: 0.8042 (mt0) cc_final: 0.7493 (mt0)
REVERT: E  173 LYS cc_start: 0.7448 (tttt) cc_final: 0.7154 (tppt)
REVERT: E  199 VAL cc_start: 0.8627 (t) cc_final: 0.8293 (t)
REVERT: E  247 ARG cc_start: 0.7274 (tpt90) cc_final: 0.6703 (pmt-80)
REVERT: F  150 LEU cc_start: 0.8754 (tp) cc_final: 0.8551 (tp)
REVERT: F  168 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7625 (tp40)
REVERT: F  228 MET cc_start: 0.8199 (ttp) cc_final: 0.7996 (ttm)
REVERT: F  244 SER cc_start: 0.8054 (t) cc_final: 0.7761 (t)
REVERT: F  247 ARG cc_start: 0.7734 (tpt90) cc_final: 0.7283 (tpm170)
REVERT: F  250 TYR cc_start: 0.7496 (t80) cc_final: 0.6904 (p90)
  outliers start: 4
  outliers final: 1
  residues processed: 335
  average time/residue: 0.1992
  time to fit residues: 84.7492
Evaluate side-chains
  230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.0270
   chunk 59 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    2.1644

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

Flipped N/Q/H residues before XYZ refinement:
A 168 GLN
A 242 GLN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
B 245 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
D 242 GLN
D 249 GLN
** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 249 GLN
F 245 GLN
F 249 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.119187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.109344 restraints weight = 15607.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.111617 restraints weight = 6389.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.112976 restraints weight = 3434.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6624  Z= 0.266
  Angle     :  0.771   6.110   9006  Z= 0.423
  Chirality :  0.059   0.197   1086
  Planarity :  0.003   0.035   1116
  Dihedral  :  7.200  25.383    896
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.76 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 239 
 PHE   0.011   0.002   PHE B 237 
 TYR   0.021   0.002   TYR E 143 
 ARG   0.003   0.001   ARG B 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  122 ASP cc_start: 0.6942 (t0) cc_final: 0.6551 (t70)
REVERT: A  191 ASP cc_start: 0.8164 (t0) cc_final: 0.7910 (t0)
REVERT: A  239 HIS cc_start: 0.7568 (t70) cc_final: 0.7075 (t70)
REVERT: A  247 ARG cc_start: 0.8554 (tpt90) cc_final: 0.7023 (tpm170)
REVERT: A  250 TYR cc_start: 0.8349 (t80) cc_final: 0.6491 (p90)
REVERT: B  122 ASP cc_start: 0.8082 (t0) cc_final: 0.7137 (t70)
REVERT: B  129 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8806 (ttmm)
REVERT: B  134 SER cc_start: 0.9192 (t) cc_final: 0.8925 (t)
REVERT: B  136 ASP cc_start: 0.8352 (p0) cc_final: 0.7982 (p0)
REVERT: B  150 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8280 (mt)
REVERT: B  161 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8211 (tp30)
REVERT: B  168 GLN cc_start: 0.8857 (tp40) cc_final: 0.8631 (tp40)
REVERT: B  180 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7135 (mtt90)
REVERT: B  190 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9102 (mt)
REVERT: B  192 MET cc_start: 0.7942 (mmm) cc_final: 0.6894 (mmm)
REVERT: B  205 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6484 (mm-30)
REVERT: B  210 MET cc_start: 0.7728 (mtp) cc_final: 0.7285 (mtp)
REVERT: B  241 GLU cc_start: 0.7958 (tt0) cc_final: 0.7734 (tt0)
REVERT: C  122 ASP cc_start: 0.8215 (t0) cc_final: 0.7470 (t0)
REVERT: C  161 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7979 (tp30)
REVERT: C  168 GLN cc_start: 0.8731 (tp40) cc_final: 0.8128 (tp40)
REVERT: C  173 LYS cc_start: 0.7260 (tttt) cc_final: 0.6450 (tppt)
REVERT: C  191 ASP cc_start: 0.8226 (t0) cc_final: 0.7997 (t0)
REVERT: C  247 ARG cc_start: 0.7738 (tpt90) cc_final: 0.6320 (pmt-80)
REVERT: D  122 ASP cc_start: 0.7785 (t0) cc_final: 0.7575 (t0)
REVERT: D  124 LYS cc_start: 0.8533 (mttp) cc_final: 0.8181 (mttp)
REVERT: D  161 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8128 (tp30)
REVERT: D  170 GLN cc_start: 0.8985 (mt0) cc_final: 0.8702 (mt0)
REVERT: D  180 ARG cc_start: 0.7788 (mtm110) cc_final: 0.6995 (mtt90)
REVERT: D  190 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9088 (mt)
REVERT: D  192 MET cc_start: 0.7900 (mmm) cc_final: 0.7609 (mmm)
REVERT: D  220 LYS cc_start: 0.9250 (tttp) cc_final: 0.9004 (tttp)
REVERT: D  223 ASN cc_start: 0.8762 (t0) cc_final: 0.8456 (t0)
REVERT: E  124 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8080 (mtmm)
REVERT: E  161 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7953 (mm-30)
REVERT: E  173 LYS cc_start: 0.7048 (tttt) cc_final: 0.6336 (tppt)
REVERT: E  180 ARG cc_start: 0.4041 (OUTLIER) cc_final: 0.2589 (mmp-170)
REVERT: E  205 GLU cc_start: 0.4149 (pm20) cc_final: 0.3815 (pm20)
REVERT: E  247 ARG cc_start: 0.7590 (tpt90) cc_final: 0.6130 (pmt-80)
REVERT: F  143 TYR cc_start: 0.8402 (t80) cc_final: 0.8075 (t80)
REVERT: F  192 MET cc_start: 0.7603 (mmm) cc_final: 0.7299 (mmm)
REVERT: F  207 MET cc_start: 0.5591 (ppp) cc_final: 0.5372 (ppp)
REVERT: F  241 GLU cc_start: 0.7482 (tt0) cc_final: 0.7077 (tt0)
REVERT: F  250 TYR cc_start: 0.8321 (t80) cc_final: 0.6366 (p90)
  outliers start: 23
  outliers final: 7
  residues processed: 246
  average time/residue: 0.2128
  time to fit residues: 66.4437
Evaluate side-chains
  226 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 215
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  232 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 249 GLN
F 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.114199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.104892 restraints weight = 16372.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.106909 restraints weight = 7059.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.108267 restraints weight = 3929.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.5379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   6624  Z= 0.453
  Angle     :  0.791   6.800   9006  Z= 0.433
  Chirality :  0.059   0.171   1086
  Planarity :  0.004   0.032   1116
  Dihedral  :  6.883  25.180    894
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.93 %
    Favored  : 79.63 %
  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: -2.38 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 239 
 PHE   0.012   0.003   PHE B 237 
 TYR   0.021   0.002   TYR D 143 
 ARG   0.004   0.001   ARG A 180 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 223
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 GLN cc_start: 0.8882 (tp40) cc_final: 0.7091 (tm-30)
REVERT: A  181 LEU cc_start: 0.8887 (mt) cc_final: 0.8599 (mt)
REVERT: A  246 GLU cc_start: 0.7065 (tt0) cc_final: 0.6785 (tt0)
REVERT: B  134 SER cc_start: 0.9350 (t) cc_final: 0.9007 (t)
REVERT: B  136 ASP cc_start: 0.8189 (p0) cc_final: 0.7930 (p0)
REVERT: B  150 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: B  161 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8142 (tp30)
REVERT: B  168 GLN cc_start: 0.9417 (tp40) cc_final: 0.8161 (tp40)
REVERT: B  180 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7140 (mpt180)
REVERT: B  194 GLN cc_start: 0.8669 (pt0) cc_final: 0.8251 (pt0)
REVERT: C  181 LEU cc_start: 0.8373 (mt) cc_final: 0.7917 (pt)
REVERT: C  192 MET cc_start: 0.8059 (mmm) cc_final: 0.6951 (pmm)
REVERT: C  241 GLU cc_start: 0.4390 (pm20) cc_final: 0.4169 (pm20)
REVERT: C  245 GLN cc_start: 0.8379 (mt0) cc_final: 0.7891 (mt0)
REVERT: C  247 ARG cc_start: 0.7791 (tpt90) cc_final: 0.6463 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8016 (tp30)
REVERT: D  180 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7127 (mtt90)
REVERT: D  192 MET cc_start: 0.7984 (mmm) cc_final: 0.7640 (mmm)
REVERT: D  220 LYS cc_start: 0.9402 (tttp) cc_final: 0.8988 (tppt)
REVERT: D  223 ASN cc_start: 0.8960 (t0) cc_final: 0.8700 (t0)
REVERT: D  245 GLN cc_start: 0.9056 (mt0) cc_final: 0.8430 (mt0)
REVERT: E  247 ARG cc_start: 0.7926 (tpt90) cc_final: 0.5702 (pmt-80)
REVERT: F  168 GLN cc_start: 0.8876 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: F  196 ASP cc_start: 0.8691 (t0) cc_final: 0.8475 (t0)
REVERT: F  241 GLU cc_start: 0.7551 (tt0) cc_final: 0.7312 (tt0)
  outliers start: 26
  outliers final: 15
  residues processed: 234
  average time/residue: 0.2060
  time to fit residues: 61.6146
Evaluate side-chains
  215 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  218 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain F residue  190 LEU
Chi-restraints excluded: chain F residue  210 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 27 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.117925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.108703 restraints weight = 15836.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.110825 restraints weight = 6493.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.112198 restraints weight = 3521.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.5711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6624  Z= 0.224
  Angle     :  0.674   6.525   9006  Z= 0.366
  Chirality :  0.056   0.173   1086
  Planarity :  0.003   0.030   1116
  Dihedral  :  6.507  26.149    894
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.25 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.012   0.002   PHE B 237 
 TYR   0.018   0.001   TYR E 143 
 ARG   0.003   0.000   ARG F 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 213
  time to evaluate  : 0.798 
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: 0.9087 (ttmm) cc_final: 0.8797 (ttmm)
REVERT: A  161 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8438 (mt-10)
REVERT: A  178 LYS cc_start: 0.7459 (tttt) cc_final: 0.7232 (tttt)
REVERT: A  245 GLN cc_start: 0.9050 (mt0) cc_final: 0.8680 (mt0)
REVERT: B  124 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8620 (mtmm)
REVERT: B  134 SER cc_start: 0.9298 (t) cc_final: 0.8956 (t)
REVERT: B  136 ASP cc_start: 0.8255 (p0) cc_final: 0.8004 (p0)
REVERT: B  150 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: B  161 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8227 (tt0)
REVERT: B  168 GLN cc_start: 0.9435 (tp40) cc_final: 0.8654 (tp40)
REVERT: B  180 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7103 (mpt180)
REVERT: B  194 GLN cc_start: 0.8656 (pt0) cc_final: 0.7691 (tm-30)
REVERT: B  205 GLU cc_start: 0.6584 (mm-30) cc_final: 0.5826 (mm-30)
REVERT: B  228 MET cc_start: 0.8787 (ttp) cc_final: 0.7611 (ttm)
REVERT: B  229 GLN cc_start: 0.7923 (mp10) cc_final: 0.6674 (mp10)
REVERT: C  192 MET cc_start: 0.7942 (mmm) cc_final: 0.6855 (ppp)
REVERT: C  245 GLN cc_start: 0.7862 (mt0) cc_final: 0.7346 (mt0)
REVERT: C  247 ARG cc_start: 0.7743 (tpt90) cc_final: 0.6339 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7660 (tp30)
REVERT: D  180 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7037 (mpt180)
REVERT: D  192 MET cc_start: 0.7921 (mmm) cc_final: 0.7720 (mmm)
REVERT: D  220 LYS cc_start: 0.9363 (tttp) cc_final: 0.8913 (tppt)
REVERT: D  227 MET cc_start: 0.8632 (mtm) cc_final: 0.8377 (mtp)
REVERT: E  120 SER cc_start: 0.8040 (p) cc_final: 0.7004 (p)
REVERT: E  124 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8392 (mtmm)
REVERT: E  192 MET cc_start: 0.7785 (mmp) cc_final: 0.6677 (ppp)
REVERT: E  247 ARG cc_start: 0.7645 (tpt90) cc_final: 0.5506 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8617 (tt0) cc_final: 0.7631 (tt0)
REVERT: F  168 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: F  181 LEU cc_start: 0.8774 (mt) cc_final: 0.8545 (mt)
REVERT: F  241 GLU cc_start: 0.7587 (tt0) cc_final: 0.7213 (tt0)
  outliers start: 15
  outliers final: 6
  residues processed: 216
  average time/residue: 0.2106
  time to fit residues: 57.6477
Evaluate side-chains
  206 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 199
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain F residue  210 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 GLN
C 249 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.112988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.103600 restraints weight = 16302.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.105720 restraints weight = 6768.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.107027 restraints weight = 3655.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   6624  Z= 0.409
  Angle     :  0.759  10.081   9006  Z= 0.406
  Chirality :  0.057   0.161   1086
  Planarity :  0.004   0.035   1116
  Dihedral  :  6.558  27.810    894
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.31 %
    Favored  : 77.51 %
  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: -2.54 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS E 239 
 PHE   0.012   0.002   PHE D 213 
 TYR   0.020   0.002   TYR D 143 
 ARG   0.004   0.001   ARG A 180 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8818 (ttmm)
REVERT: A  161 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7807 (mt-10)
REVERT: A  163 GLU cc_start: 0.7964 (mp0) cc_final: 0.7155 (mp0)
REVERT: B  124 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8267 (mttp)
REVERT: B  134 SER cc_start: 0.9273 (t) cc_final: 0.8935 (t)
REVERT: B  136 ASP cc_start: 0.8329 (p0) cc_final: 0.8100 (p0)
REVERT: B  150 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8529 (mt)
REVERT: B  161 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8082 (tp30)
REVERT: B  168 GLN cc_start: 0.9525 (tp40) cc_final: 0.8172 (tp40)
REVERT: B  180 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7153 (mpt180)
REVERT: B  194 GLN cc_start: 0.8608 (pt0) cc_final: 0.8279 (pt0)
REVERT: B  196 ASP cc_start: 0.8450 (t0) cc_final: 0.8241 (t0)
REVERT: B  205 GLU cc_start: 0.6570 (mm-30) cc_final: 0.5683 (mm-30)
REVERT: C  124 LYS cc_start: 0.8146 (mptp) cc_final: 0.7559 (mmtm)
REVERT: C  213 PHE cc_start: 0.8061 (t80) cc_final: 0.7821 (t80)
REVERT: C  229 GLN cc_start: 0.7907 (mp10) cc_final: 0.7549 (mp10)
REVERT: C  245 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7719 (mt0)
REVERT: C  247 ARG cc_start: 0.7738 (tpt90) cc_final: 0.6413 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8033 (tp30)
REVERT: D  180 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7098 (mpt180)
REVERT: D  192 MET cc_start: 0.7887 (mmm) cc_final: 0.7511 (mmm)
REVERT: D  194 GLN cc_start: 0.8646 (pt0) cc_final: 0.8239 (pt0)
REVERT: D  220 LYS cc_start: 0.9351 (tttp) cc_final: 0.8902 (tppt)
REVERT: E  120 SER cc_start: 0.8249 (p) cc_final: 0.7212 (p)
REVERT: E  124 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8368 (mtmm)
REVERT: E  171 PHE cc_start: 0.8404 (t80) cc_final: 0.8064 (t80)
REVERT: E  216 LEU cc_start: 0.9178 (pt) cc_final: 0.7813 (mt)
REVERT: E  247 ARG cc_start: 0.7773 (tpt90) cc_final: 0.5678 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8898 (tt0) cc_final: 0.8416 (mt-10)
REVERT: F  168 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: F  190 LEU cc_start: 0.9340 (mm) cc_final: 0.9062 (mt)
REVERT: F  193 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4149 (pttm)
REVERT: F  241 GLU cc_start: 0.7568 (tt0) cc_final: 0.7242 (tt0)
  outliers start: 24
  outliers final: 12
  residues processed: 216
  average time/residue: 0.2161
  time to fit residues: 59.2858
Evaluate side-chains
  210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 195
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  210 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0980
   chunk 43 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 145 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.115595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.106322 restraints weight = 15711.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.108501 restraints weight = 6558.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.109828 restraints weight = 3521.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.6242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6624  Z= 0.255
  Angle     :  0.685   8.425   9006  Z= 0.366
  Chirality :  0.055   0.155   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.288  27.438    894
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.77 %
    Favored  : 76.72 %
  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: -2.51 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 239 
 PHE   0.012   0.002   PHE B 237 
 TYR   0.020   0.002   TYR B 143 
 ARG   0.002   0.000   ARG F 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 205
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8855 (ttmm)
REVERT: A  161 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7893 (mt-10)
REVERT: A  163 GLU cc_start: 0.8119 (mp0) cc_final: 0.7199 (mp0)
REVERT: A  168 GLN cc_start: 0.8770 (tp40) cc_final: 0.7438 (tm-30)
REVERT: B  124 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8081 (mttp)
REVERT: B  134 SER cc_start: 0.9223 (t) cc_final: 0.8877 (t)
REVERT: B  136 ASP cc_start: 0.8292 (p0) cc_final: 0.8077 (p0)
REVERT: B  150 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8524 (mt)
REVERT: B  161 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8214 (tt0)
REVERT: B  180 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7161 (mpt180)
REVERT: B  194 GLN cc_start: 0.8598 (pt0) cc_final: 0.8318 (pt0)
REVERT: B  196 ASP cc_start: 0.8514 (t0) cc_final: 0.8288 (t0)
REVERT: B  205 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5855 (mm-30)
REVERT: B  228 MET cc_start: 0.8929 (ttp) cc_final: 0.7567 (ttm)
REVERT: B  229 GLN cc_start: 0.8167 (mp10) cc_final: 0.6761 (mp10)
REVERT: C  124 LYS cc_start: 0.8203 (mttp) cc_final: 0.7621 (mmtm)
REVERT: C  192 MET cc_start: 0.7855 (mmm) cc_final: 0.6941 (ppp)
REVERT: C  213 PHE cc_start: 0.8079 (t80) cc_final: 0.7830 (t80)
REVERT: C  229 GLN cc_start: 0.8004 (mp10) cc_final: 0.7582 (mp10)
REVERT: C  236 TYR cc_start: 0.8533 (t80) cc_final: 0.8308 (t80)
REVERT: C  245 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7566 (mt0)
REVERT: C  247 ARG cc_start: 0.7627 (tpt90) cc_final: 0.6369 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8280 (tttp)
REVERT: D  161 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8253 (tp30)
REVERT: D  180 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7138 (mpt180)
REVERT: D  192 MET cc_start: 0.7904 (mmm) cc_final: 0.7501 (mmm)
REVERT: D  210 MET cc_start: 0.8147 (tpp) cc_final: 0.7602 (tpp)
REVERT: D  220 LYS cc_start: 0.9355 (tttp) cc_final: 0.8918 (tppt)
REVERT: E  120 SER cc_start: 0.8309 (p) cc_final: 0.7376 (p)
REVERT: E  124 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8572 (mtmm)
REVERT: E  171 PHE cc_start: 0.8429 (t80) cc_final: 0.8028 (t80)
REVERT: E  182 ASN cc_start: 0.8583 (t0) cc_final: 0.8324 (t0)
REVERT: E  216 LEU cc_start: 0.9119 (pt) cc_final: 0.7852 (mt)
REVERT: E  247 ARG cc_start: 0.7626 (tpt90) cc_final: 0.5731 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8875 (tt0) cc_final: 0.8540 (mt-10)
REVERT: F  168 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8514 (tm-30)
REVERT: F  241 GLU cc_start: 0.7560 (tt0) cc_final: 0.7225 (tt0)
REVERT: F  252 ASP cc_start: 0.8212 (t0) cc_final: 0.7862 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 214
  average time/residue: 0.2113
  time to fit residues: 57.1555
Evaluate side-chains
  208 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 194
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.113447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.104144 restraints weight = 16077.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.106329 restraints weight = 6731.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.107680 restraints weight = 3607.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.6410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6624  Z= 0.396
  Angle     :  0.748   7.621   9006  Z= 0.399
  Chirality :  0.056   0.158   1086
  Planarity :  0.003   0.037   1116
  Dihedral  :  6.357  27.992    894
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.84 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.002   HIS E 239 
 PHE   0.011   0.002   PHE E 237 
 TYR   0.022   0.002   TYR E 236 
 ARG   0.004   0.000   ARG A 180 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8894 (ttmm)
REVERT: A  161 GLU cc_start: 0.8680 (mt-10) cc_final: 0.7801 (mt-10)
REVERT: A  163 GLU cc_start: 0.7969 (mp0) cc_final: 0.7237 (mp0)
REVERT: A  180 ARG cc_start: 0.5166 (OUTLIER) cc_final: 0.4818 (pmt-80)
REVERT: A  193 LYS cc_start: 0.4656 (OUTLIER) cc_final: 0.3445 (pttm)
REVERT: B  124 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8102 (mtmm)
REVERT: B  134 SER cc_start: 0.9275 (t) cc_final: 0.8923 (t)
REVERT: B  150 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8536 (mt)
REVERT: B  161 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7999 (tp30)
REVERT: B  163 GLU cc_start: 0.6908 (pm20) cc_final: 0.6676 (pm20)
REVERT: B  180 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7169 (mpt180)
REVERT: B  194 GLN cc_start: 0.8630 (pt0) cc_final: 0.7796 (tm-30)
REVERT: B  205 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6578 (mm-30)
REVERT: B  228 MET cc_start: 0.8909 (ttp) cc_final: 0.7580 (ttm)
REVERT: B  229 GLN cc_start: 0.8280 (mp10) cc_final: 0.6642 (mp10)
REVERT: C  191 ASP cc_start: 0.8111 (t0) cc_final: 0.7860 (t0)
REVERT: C  213 PHE cc_start: 0.8030 (t80) cc_final: 0.7806 (t80)
REVERT: C  229 GLN cc_start: 0.8447 (mp10) cc_final: 0.7817 (mp10)
REVERT: C  245 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7841 (mt0)
REVERT: C  247 ARG cc_start: 0.7590 (tpt90) cc_final: 0.6373 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8312 (tttp)
REVERT: D  161 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8192 (tp30)
REVERT: D  180 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7108 (mpt180)
REVERT: D  192 MET cc_start: 0.7925 (mmm) cc_final: 0.7503 (mmm)
REVERT: D  220 LYS cc_start: 0.9394 (tttp) cc_final: 0.8852 (tppt)
REVERT: E  171 PHE cc_start: 0.8482 (t80) cc_final: 0.8110 (t80)
REVERT: E  180 ARG cc_start: 0.4631 (OUTLIER) cc_final: 0.3507 (mmp-170)
REVERT: E  182 ASN cc_start: 0.8622 (t0) cc_final: 0.8358 (t0)
REVERT: E  216 LEU cc_start: 0.9094 (pt) cc_final: 0.7764 (mt)
REVERT: E  229 GLN cc_start: 0.8449 (mp10) cc_final: 0.8153 (mp10)
REVERT: E  247 ARG cc_start: 0.7710 (tpt90) cc_final: 0.6339 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8627 (mt-10)
REVERT: F  168 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8630 (tm-30)
REVERT: F  180 ARG cc_start: 0.5275 (OUTLIER) cc_final: 0.2993 (pmt-80)
REVERT: F  193 LYS cc_start: 0.4986 (OUTLIER) cc_final: 0.3660 (pttm)
REVERT: F  241 GLU cc_start: 0.7575 (tt0) cc_final: 0.7280 (tt0)
REVERT: F  252 ASP cc_start: 0.8290 (t0) cc_final: 0.7899 (t0)
  outliers start: 35
  outliers final: 21
  residues processed: 214
  average time/residue: 0.2151
  time to fit residues: 58.5609
Evaluate side-chains
  219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue  130 SER
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  181 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  161 GLU
Chi-restraints excluded: chain F residue  180 ARG
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  218 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.117504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.108393 restraints weight = 15614.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.110503 restraints weight = 6507.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.111895 restraints weight = 3528.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.6628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6624  Z= 0.226
  Angle     :  0.719  12.958   9006  Z= 0.375
  Chirality :  0.055   0.168   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.186  27.274    894
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.49 %
    Favored  : 73.81 %
  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: -2.52 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS E 239 
 PHE   0.013   0.001   PHE D 237 
 TYR   0.021   0.002   TYR D 236 
 ARG   0.002   0.000   ARG E 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8395 (tttp)
REVERT: A  161 GLU cc_start: 0.8680 (mt-10) cc_final: 0.7680 (mt-10)
REVERT: A  163 GLU cc_start: 0.8052 (mp0) cc_final: 0.7278 (mp0)
REVERT: A  168 GLN cc_start: 0.8793 (tp40) cc_final: 0.7453 (tm-30)
REVERT: A  193 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.3522 (pttm)
REVERT: B  124 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8024 (mtmm)
REVERT: B  134 SER cc_start: 0.9240 (t) cc_final: 0.8898 (t)
REVERT: B  144 LEU cc_start: 0.8352 (tt) cc_final: 0.7930 (tp)
REVERT: B  145 ASN cc_start: 0.7849 (m-40) cc_final: 0.7093 (t0)
REVERT: B  150 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8542 (mt)
REVERT: B  161 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7974 (tp30)
REVERT: B  163 GLU cc_start: 0.6884 (pm20) cc_final: 0.6589 (pm20)
REVERT: B  180 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7142 (mpt180)
REVERT: B  194 GLN cc_start: 0.8577 (pt0) cc_final: 0.7808 (tm-30)
REVERT: B  205 GLU cc_start: 0.6226 (mm-30) cc_final: 0.5794 (mm-30)
REVERT: C  120 SER cc_start: 0.8157 (p) cc_final: 0.7681 (p)
REVERT: C  192 MET cc_start: 0.7337 (mmm) cc_final: 0.6361 (ppp)
REVERT: C  210 MET cc_start: 0.3341 (OUTLIER) cc_final: 0.2516 (pmm)
REVERT: C  213 PHE cc_start: 0.8063 (t80) cc_final: 0.7840 (t80)
REVERT: C  229 GLN cc_start: 0.8274 (mp10) cc_final: 0.7428 (mp10)
REVERT: C  236 TYR cc_start: 0.8498 (t80) cc_final: 0.8253 (t80)
REVERT: C  245 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7748 (mt0)
REVERT: C  247 ARG cc_start: 0.7615 (tpt90) cc_final: 0.6393 (pmt-80)
REVERT: D  120 SER cc_start: 0.7759 (p) cc_final: 0.7075 (p)
REVERT: D  129 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8286 (tttp)
REVERT: D  145 ASN cc_start: 0.7054 (m-40) cc_final: 0.6489 (t0)
REVERT: D  180 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7146 (mpt180)
REVERT: D  192 MET cc_start: 0.7947 (mmm) cc_final: 0.7681 (mmm)
REVERT: D  194 GLN cc_start: 0.8440 (pt0) cc_final: 0.7859 (tm-30)
REVERT: D  220 LYS cc_start: 0.9382 (tttp) cc_final: 0.8945 (ttmt)
REVERT: D  222 HIS cc_start: 0.8760 (m-70) cc_final: 0.8460 (m90)
REVERT: D  228 MET cc_start: 0.7950 (ttt) cc_final: 0.7528 (ttt)
REVERT: D  229 GLN cc_start: 0.7860 (mp10) cc_final: 0.7190 (mp10)
REVERT: E  120 SER cc_start: 0.7449 (t) cc_final: 0.6444 (p)
REVERT: E  145 ASN cc_start: 0.7169 (m-40) cc_final: 0.6728 (t0)
REVERT: E  182 ASN cc_start: 0.8646 (t0) cc_final: 0.8362 (t0)
REVERT: E  192 MET cc_start: 0.7619 (mmp) cc_final: 0.7136 (ppp)
REVERT: E  216 LEU cc_start: 0.9045 (pt) cc_final: 0.7727 (mt)
REVERT: E  247 ARG cc_start: 0.7515 (tpt90) cc_final: 0.5700 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8631 (mt-10)
REVERT: F  168 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8576 (tm-30)
REVERT: F  205 GLU cc_start: 0.8285 (mp0) cc_final: 0.7973 (mp0)
REVERT: F  241 GLU cc_start: 0.7550 (tt0) cc_final: 0.6815 (tt0)
REVERT: F  252 ASP cc_start: 0.8150 (t0) cc_final: 0.7752 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 218
  average time/residue: 0.2095
  time to fit residues: 58.0947
Evaluate side-chains
  218 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 194
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  161 GLU
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
B 242 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.118024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.108977 restraints weight = 15711.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.111126 restraints weight = 6583.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.112466 restraints weight = 3515.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.6765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6624  Z= 0.239
  Angle     :  0.722  10.355   9006  Z= 0.375
  Chirality :  0.055   0.164   1086
  Planarity :  0.003   0.033   1116
  Dihedral  :  6.069  26.535    894
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.62 %
    Favored  : 73.81 %
  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: -2.53 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.001   HIS E 239 
 PHE   0.012   0.001   PHE D 237 
 TYR   0.026   0.002   TYR E 236 
 ARG   0.002   0.000   ARG F 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8398 (tttm)
REVERT: A  161 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: A  163 GLU cc_start: 0.8056 (mp0) cc_final: 0.7561 (mp0)
REVERT: A  168 GLN cc_start: 0.8804 (tp40) cc_final: 0.8182 (tm-30)
REVERT: A  180 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.3094 (pmt-80)
REVERT: A  193 LYS cc_start: 0.4778 (OUTLIER) cc_final: 0.3554 (pttm)
REVERT: B  124 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8065 (mtmm)
REVERT: B  134 SER cc_start: 0.9246 (t) cc_final: 0.8904 (t)
REVERT: B  145 ASN cc_start: 0.7699 (m-40) cc_final: 0.7193 (t0)
REVERT: B  150 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8655 (mt)
REVERT: B  161 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8004 (tp30)
REVERT: B  163 GLU cc_start: 0.6930 (pm20) cc_final: 0.6609 (pm20)
REVERT: B  180 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7167 (mpt180)
REVERT: B  194 GLN cc_start: 0.8604 (pt0) cc_final: 0.7829 (tm-30)
REVERT: B  205 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5416 (mm-30)
REVERT: B  228 MET cc_start: 0.8740 (ttp) cc_final: 0.7671 (ttm)
REVERT: B  229 GLN cc_start: 0.8241 (mp10) cc_final: 0.6933 (mp10)
REVERT: C  191 ASP cc_start: 0.8254 (t0) cc_final: 0.8006 (t0)
REVERT: C  192 MET cc_start: 0.7218 (mmm) cc_final: 0.6222 (ppp)
REVERT: C  210 MET cc_start: 0.3485 (OUTLIER) cc_final: 0.2665 (pmm)
REVERT: C  213 PHE cc_start: 0.8042 (t80) cc_final: 0.7804 (t80)
REVERT: C  229 GLN cc_start: 0.8197 (mp10) cc_final: 0.7626 (mp10)
REVERT: C  236 TYR cc_start: 0.8515 (t80) cc_final: 0.8262 (t80)
REVERT: C  247 ARG cc_start: 0.7557 (tpt90) cc_final: 0.6373 (pmt-80)
REVERT: D  120 SER cc_start: 0.7745 (p) cc_final: 0.7056 (p)
REVERT: D  129 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8275 (tttp)
REVERT: D  145 ASN cc_start: 0.7441 (m-40) cc_final: 0.6950 (t0)
REVERT: D  180 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7151 (mpt180)
REVERT: D  192 MET cc_start: 0.7908 (mmm) cc_final: 0.7638 (mmm)
REVERT: D  194 GLN cc_start: 0.8478 (pt0) cc_final: 0.7821 (tm-30)
REVERT: D  220 LYS cc_start: 0.9394 (tttp) cc_final: 0.9031 (tppt)
REVERT: E  120 SER cc_start: 0.7015 (t) cc_final: 0.6178 (p)
REVERT: E  124 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8109 (mptt)
REVERT: E  145 ASN cc_start: 0.7266 (m-40) cc_final: 0.6729 (t0)
REVERT: E  182 ASN cc_start: 0.8658 (t0) cc_final: 0.8379 (t0)
REVERT: E  192 MET cc_start: 0.7677 (mmp) cc_final: 0.6944 (ppp)
REVERT: E  216 LEU cc_start: 0.9079 (pt) cc_final: 0.7785 (mt)
REVERT: E  247 ARG cc_start: 0.7558 (tpt90) cc_final: 0.5691 (pmt-80)
REVERT: F  168 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8607 (tm-30)
REVERT: F  193 LYS cc_start: 0.4892 (OUTLIER) cc_final: 0.3621 (pttm)
REVERT: F  205 GLU cc_start: 0.8159 (mp0) cc_final: 0.7813 (mp0)
REVERT: F  241 GLU cc_start: 0.7552 (tt0) cc_final: 0.6810 (tt0)
REVERT: F  246 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.2467 (pm20)
REVERT: F  252 ASP cc_start: 0.8114 (t0) cc_final: 0.7739 (t0)
  outliers start: 27
  outliers final: 15
  residues processed: 214
  average time/residue: 0.2049
  time to fit residues: 55.6165
Evaluate side-chains
  215 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 193
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Chi-restraints excluded: chain F residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0670
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.4126

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

Flipped N/Q/H residues before XYZ refinement:
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.118892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.109773 restraints weight = 15689.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.111945 restraints weight = 6556.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.113331 restraints weight = 3508.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.6860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6624  Z= 0.223
  Angle     :  0.710  10.367   9006  Z= 0.371
  Chirality :  0.055   0.167   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.019  25.843    894
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.28 %
    Favored  : 73.41 %
  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: -2.46 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.002   HIS E 239 
 PHE   0.011   0.001   PHE D 237 
 TYR   0.021   0.002   TYR E 236 
 ARG   0.002   0.000   ARG F 247 

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8423 (tttp)
REVERT: A  161 GLU cc_start: 0.8705 (mt-10) cc_final: 0.7731 (mt-10)
REVERT: A  163 GLU cc_start: 0.8063 (mp0) cc_final: 0.7346 (mp0)
REVERT: A  193 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.3580 (pttm)
REVERT: A  245 GLN cc_start: 0.9047 (mt0) cc_final: 0.8546 (mt0)
REVERT: B  124 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8051 (mtmm)
REVERT: B  134 SER cc_start: 0.9237 (t) cc_final: 0.8892 (t)
REVERT: B  145 ASN cc_start: 0.7698 (m-40) cc_final: 0.7238 (t0)
REVERT: B  150 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8674 (mt)
REVERT: B  156 ASN cc_start: 0.9171 (m-40) cc_final: 0.8935 (m-40)
REVERT: B  161 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7996 (tp30)
REVERT: B  163 GLU cc_start: 0.6969 (pm20) cc_final: 0.6584 (pm20)
REVERT: B  180 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7175 (mpt180)
REVERT: B  194 GLN cc_start: 0.8587 (pt0) cc_final: 0.7821 (tm-30)
REVERT: B  205 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6225 (mm-30)
REVERT: B  227 MET cc_start: 0.8820 (mtm) cc_final: 0.8580 (mtm)
REVERT: B  228 MET cc_start: 0.8651 (ttp) cc_final: 0.7624 (ttm)
REVERT: B  229 GLN cc_start: 0.8125 (mp10) cc_final: 0.6930 (mp10)
REVERT: C  191 ASP cc_start: 0.8283 (t0) cc_final: 0.8035 (t0)
REVERT: C  192 MET cc_start: 0.7143 (mmm) cc_final: 0.6225 (ppp)
REVERT: C  210 MET cc_start: 0.3665 (OUTLIER) cc_final: 0.2975 (pmm)
REVERT: C  213 PHE cc_start: 0.8050 (t80) cc_final: 0.7814 (t80)
REVERT: C  229 GLN cc_start: 0.8168 (mp10) cc_final: 0.7609 (mp10)
REVERT: C  236 TYR cc_start: 0.8505 (t80) cc_final: 0.8263 (t80)
REVERT: C  247 ARG cc_start: 0.7567 (tpt90) cc_final: 0.6358 (pmt-80)
REVERT: D  120 SER cc_start: 0.7881 (p) cc_final: 0.7150 (p)
REVERT: D  129 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8269 (tttp)
REVERT: D  145 ASN cc_start: 0.7403 (m-40) cc_final: 0.6877 (t0)
REVERT: D  180 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7137 (mpt180)
REVERT: D  192 MET cc_start: 0.7916 (mmm) cc_final: 0.7638 (mmm)
REVERT: D  194 GLN cc_start: 0.8354 (pt0) cc_final: 0.7757 (tm-30)
REVERT: D  220 LYS cc_start: 0.9460 (tttp) cc_final: 0.9016 (tppt)
REVERT: E  120 SER cc_start: 0.6900 (t) cc_final: 0.6060 (p)
REVERT: E  124 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8058 (mptt)
REVERT: E  145 ASN cc_start: 0.7140 (m-40) cc_final: 0.6795 (t0)
REVERT: E  182 ASN cc_start: 0.8660 (t0) cc_final: 0.8377 (t0)
REVERT: E  192 MET cc_start: 0.7735 (mmp) cc_final: 0.6745 (ppp)
REVERT: E  216 LEU cc_start: 0.8977 (pt) cc_final: 0.7797 (mt)
REVERT: E  229 GLN cc_start: 0.7971 (mp10) cc_final: 0.7159 (mp10)
REVERT: E  247 ARG cc_start: 0.7484 (tpt90) cc_final: 0.5666 (pmt-80)
REVERT: F  168 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: F  193 LYS cc_start: 0.4926 (OUTLIER) cc_final: 0.3665 (pttm)
REVERT: F  205 GLU cc_start: 0.8001 (mp0) cc_final: 0.7740 (mp0)
REVERT: F  239 HIS cc_start: 0.7772 (t70) cc_final: 0.7365 (t-170)
REVERT: F  241 GLU cc_start: 0.7590 (tt0) cc_final: 0.6822 (tt0)
REVERT: F  252 ASP cc_start: 0.8115 (t0) cc_final: 0.7706 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 221
  average time/residue: 0.2045
  time to fit residues: 57.5510
Evaluate side-chains
  220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0070
   chunk 20 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.4004

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

Flipped N/Q/H residues before XYZ refinement:
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.119765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.110610 restraints weight = 15636.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.112818 restraints weight = 6445.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.114228 restraints weight = 3427.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.6953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6624  Z= 0.220
  Angle     :  0.706  11.842   9006  Z= 0.368
  Chirality :  0.054   0.152   1086
  Planarity :  0.003   0.032   1116
  Dihedral  :  5.916  25.173    894
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.54 %
    Favored  : 73.15 %
  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: -2.44 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.002   HIS E 239 
 PHE   0.016   0.001   PHE F 171 
 TYR   0.018   0.002   TYR E 236 
 ARG   0.002   0.000   ARG F 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2595.98 seconds
wall clock time: 47 minutes 35.82 seconds (2855.82 seconds total)