Starting phenix.real_space_refine
on Thu Jun  5 17:46:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvf_14176/06_2025/7qvf_14176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvf_14176/06_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_14176/06_2025/7qvf_14176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvf_14176/06_2025/7qvf_14176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvf_14176/06_2025/7qvf_14176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvf_14176/06_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-5710/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: 5.86, per 1000 atoms: 0.90
  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: 1.32
  Conformation dependent library (CDL) restraints added in 956.7 milliseconds
  

  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: 0.98
  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: 1.77

  Time building geometry restraints manager: 1.63 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:             34.830
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.780
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.970
-------------------------------------------------------------------------------
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   6630  Z= 0.697
  Angle     :  2.102  11.556   9018  Z= 1.356
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08156 (  151)
  hydrogen bonds       : angle       7.92598 (  453)
  SS BOND              : bond        0.01562 (    6)
  SS BOND              : angle       1.52695 (   12)
  covalent geometry    : bond        0.01209 ( 6624)
  covalent geometry    : angle       2.10293 ( 9006)

*********************** 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  : 0.743 
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: 0.1919
  time to fit residues: 81.8402
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  : 0.706 
-------------------------------------------------------------------------------
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 = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.109345 restraints weight = 15607.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.111615 restraints weight = 6388.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.112973 restraints weight = 3431.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
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   6630  Z= 0.181
  Angle     :  0.771   6.110   9018  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02924 (  151)
  hydrogen bonds       : angle       5.48642 (  453)
  SS BOND              : bond        0.00159 (    6)
  SS BOND              : angle       0.42817 (   12)
  covalent geometry    : bond        0.00407 ( 6624)
  covalent geometry    : angle       0.77147 ( 9006)

*********************** 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  : 0.782 
Fit side-chains
REVERT: A  122 ASP cc_start: 0.6941 (t0) cc_final: 0.6551 (t70)
REVERT: A  191 ASP cc_start: 0.8165 (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: 0.8350 (t80) cc_final: 0.6491 (p90)
REVERT: B  122 ASP cc_start: 0.8082 (t0) cc_final: 0.7136 (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: 0.7983 (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: 0.8858 (tp40) cc_final: 0.8632 (tp40)
REVERT: B  180 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7135 (mtt90)
REVERT: B  190 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9101 (mt)
REVERT: B  192 MET cc_start: 0.7946 (mmm) cc_final: 0.6898 (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: 0.7259 (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: 0.7737 (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: 0.8180 (mttp)
REVERT: D  161 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8127 (tp30)
REVERT: D  170 GLN cc_start: 0.8985 (mt0) cc_final: 0.8702 (mt0)
REVERT: D  180 ARG cc_start: 0.7787 (mtm110) cc_final: 0.6995 (mtt90)
REVERT: D  190 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9087 (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: 0.8763 (t0) cc_final: 0.8457 (t0)
REVERT: E  124 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8079 (mtmm)
REVERT: E  161 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7953 (mm-30)
REVERT: E  173 LYS cc_start: 0.7047 (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: 0.4148 (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: 0.5590 (ppp) cc_final: 0.5372 (ppp)
REVERT: F  241 GLU cc_start: 0.7481 (tt0) cc_final: 0.7076 (tt0)
REVERT: F  250 TYR cc_start: 0.8321 (t80) cc_final: 0.6365 (p90)
  outliers start: 23
  outliers final: 7
  residues processed: 246
  average time/residue: 0.2138
  time to fit residues: 67.2422
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  : 0.812 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.9186

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.118161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.108681 restraints weight = 16111.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.110839 restraints weight = 6825.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.112219 restraints weight = 3704.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6630  Z= 0.202
  Angle     :  0.715   5.450   9018  Z= 0.392
  Chirality :  0.057   0.166   1086
  Planarity :  0.003   0.025   1116
  Dihedral  :  6.663  24.050    894
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.93 %
    Favored  : 80.56 %
  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: -2.25 (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   0.018   0.002   TYR D 143 
 ARG   0.004   0.001   ARG F 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  151)
  hydrogen bonds       : angle       5.04063 (  453)
  SS BOND              : bond        0.00231 (    6)
  SS BOND              : angle       0.22081 (   12)
  covalent geometry    : bond        0.00472 ( 6624)
  covalent geometry    : angle       0.71590 ( 9006)

*********************** 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
  239 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ASP cc_start: 0.7301 (t0) cc_final: 0.6830 (t70)
REVERT: A  163 GLU cc_start: 0.7475 (mp0) cc_final: 0.7203 (mp0)
REVERT: A  168 GLN cc_start: 0.8762 (tp40) cc_final: 0.7223 (tm-30)
REVERT: A  246 GLU cc_start: 0.6999 (tt0) cc_final: 0.6661 (tt0)
REVERT: B  124 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8333 (mtmm)
REVERT: B  134 SER cc_start: 0.9268 (t) cc_final: 0.8965 (t)
REVERT: B  136 ASP cc_start: 0.8200 (p0) cc_final: 0.7932 (p0)
REVERT: B  150 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8489 (mt)
REVERT: B  161 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8173 (tp30)
REVERT: B  168 GLN cc_start: 0.9344 (tp40) cc_final: 0.8313 (tp40)
REVERT: B  180 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7173 (mpt180)
REVERT: B  194 GLN cc_start: 0.8615 (pt0) cc_final: 0.7767 (tm-30)
REVERT: B  205 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6338 (mm-30)
REVERT: B  228 MET cc_start: 0.8787 (ttp) cc_final: 0.7864 (ttp)
REVERT: C  124 LYS cc_start: 0.8163 (mptp) cc_final: 0.7850 (mmtm)
REVERT: C  181 LEU cc_start: 0.8322 (mt) cc_final: 0.7880 (pt)
REVERT: C  192 MET cc_start: 0.8021 (mmm) cc_final: 0.6714 (ppp)
REVERT: C  229 GLN cc_start: 0.8426 (mp10) cc_final: 0.8153 (mp10)
REVERT: C  245 GLN cc_start: 0.8156 (mt0) cc_final: 0.7862 (mt0)
REVERT: C  247 ARG cc_start: 0.7673 (tpt90) cc_final: 0.6376 (pmt-80)
REVERT: D  122 ASP cc_start: 0.7881 (t0) cc_final: 0.7576 (t0)
REVERT: D  161 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7700 (tp30)
REVERT: D  180 ARG cc_start: 0.7811 (mtm110) cc_final: 0.6995 (mtt90)
REVERT: D  191 ASP cc_start: 0.8388 (t0) cc_final: 0.8159 (t0)
REVERT: D  192 MET cc_start: 0.7934 (mmm) cc_final: 0.7326 (mmt)
REVERT: D  196 ASP cc_start: 0.8697 (t0) cc_final: 0.8442 (t0)
REVERT: D  220 LYS cc_start: 0.9368 (tttp) cc_final: 0.9007 (ttmt)
REVERT: E  124 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8423 (mttp)
REVERT: E  161 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7782 (tp30)
REVERT: E  207 MET cc_start: 0.6197 (tpt) cc_final: 0.5898 (tpt)
REVERT: E  247 ARG cc_start: 0.7673 (tpt90) cc_final: 0.5535 (pmt-80)
REVERT: F  181 LEU cc_start: 0.8769 (mt) cc_final: 0.8525 (mt)
REVERT: F  196 ASP cc_start: 0.8673 (t0) cc_final: 0.8458 (t0)
REVERT: F  241 GLU cc_start: 0.7475 (tt0) cc_final: 0.7234 (tt0)
REVERT: F  250 TYR cc_start: 0.8600 (t80) cc_final: 0.6628 (p90)
  outliers start: 19
  outliers final: 11
  residues processed: 225
  average time/residue: 0.2472
  time to fit residues: 70.9765
Evaluate side-chains
  211 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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  190 LEU
Chi-restraints excluded: chain C residue  218 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue  216 LEU
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:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0670
   overall best weight:    2.9524

-------------------------------------------------------------------------------
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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 GLN
** E 145 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.116594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.107361 restraints weight = 16129.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.109543 restraints weight = 6636.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.110833 restraints weight = 3544.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.5592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6630  Z= 0.210
  Angle     :  0.701   7.493   9018  Z= 0.382
  Chirality :  0.056   0.167   1086
  Planarity :  0.003   0.031   1116
  Dihedral  :  6.519  24.745    894
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.67 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 239 
 PHE   0.011   0.002   PHE B 237 
 TYR   0.020   0.002   TYR E 143 
 ARG   0.003   0.000   ARG F 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02572 (  151)
  hydrogen bonds       : angle       4.97658 (  453)
  SS BOND              : bond        0.00096 (    6)
  SS BOND              : angle       0.27844 (   12)
  covalent geometry    : bond        0.00482 ( 6624)
  covalent geometry    : angle       0.70118 ( 9006)

*********************** 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
  241 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 215
  time to evaluate  : 1.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7276 (tttt) cc_final: 0.7052 (tttt)
REVERT: A  181 LEU cc_start: 0.8823 (mt) cc_final: 0.8562 (mt)
REVERT: B  124 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8425 (mtmm)
REVERT: B  134 SER cc_start: 0.9208 (t) cc_final: 0.8885 (t)
REVERT: B  136 ASP cc_start: 0.8291 (p0) cc_final: 0.8024 (p0)
REVERT: B  150 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: B  161 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8168 (tp30)
REVERT: B  168 GLN cc_start: 0.9392 (tp40) cc_final: 0.8356 (tp40)
REVERT: B  180 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7079 (mpt180)
REVERT: B  194 GLN cc_start: 0.8659 (pt0) cc_final: 0.7731 (tm-30)
REVERT: C  192 MET cc_start: 0.8043 (mmm) cc_final: 0.6882 (ppp)
REVERT: C  228 MET cc_start: 0.8541 (ttp) cc_final: 0.7616 (ptm)
REVERT: C  229 GLN cc_start: 0.7968 (mp10) cc_final: 0.6977 (mp10)
REVERT: C  245 GLN cc_start: 0.7865 (mt0) cc_final: 0.7453 (mt0)
REVERT: C  247 ARG cc_start: 0.7730 (tpt90) cc_final: 0.6357 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7703 (tp30)
REVERT: D  163 GLU cc_start: 0.7298 (mp0) cc_final: 0.7033 (mp0)
REVERT: D  180 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7087 (mtt90)
REVERT: D  191 ASP cc_start: 0.8336 (t0) cc_final: 0.8106 (t0)
REVERT: D  220 LYS cc_start: 0.9340 (tttp) cc_final: 0.8880 (tppt)
REVERT: D  227 MET cc_start: 0.8815 (mtm) cc_final: 0.8466 (mtp)
REVERT: E  120 SER cc_start: 0.8356 (p) cc_final: 0.7313 (p)
REVERT: E  161 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7684 (tp30)
REVERT: E  192 MET cc_start: 0.7795 (mmp) cc_final: 0.6681 (ppp)
REVERT: E  247 ARG cc_start: 0.7735 (tpt90) cc_final: 0.5514 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8684 (tt0) cc_final: 0.7477 (tt0)
REVERT: F  168 GLN cc_start: 0.8966 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: F  181 LEU cc_start: 0.8851 (mt) cc_final: 0.8624 (mt)
REVERT: F  190 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8966 (mt)
REVERT: F  194 GLN cc_start: 0.8185 (mp10) cc_final: 0.7500 (pp30)
REVERT: F  196 ASP cc_start: 0.8599 (t0) cc_final: 0.8379 (t0)
REVERT: F  239 HIS cc_start: 0.7917 (t70) cc_final: 0.7430 (t-170)
REVERT: F  241 GLU cc_start: 0.7543 (tt0) cc_final: 0.7234 (tt0)
  outliers start: 26
  outliers final: 18
  residues processed: 226
  average time/residue: 0.3146
  time to fit residues: 92.3937
Evaluate side-chains
  219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
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 B residue  216 LEU
Chi-restraints excluded: chain B residue  246 GLU
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  224 ILE
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  190 LEU
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:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 145 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.115357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.106260 restraints weight = 16166.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.108344 restraints weight = 6910.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.109632 restraints weight = 3779.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6630  Z= 0.248
  Angle     :  0.734   7.147   9018  Z= 0.396
  Chirality :  0.056   0.167   1086
  Planarity :  0.003   0.036   1116
  Dihedral  :  6.522  26.794    894
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.92 %
    Favored  : 77.78 %
  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 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS C 239 
 PHE   0.011   0.002   PHE D 237 
 TYR   0.021   0.002   TYR D 143 
 ARG   0.003   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02605 (  151)
  hydrogen bonds       : angle       4.88688 (  453)
  SS BOND              : bond        0.00107 (    6)
  SS BOND              : angle       0.32237 (   12)
  covalent geometry    : bond        0.00573 ( 6624)
  covalent geometry    : angle       0.73453 ( 9006)

*********************** 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
  231 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8489 (mt-10)
REVERT: A  168 GLN cc_start: 0.8859 (tp40) cc_final: 0.7788 (tm-30)
REVERT: A  181 LEU cc_start: 0.8889 (mt) cc_final: 0.8660 (mt)
REVERT: B  124 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8542 (mttp)
REVERT: B  134 SER cc_start: 0.9363 (t) cc_final: 0.9026 (t)
REVERT: B  150 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: B  161 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8262 (tp30)
REVERT: B  168 GLN cc_start: 0.9523 (tp40) cc_final: 0.8315 (tp40)
REVERT: B  180 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7212 (mpt180)
REVERT: B  194 GLN cc_start: 0.8736 (pt0) cc_final: 0.8417 (pt0)
REVERT: B  228 MET cc_start: 0.8807 (ttp) cc_final: 0.7579 (ttm)
REVERT: B  229 GLN cc_start: 0.8405 (mp10) cc_final: 0.7095 (mp10)
REVERT: C  124 LYS cc_start: 0.8250 (mttp) cc_final: 0.7957 (mmtm)
REVERT: C  213 PHE cc_start: 0.8016 (t80) cc_final: 0.7804 (t80)
REVERT: C  228 MET cc_start: 0.8609 (ttp) cc_final: 0.7586 (ptm)
REVERT: C  229 GLN cc_start: 0.8156 (mp10) cc_final: 0.7668 (mp10)
REVERT: C  245 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7793 (mt0)
REVERT: C  247 ARG cc_start: 0.7704 (tpt90) cc_final: 0.6488 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7899 (tp30)
REVERT: D  180 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7035 (mtt90)
REVERT: D  220 LYS cc_start: 0.9412 (tttp) cc_final: 0.8996 (tppt)
REVERT: D  227 MET cc_start: 0.8579 (mtm) cc_final: 0.8272 (mtp)
REVERT: E  120 SER cc_start: 0.8364 (p) cc_final: 0.7437 (p)
REVERT: E  171 PHE cc_start: 0.8504 (t80) cc_final: 0.8187 (t80)
REVERT: E  192 MET cc_start: 0.7745 (mmp) cc_final: 0.6505 (ppp)
REVERT: E  247 ARG cc_start: 0.7785 (tpt90) cc_final: 0.5631 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8604 (tt0) cc_final: 0.8259 (mt-10)
REVERT: F  190 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8979 (mt)
REVERT: F  194 GLN cc_start: 0.8371 (mp10) cc_final: 0.7502 (pp30)
REVERT: F  241 GLU cc_start: 0.7439 (tt0) cc_final: 0.7153 (tt0)
  outliers start: 25
  outliers final: 14
  residues processed: 216
  average time/residue: 0.2743
  time to fit residues: 75.6048
Evaluate side-chains
  211 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
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 B residue  246 GLU
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  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  190 LEU
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:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.114230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.105283 restraints weight = 15897.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.107373 restraints weight = 6805.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.108646 restraints weight = 3707.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.6170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6630  Z= 0.248
  Angle     :  0.745  11.716   9018  Z= 0.395
  Chirality :  0.056   0.166   1086
  Planarity :  0.003   0.038   1116
  Dihedral  :  6.447  27.320    894
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.84 %
    Favored  : 76.59 %
  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 : -1.90 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 239 
 PHE   0.010   0.002   PHE B 237 
 TYR   0.022   0.002   TYR F 143 
 ARG   0.004   0.000   ARG F 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02620 (  151)
  hydrogen bonds       : angle       4.92199 (  453)
  SS BOND              : bond        0.00074 (    6)
  SS BOND              : angle       0.36059 (   12)
  covalent geometry    : bond        0.00570 ( 6624)
  covalent geometry    : angle       0.74534 ( 9006)

*********************** 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
  232 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 1.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 GLU cc_start: 0.7901 (mp0) cc_final: 0.7075 (mp0)
REVERT: A  168 GLN cc_start: 0.8831 (tp40) cc_final: 0.7504 (tm-30)
REVERT: A  181 LEU cc_start: 0.8861 (mt) cc_final: 0.8554 (mt)
REVERT: B  134 SER cc_start: 0.9293 (t) cc_final: 0.8995 (t)
REVERT: B  150 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8500 (mt)
REVERT: B  161 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8106 (tp30)
REVERT: B  180 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7212 (mpt180)
REVERT: B  194 GLN cc_start: 0.8688 (pt0) cc_final: 0.8373 (pt0)
REVERT: B  205 GLU cc_start: 0.6945 (mm-30) cc_final: 0.5378 (mm-30)
REVERT: C  124 LYS cc_start: 0.8278 (mttp) cc_final: 0.8048 (mmtm)
REVERT: C  192 MET cc_start: 0.7778 (mmm) cc_final: 0.6918 (ppp)
REVERT: C  205 GLU cc_start: 0.3005 (pm20) cc_final: 0.2728 (pm20)
REVERT: C  213 PHE cc_start: 0.8025 (t80) cc_final: 0.7795 (t80)
REVERT: C  229 GLN cc_start: 0.8125 (mp10) cc_final: 0.7446 (mp10)
REVERT: C  245 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7674 (mt0)
REVERT: C  247 ARG cc_start: 0.7630 (tpt90) cc_final: 0.6465 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7941 (tp30)
REVERT: D  163 GLU cc_start: 0.7554 (mp0) cc_final: 0.7109 (mp0)
REVERT: D  180 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7260 (mpt180)
REVERT: D  220 LYS cc_start: 0.9400 (tttp) cc_final: 0.8979 (tppt)
REVERT: D  227 MET cc_start: 0.8643 (mtm) cc_final: 0.8328 (mtp)
REVERT: E  120 SER cc_start: 0.8350 (p) cc_final: 0.7457 (p)
REVERT: E  171 PHE cc_start: 0.8539 (t80) cc_final: 0.8174 (t80)
REVERT: E  182 ASN cc_start: 0.8524 (t0) cc_final: 0.8272 (t0)
REVERT: E  192 MET cc_start: 0.7393 (mmp) cc_final: 0.6358 (ppp)
REVERT: E  247 ARG cc_start: 0.7752 (tpt90) cc_final: 0.5778 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8800 (tt0) cc_final: 0.8577 (mt-10)
REVERT: F  190 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9038 (mt)
REVERT: F  193 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.4338 (pttm)
REVERT: F  241 GLU cc_start: 0.7518 (tt0) cc_final: 0.7196 (tt0)
  outliers start: 27
  outliers final: 18
  residues processed: 218
  average time/residue: 0.3705
  time to fit residues: 105.1707
Evaluate side-chains
  216 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
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  149 THR
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  162 VAL
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  190 LEU
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  218 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   chunk 53 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.4986

-------------------------------------------------------------------------------
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 = 0.4286 r_free = 0.4286 target = 0.116128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.107008 restraints weight = 15791.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.109181 restraints weight = 6514.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.110556 restraints weight = 3469.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.6309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6630  Z= 0.189
  Angle     :  0.752  11.593   9018  Z= 0.391
  Chirality :  0.056   0.161   1086
  Planarity :  0.003   0.039   1116
  Dihedral  :  6.336  27.030    894
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 21.03 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 239 
 PHE   0.010   0.001   PHE B 237 
 TYR   0.019   0.002   TYR A 143 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02516 (  151)
  hydrogen bonds       : angle       4.97321 (  453)
  SS BOND              : bond        0.00093 (    6)
  SS BOND              : angle       0.31500 (   12)
  covalent geometry    : bond        0.00441 ( 6624)
  covalent geometry    : angle       0.75202 ( 9006)

*********************** 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: 30
    poor density    : 202
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 GLU cc_start: 0.7945 (mp0) cc_final: 0.7101 (mp0)
REVERT: A  168 GLN cc_start: 0.8799 (tp40) cc_final: 0.7455 (tm-30)
REVERT: A  181 LEU cc_start: 0.8905 (mt) cc_final: 0.8623 (mt)
REVERT: B  124 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8000 (mtmm)
REVERT: B  134 SER cc_start: 0.9252 (t) cc_final: 0.8930 (t)
REVERT: B  150 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8517 (mt)
REVERT: B  161 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7998 (tp30)
REVERT: B  180 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7347 (mpt180)
REVERT: B  194 GLN cc_start: 0.8643 (pt0) cc_final: 0.8313 (pt0)
REVERT: B  228 MET cc_start: 0.8812 (ttp) cc_final: 0.7609 (ttm)
REVERT: B  229 GLN cc_start: 0.8286 (mp10) cc_final: 0.6802 (mp10)
REVERT: C  192 MET cc_start: 0.7845 (mmm) cc_final: 0.6924 (ppp)
REVERT: C  213 PHE cc_start: 0.8056 (t80) cc_final: 0.7825 (t80)
REVERT: C  229 GLN cc_start: 0.8136 (mp10) cc_final: 0.7625 (mp10)
REVERT: C  247 ARG cc_start: 0.7640 (tpt90) cc_final: 0.6413 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8293 (tttp)
REVERT: D  138 GLN cc_start: 0.8174 (tp40) cc_final: 0.7407 (tm-30)
REVERT: D  161 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7863 (tp30)
REVERT: D  163 GLU cc_start: 0.7611 (mp0) cc_final: 0.7016 (mp0)
REVERT: D  180 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7148 (mpt180)
REVERT: D  194 GLN cc_start: 0.8442 (pt0) cc_final: 0.7793 (tm-30)
REVERT: D  220 LYS cc_start: 0.9376 (tttp) cc_final: 0.8823 (tppt)
REVERT: D  222 HIS cc_start: 0.8764 (m-70) cc_final: 0.8326 (m90)
REVERT: D  227 MET cc_start: 0.8676 (mtm) cc_final: 0.8324 (mtp)
REVERT: E  120 SER cc_start: 0.8378 (p) cc_final: 0.7549 (p)
REVERT: E  171 PHE cc_start: 0.8479 (t80) cc_final: 0.8091 (t80)
REVERT: E  182 ASN cc_start: 0.8543 (t0) cc_final: 0.8294 (t0)
REVERT: E  247 ARG cc_start: 0.7648 (tpt90) cc_final: 0.5687 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8783 (tt0) cc_final: 0.8582 (mt-10)
REVERT: F  193 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4219 (pttm)
REVERT: F  241 GLU cc_start: 0.7607 (tt0) cc_final: 0.7258 (tt0)
REVERT: F  252 ASP cc_start: 0.8174 (t0) cc_final: 0.7763 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 214
  average time/residue: 0.2419
  time to fit residues: 67.0571
Evaluate side-chains
  215 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
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  120 SER
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  149 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  216 LEU
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  162 VAL
Chi-restraints excluded: chain D residue  241 GLU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  120 SER
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
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:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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**
** 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 = 0.4283 r_free = 0.4283 target = 0.115952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.106783 restraints weight = 15863.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.108984 restraints weight = 6569.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.110357 restraints weight = 3502.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.6497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6630  Z= 0.196
  Angle     :  0.758  11.664   9018  Z= 0.397
  Chirality :  0.055   0.150   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.302  26.712    894
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.22 %
    Favored  : 73.94 %
  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: -2.57 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C 239 
 PHE   0.012   0.001   PHE D 237 
 TYR   0.027   0.002   TYR D 236 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02592 (  151)
  hydrogen bonds       : angle       5.04373 (  453)
  SS BOND              : bond        0.00082 (    6)
  SS BOND              : angle       0.32506 (   12)
  covalent geometry    : bond        0.00466 ( 6624)
  covalent geometry    : angle       0.75857 ( 9006)

*********************** 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
  218 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8422 (tttm)
REVERT: A  161 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7846 (mt-10)
REVERT: A  163 GLU cc_start: 0.7917 (mp0) cc_final: 0.7073 (mp0)
REVERT: A  168 GLN cc_start: 0.8802 (tp40) cc_final: 0.8152 (tm-30)
REVERT: A  181 LEU cc_start: 0.8888 (mt) cc_final: 0.8604 (mt)
REVERT: B  124 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8155 (mtmm)
REVERT: B  134 SER cc_start: 0.9244 (t) cc_final: 0.8927 (t)
REVERT: B  150 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8575 (mt)
REVERT: B  161 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8050 (tp30)
REVERT: B  180 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7340 (mpt180)
REVERT: B  194 GLN cc_start: 0.8610 (pt0) cc_final: 0.8276 (pt0)
REVERT: B  228 MET cc_start: 0.8778 (ttp) cc_final: 0.7477 (ttm)
REVERT: B  229 GLN cc_start: 0.8196 (mp10) cc_final: 0.6734 (mp10)
REVERT: C  124 LYS cc_start: 0.8257 (mttp) cc_final: 0.6752 (mmtt)
REVERT: C  192 MET cc_start: 0.7874 (mmm) cc_final: 0.6778 (ppp)
REVERT: C  213 PHE cc_start: 0.8036 (t80) cc_final: 0.7807 (t80)
REVERT: C  229 GLN cc_start: 0.8087 (mp10) cc_final: 0.7291 (mp10)
REVERT: C  247 ARG cc_start: 0.7616 (tpt90) cc_final: 0.6407 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8293 (tttp)
REVERT: D  161 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7919 (tp30)
REVERT: D  163 GLU cc_start: 0.7753 (mp0) cc_final: 0.7272 (mp0)
REVERT: D  180 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7203 (mpt180)
REVERT: D  194 GLN cc_start: 0.8408 (pt0) cc_final: 0.7805 (tm-30)
REVERT: D  220 LYS cc_start: 0.9374 (tttp) cc_final: 0.9047 (tppt)
REVERT: D  227 MET cc_start: 0.8710 (mtm) cc_final: 0.8391 (mtp)
REVERT: E  120 SER cc_start: 0.8377 (p) cc_final: 0.7563 (p)
REVERT: E  171 PHE cc_start: 0.8426 (t80) cc_final: 0.8022 (t80)
REVERT: E  182 ASN cc_start: 0.8662 (t0) cc_final: 0.8401 (t0)
REVERT: E  216 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.7856 (mt)
REVERT: E  247 ARG cc_start: 0.7608 (tpt90) cc_final: 0.5722 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8799 (tt0) cc_final: 0.8556 (mt-10)
REVERT: F  241 GLU cc_start: 0.7572 (tt0) cc_final: 0.7225 (tt0)
REVERT: F  252 ASP cc_start: 0.8183 (t0) cc_final: 0.7796 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 205
  average time/residue: 0.2100
  time to fit residues: 54.7201
Evaluate side-chains
  205 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 SER
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  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  149 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 THR
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  162 VAL
Chi-restraints excluded: chain D residue  241 GLU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  120 SER
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:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 HIS ** 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 = 0.4335 r_free = 0.4335 target = 0.119024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.109887 restraints weight = 15529.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.112046 restraints weight = 6532.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.113405 restraints weight = 3512.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.6673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6630  Z= 0.143
  Angle     :  0.708  10.269   9018  Z= 0.371
  Chirality :  0.055   0.147   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.074  25.469    894
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.96 %
    Favored  : 74.47 %
  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: -2.48 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 239 
 PHE   0.012   0.001   PHE D 237 
 TYR   0.019   0.002   TYR D 236 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02346 (  151)
  hydrogen bonds       : angle       4.99182 (  453)
  SS BOND              : bond        0.00123 (    6)
  SS BOND              : angle       0.24572 (   12)
  covalent geometry    : bond        0.00334 ( 6624)
  covalent geometry    : angle       0.70886 ( 9006)

*********************** 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
  229 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9223 (ttmm) cc_final: 0.8466 (tttm)
REVERT: A  161 GLU cc_start: 0.8770 (mt-10) cc_final: 0.7808 (mt-10)
REVERT: A  163 GLU cc_start: 0.7992 (mp0) cc_final: 0.7189 (mp0)
REVERT: A  168 GLN cc_start: 0.8778 (tp40) cc_final: 0.8154 (tm-30)
REVERT: A  181 LEU cc_start: 0.8880 (mt) cc_final: 0.8592 (mt)
REVERT: A  245 GLN cc_start: 0.9112 (mt0) cc_final: 0.8727 (mt0)
REVERT: B  124 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8294 (mtmm)
REVERT: B  134 SER cc_start: 0.9221 (t) cc_final: 0.8905 (t)
REVERT: B  150 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8684 (mt)
REVERT: B  161 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7999 (tp30)
REVERT: B  163 GLU cc_start: 0.7104 (pm20) cc_final: 0.6830 (pm20)
REVERT: B  180 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7335 (mpt180)
REVERT: B  194 GLN cc_start: 0.8609 (pt0) cc_final: 0.7728 (tm-30)
REVERT: B  228 MET cc_start: 0.8692 (ttp) cc_final: 0.7447 (ttm)
REVERT: B  229 GLN cc_start: 0.8141 (mp10) cc_final: 0.6697 (mp10)
REVERT: C  124 LYS cc_start: 0.8249 (mttp) cc_final: 0.6766 (mmtt)
REVERT: C  145 ASN cc_start: 0.7724 (m-40) cc_final: 0.7042 (t0)
REVERT: C  192 MET cc_start: 0.7525 (mmm) cc_final: 0.6675 (ppp)
REVERT: C  213 PHE cc_start: 0.8062 (t80) cc_final: 0.7832 (t80)
REVERT: C  229 GLN cc_start: 0.8025 (mp10) cc_final: 0.7250 (mp10)
REVERT: C  247 ARG cc_start: 0.7555 (tpt90) cc_final: 0.6373 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8346 (tttp)
REVERT: D  145 ASN cc_start: 0.7136 (m-40) cc_final: 0.6706 (t0)
REVERT: D  161 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8312 (mt-10)
REVERT: D  180 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7127 (mpt180)
REVERT: D  194 GLN cc_start: 0.8313 (pt0) cc_final: 0.7803 (tm-30)
REVERT: D  210 MET cc_start: 0.8025 (tpp) cc_final: 0.7656 (tpp)
REVERT: D  220 LYS cc_start: 0.9443 (tttp) cc_final: 0.9079 (tppt)
REVERT: E  120 SER cc_start: 0.8437 (p) cc_final: 0.7879 (p)
REVERT: E  182 ASN cc_start: 0.8596 (t0) cc_final: 0.8308 (t0)
REVERT: E  191 ASP cc_start: 0.8371 (t0) cc_final: 0.8137 (t0)
REVERT: E  192 MET cc_start: 0.7057 (mmp) cc_final: 0.6243 (pmm)
REVERT: E  216 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.7772 (mt)
REVERT: E  247 ARG cc_start: 0.7444 (tpt90) cc_final: 0.5615 (pmt-80)
REVERT: F  180 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.2843 (pmt-80)
REVERT: F  190 LEU cc_start: 0.9333 (mm) cc_final: 0.9096 (mt)
REVERT: F  205 GLU cc_start: 0.8149 (mp0) cc_final: 0.7947 (mp0)
REVERT: F  239 HIS cc_start: 0.8029 (t70) cc_final: 0.7418 (t-170)
REVERT: F  241 GLU cc_start: 0.7542 (tt0) cc_final: 0.7281 (tt0)
REVERT: F  252 ASP cc_start: 0.8117 (t0) cc_final: 0.7730 (t0)
  outliers start: 27
  outliers final: 17
  residues processed: 216
  average time/residue: 0.2014
  time to fit residues: 55.3279
Evaluate side-chains
  212 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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 B residue  124 LYS
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  210 MET
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  216 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  162 VAL
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  180 ARG
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 54 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0770
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    2.4144

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 HIS ** 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 = 0.4312 r_free = 0.4312 target = 0.117664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.108453 restraints weight = 15753.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.110557 restraints weight = 6689.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.111960 restraints weight = 3664.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.6720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6630  Z= 0.185
  Angle     :  0.739   9.735   9018  Z= 0.387
  Chirality :  0.055   0.161   1086
  Planarity :  0.003   0.032   1116
  Dihedral  :  6.084  25.622    894
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.35 %
    Favored  : 74.60 %
  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: -2.50 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS C 239 
 PHE   0.011   0.001   PHE D 237 
 TYR   0.019   0.002   TYR D 236 
 ARG   0.002   0.000   ARG F 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02431 (  151)
  hydrogen bonds       : angle       4.93753 (  453)
  SS BOND              : bond        0.00064 (    6)
  SS BOND              : angle       0.31494 (   12)
  covalent geometry    : bond        0.00436 ( 6624)
  covalent geometry    : angle       0.73983 ( 9006)

********************** 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
  220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8498 (tttm)
REVERT: A  161 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: A  163 GLU cc_start: 0.8006 (mp0) cc_final: 0.7253 (mp0)
REVERT: A  180 ARG cc_start: 0.5369 (OUTLIER) cc_final: 0.2846 (pmt-80)
REVERT: A  181 LEU cc_start: 0.8892 (mt) cc_final: 0.8661 (mt)
REVERT: A  245 GLN cc_start: 0.9187 (mt0) cc_final: 0.8791 (mt0)
REVERT: B  124 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8219 (mtmm)
REVERT: B  134 SER cc_start: 0.9237 (t) cc_final: 0.8911 (t)
REVERT: B  150 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8641 (mt)
REVERT: B  161 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8020 (tp30)
REVERT: B  163 GLU cc_start: 0.7166 (pm20) cc_final: 0.6776 (pm20)
REVERT: B  180 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7334 (mpt180)
REVERT: B  194 GLN cc_start: 0.8590 (pt0) cc_final: 0.8249 (pt0)
REVERT: B  228 MET cc_start: 0.8701 (ttp) cc_final: 0.7461 (ttm)
REVERT: B  229 GLN cc_start: 0.8183 (mp10) cc_final: 0.6750 (mp10)
REVERT: C  120 SER cc_start: 0.8098 (p) cc_final: 0.7613 (p)
REVERT: C  124 LYS cc_start: 0.8308 (mttp) cc_final: 0.6781 (mmtt)
REVERT: C  145 ASN cc_start: 0.7756 (m-40) cc_final: 0.7051 (t0)
REVERT: C  192 MET cc_start: 0.7954 (mmm) cc_final: 0.6768 (ppp)
REVERT: C  213 PHE cc_start: 0.8039 (t80) cc_final: 0.7808 (t80)
REVERT: C  229 GLN cc_start: 0.8020 (mp10) cc_final: 0.7337 (mp10)
REVERT: C  247 ARG cc_start: 0.7609 (tpt90) cc_final: 0.6471 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8325 (tttp)
REVERT: D  145 ASN cc_start: 0.7116 (m-40) cc_final: 0.6719 (t0)
REVERT: D  180 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7231 (mpt180)
REVERT: D  194 GLN cc_start: 0.8344 (pt0) cc_final: 0.7804 (tm-30)
REVERT: D  220 LYS cc_start: 0.9452 (tttp) cc_final: 0.9055 (tppt)
REVERT: E  120 SER cc_start: 0.8470 (p) cc_final: 0.7891 (p)
REVERT: E  182 ASN cc_start: 0.8686 (t0) cc_final: 0.8405 (t0)
REVERT: E  216 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.7802 (mt)
REVERT: E  227 MET cc_start: 0.6558 (mtm) cc_final: 0.6171 (ptt)
REVERT: E  247 ARG cc_start: 0.7499 (tpt90) cc_final: 0.5707 (pmt-80)
REVERT: F  145 ASN cc_start: 0.8007 (m-40) cc_final: 0.7710 (m-40)
REVERT: F  180 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.2676 (pmt-80)
REVERT: F  190 LEU cc_start: 0.9368 (mm) cc_final: 0.9116 (mt)
REVERT: F  193 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.3988 (pttm)
REVERT: F  239 HIS cc_start: 0.7997 (t70) cc_final: 0.7504 (t-170)
REVERT: F  252 ASP cc_start: 0.8207 (t0) cc_final: 0.7777 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 210
  average time/residue: 0.2159
  time to fit residues: 57.8805
Evaluate side-chains
  209 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 188
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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 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  185 THR
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 E residue  153 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  180 ARG
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:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 222 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.119382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.110094 restraints weight = 15698.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.112268 restraints weight = 6670.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.113691 restraints weight = 3614.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.6815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6630  Z= 0.150
  Angle     :  0.724   9.313   9018  Z= 0.378
  Chirality :  0.055   0.144   1086
  Planarity :  0.003   0.033   1116
  Dihedral  :  5.986  25.117    894
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.69 %
    Favored  : 74.74 %
  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: -2.41 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 222 
 PHE   0.011   0.001   PHE D 237 
 TYR   0.019   0.002   TYR E 236 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02375 (  151)
  hydrogen bonds       : angle       4.91310 (  453)
  SS BOND              : bond        0.00086 (    6)
  SS BOND              : angle       0.20804 (   12)
  covalent geometry    : bond        0.00351 ( 6624)
  covalent geometry    : angle       0.72435 ( 9006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3147.57 seconds
wall clock time: 58 minutes 25.12 seconds (3505.12 seconds total)