Starting phenix.real_space_refine
on Fri Aug 22 17:40:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvf_14176/08_2025/7qvf_14176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvf_14176/08_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_14176/08_2025/7qvf_14176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvf_14176/08_2025/7qvf_14176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvf_14176/08_2025/7qvf_14176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvf_14176/08_2025/7qvf_14176.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.25
  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: 0.48
  Conformation dependent library (CDL) restraints added in 369.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.00

  Time building geometry restraints manager: 0.66 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: 0.00
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:             7.850
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.470
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.620
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 247 
 TYR   0.138   0.025   TYR A 143 
 PHE   0.032   0.010   PHE F 171 
 HIS   0.016   0.005   HIS B 239 

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

*********************** 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  : 0.190 
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: 0.8438 (tp)
REVERT: A  168 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7841 (tp40)
REVERT: A  247 ARG cc_start: 0.7785 (tpt90) cc_final: 0.7520 (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: 0.8586 (t)
REVERT: B  228 MET cc_start: 0.8416 (ttp) cc_final: 0.7376 (ttm)
REVERT: C  173 LYS cc_start: 0.7530 (tttt) cc_final: 0.7273 (tppt)
REVERT: C  228 MET cc_start: 0.8256 (ttp) cc_final: 0.7421 (ttm)
REVERT: C  245 GLN cc_start: 0.7761 (mt0) cc_final: 0.7111 (mt0)
REVERT: C  247 ARG cc_start: 0.7087 (tpt90) cc_final: 0.6397 (pmt-80)
REVERT: D  154 ASN cc_start: 0.7800 (t0) cc_final: 0.7579 (t0)
REVERT: D  228 MET cc_start: 0.8431 (ttp) cc_final: 0.7842 (ttm)
REVERT: D  245 GLN cc_start: 0.8042 (mt0) cc_final: 0.7491 (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: 0.8296 (t)
REVERT: E  242 GLN cc_start: 0.7857 (mt0) cc_final: 0.7628 (mt0)
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: 0.8552 (tp)
REVERT: F  168 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7626 (tp40)
REVERT: F  228 MET cc_start: 0.8199 (ttp) cc_final: 0.7955 (ttm)
REVERT: F  244 SER cc_start: 0.8054 (t) cc_final: 0.7755 (t)
REVERT: F  247 ARG cc_start: 0.7734 (tpt90) cc_final: 0.7281 (tpm170)
REVERT: F  250 TYR cc_start: 0.7496 (t80) cc_final: 0.6901 (p90)
  outliers start: 4
  outliers final: 1
  residues processed: 335
  average time/residue: 0.0817
  time to fit residues: 35.2835
Evaluate side-chains
  231 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    0.0370
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 249 GLN
** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 154 ASN
E 249 GLN
F 245 GLN
F 249 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.121607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.111636 restraints weight = 15661.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.113994 restraints weight = 6398.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.115410 restraints weight = 3436.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.116375 restraints weight = 2189.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.116973 restraints weight = 1573.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6630  Z= 0.160
  Angle     :  0.775   6.327   9018  Z= 0.424
  Chirality :  0.060   0.213   1086
  Planarity :  0.003   0.025   1116
  Dihedral  :  7.133  26.658    896
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.36 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 247 
 TYR   0.022   0.002   TYR E 143 
 PHE   0.011   0.001   PHE B 237 
 HIS   0.002   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6624)
  covalent geometry    : angle       0.77545 ( 9006)
  SS BOND              : bond        0.00312 (    6)
  SS BOND              : angle       0.38110 (   12)
  hydrogen bonds       : bond        0.02878 (  151)
  hydrogen bonds       : angle       5.57684 (  453)

*********************** 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
  264 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ASP cc_start: 0.6811 (t0) cc_final: 0.6347 (t70)
REVERT: A  191 ASP cc_start: 0.8230 (t0) cc_final: 0.7985 (t0)
REVERT: A  207 MET cc_start: 0.5495 (ppp) cc_final: 0.5082 (ppp)
REVERT: A  247 ARG cc_start: 0.8472 (tpt90) cc_final: 0.6932 (tpm170)
REVERT: A  250 TYR cc_start: 0.8131 (t80) cc_final: 0.6469 (p90)
REVERT: B  122 ASP cc_start: 0.7921 (t0) cc_final: 0.6986 (t70)
REVERT: B  129 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8867 (ttmm)
REVERT: B  134 SER cc_start: 0.9143 (t) cc_final: 0.8899 (t)
REVERT: B  136 ASP cc_start: 0.8284 (p0) cc_final: 0.7925 (p0)
REVERT: B  150 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8321 (mt)
REVERT: B  180 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7129 (mtt90)
REVERT: B  190 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9015 (mt)
REVERT: B  205 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6354 (mm-30)
REVERT: B  210 MET cc_start: 0.7507 (mtp) cc_final: 0.7184 (mtp)
REVERT: C  122 ASP cc_start: 0.8088 (t0) cc_final: 0.7407 (t0)
REVERT: C  168 GLN cc_start: 0.8799 (tp40) cc_final: 0.8139 (tp40)
REVERT: C  173 LYS cc_start: 0.7278 (tttt) cc_final: 0.6512 (tppt)
REVERT: C  192 MET cc_start: 0.8216 (mmm) cc_final: 0.6727 (ppp)
REVERT: C  228 MET cc_start: 0.8289 (ttp) cc_final: 0.7736 (ttp)
REVERT: C  229 GLN cc_start: 0.7691 (mp10) cc_final: 0.6905 (mp10)
REVERT: C  247 ARG cc_start: 0.7676 (tpt90) cc_final: 0.6250 (pmt-80)
REVERT: D  122 ASP cc_start: 0.7628 (t0) cc_final: 0.7427 (t0)
REVERT: D  124 LYS cc_start: 0.8367 (mttp) cc_final: 0.8100 (mptp)
REVERT: D  161 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8129 (tp30)
REVERT: D  180 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7036 (mtt90)
REVERT: D  190 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9084 (mt)
REVERT: D  191 ASP cc_start: 0.8406 (t0) cc_final: 0.8186 (t0)
REVERT: D  192 MET cc_start: 0.7848 (mmm) cc_final: 0.7101 (mmt)
REVERT: D  194 GLN cc_start: 0.8632 (pt0) cc_final: 0.7665 (tm-30)
REVERT: D  205 GLU cc_start: 0.6985 (mp0) cc_final: 0.6724 (mp0)
REVERT: E  170 GLN cc_start: 0.8301 (mt0) cc_final: 0.8028 (mt0)
REVERT: E  173 LYS cc_start: 0.7063 (tttt) cc_final: 0.6376 (tppt)
REVERT: E  180 ARG cc_start: 0.3967 (OUTLIER) cc_final: 0.2832 (mmp-170)
REVERT: E  205 GLU cc_start: 0.4470 (pm20) cc_final: 0.4169 (pm20)
REVERT: E  242 GLN cc_start: 0.8316 (mt0) cc_final: 0.7886 (mt0)
REVERT: E  247 ARG cc_start: 0.7557 (tpt90) cc_final: 0.5549 (pmt-80)
REVERT: F  143 TYR cc_start: 0.8408 (t80) cc_final: 0.8043 (t80)
REVERT: F  192 MET cc_start: 0.7581 (mmm) cc_final: 0.7187 (mmm)
REVERT: F  205 GLU cc_start: 0.7287 (mp0) cc_final: 0.7042 (mp0)
REVERT: F  207 MET cc_start: 0.5524 (ppp) cc_final: 0.5311 (tpt)
REVERT: F  247 ARG cc_start: 0.8530 (tpt90) cc_final: 0.7330 (tpm170)
REVERT: F  250 TYR cc_start: 0.8086 (t80) cc_final: 0.6377 (p90)
  outliers start: 24
  outliers final: 6
  residues processed: 252
  average time/residue: 0.0847
  time to fit residues: 27.5282
Evaluate side-chains
  229 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 219
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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 C residue  224 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  232 VAL
Chi-restraints excluded: chain F residue  218 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 76 optimal weight:    0.2980
   chunk 7 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    4.8588

-------------------------------------------------------------------------------
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 229 GLN
B 242 GLN
** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 154 ASN
E 249 GLN
F 245 GLN
F 249 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.113957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.104624 restraints weight = 16286.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.106755 restraints weight = 6749.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.108096 restraints weight = 3634.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.108984 restraints weight = 2300.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.109551 restraints weight = 1646.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   6630  Z= 0.310
  Angle     :  0.797   6.909   9018  Z= 0.436
  Chirality :  0.059   0.172   1086
  Planarity :  0.004   0.029   1116
  Dihedral  :  6.887  22.645    894
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.12 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 180 
 TYR   0.019   0.003   TYR D 248 
 PHE   0.012   0.003   PHE E 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00718 ( 6624)
  covalent geometry    : angle       0.79731 ( 9006)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.28426 (   12)
  hydrogen bonds       : bond        0.03027 (  151)
  hydrogen bonds       : angle       4.95582 (  453)

*********************** 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
  238 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 LEU cc_start: 0.9268 (mm) cc_final: 0.9000 (mt)
REVERT: A  246 GLU cc_start: 0.7060 (tt0) cc_final: 0.6823 (tt0)
REVERT: B  134 SER cc_start: 0.9287 (t) cc_final: 0.8941 (t)
REVERT: B  136 ASP cc_start: 0.8222 (p0) cc_final: 0.7945 (p0)
REVERT: B  150 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8407 (mt)
REVERT: B  161 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8093 (tp30)
REVERT: B  180 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7106 (mpt180)
REVERT: B  192 MET cc_start: 0.8035 (mmm) cc_final: 0.7717 (mmm)
REVERT: B  194 GLN cc_start: 0.8654 (pt0) cc_final: 0.8436 (pt0)
REVERT: B  205 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6292 (mm-30)
REVERT: B  210 MET cc_start: 0.7708 (mtp) cc_final: 0.7314 (mtp)
REVERT: B  228 MET cc_start: 0.8902 (ttp) cc_final: 0.7606 (ttm)
REVERT: B  229 GLN cc_start: 0.8562 (mp-120) cc_final: 0.7785 (mp10)
REVERT: C  228 MET cc_start: 0.8707 (ttp) cc_final: 0.8276 (ttm)
REVERT: C  245 GLN cc_start: 0.8503 (mt0) cc_final: 0.8002 (mt0)
REVERT: C  247 ARG cc_start: 0.7804 (tpt90) cc_final: 0.6350 (pmt-80)
REVERT: D  122 ASP cc_start: 0.8084 (t0) cc_final: 0.7667 (t0)
REVERT: D  124 LYS cc_start: 0.8537 (mttp) cc_final: 0.8188 (mttp)
REVERT: D  161 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7984 (tp30)
REVERT: D  180 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7146 (mmt180)
REVERT: D  192 MET cc_start: 0.8090 (mmm) cc_final: 0.7734 (mmm)
REVERT: D  210 MET cc_start: 0.8168 (tpp) cc_final: 0.7527 (tpp)
REVERT: D  220 LYS cc_start: 0.9322 (tttp) cc_final: 0.9102 (mttp)
REVERT: E  120 SER cc_start: 0.8515 (p) cc_final: 0.7928 (p)
REVERT: E  207 MET cc_start: 0.6443 (tpt) cc_final: 0.6227 (tpt)
REVERT: E  242 GLN cc_start: 0.8274 (mt0) cc_final: 0.7750 (mt0)
REVERT: E  247 ARG cc_start: 0.7856 (tpt90) cc_final: 0.5574 (pmt-80)
REVERT: F  168 GLN cc_start: 0.8780 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: F  194 GLN cc_start: 0.8523 (mp10) cc_final: 0.8318 (mp10)
REVERT: F  196 ASP cc_start: 0.8685 (t0) cc_final: 0.8469 (t0)
REVERT: F  207 MET cc_start: 0.5557 (ppp) cc_final: 0.5348 (ppp)
  outliers start: 21
  outliers final: 8
  residues processed: 224
  average time/residue: 0.0923
  time to fit residues: 26.5348
Evaluate side-chains
  207 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 198
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  218 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  218 SER
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 42 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.114790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.105281 restraints weight = 16090.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.107394 restraints weight = 6713.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.108747 restraints weight = 3680.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.109708 restraints weight = 2339.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.110339 restraints weight = 1668.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.5696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6630  Z= 0.215
  Angle     :  0.694   6.017   9018  Z= 0.380
  Chirality :  0.056   0.157   1086
  Planarity :  0.003   0.033   1116
  Dihedral  :  6.566  25.874    894
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.99 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.40 (0.25), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.19), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 247 
 TYR   0.019   0.002   TYR E 143 
 PHE   0.009   0.002   PHE D 237 
 HIS   0.009   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 6624)
  covalent geometry    : angle       0.69438 ( 9006)
  SS BOND              : bond        0.00105 (    6)
  SS BOND              : angle       0.34154 (   12)
  hydrogen bonds       : bond        0.02637 (  151)
  hydrogen bonds       : angle       4.87387 (  453)

*********************** 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
  234 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 LEU cc_start: 0.8796 (mt) cc_final: 0.8541 (mt)
REVERT: A  190 LEU cc_start: 0.9293 (mm) cc_final: 0.9071 (mt)
REVERT: B  124 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8551 (mmmt)
REVERT: B  134 SER cc_start: 0.9251 (t) cc_final: 0.8928 (t)
REVERT: B  136 ASP cc_start: 0.8226 (p0) cc_final: 0.7978 (p0)
REVERT: B  150 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8433 (mt)
REVERT: B  161 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8144 (tp30)
REVERT: B  180 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7110 (mpt180)
REVERT: B  192 MET cc_start: 0.8042 (mmm) cc_final: 0.7449 (mmm)
REVERT: B  194 GLN cc_start: 0.8685 (pt0) cc_final: 0.8475 (pt0)
REVERT: B  205 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6795 (mm-30)
REVERT: B  210 MET cc_start: 0.7785 (mtp) cc_final: 0.7410 (mtp)
REVERT: B  226 LEU cc_start: 0.9385 (mt) cc_final: 0.9157 (mt)
REVERT: B  228 MET cc_start: 0.8827 (ttp) cc_final: 0.7580 (ttm)
REVERT: B  229 GLN cc_start: 0.8395 (mp-120) cc_final: 0.7736 (mp10)
REVERT: C  191 ASP cc_start: 0.8355 (t0) cc_final: 0.7857 (t0)
REVERT: C  228 MET cc_start: 0.8676 (ttp) cc_final: 0.8258 (ttm)
REVERT: C  245 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7631 (mt0)
REVERT: C  247 ARG cc_start: 0.7764 (tpt90) cc_final: 0.6309 (pmt-80)
REVERT: D  122 ASP cc_start: 0.8057 (t0) cc_final: 0.7820 (t0)
REVERT: D  161 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7637 (tp30)
REVERT: D  180 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7099 (mtt90)
REVERT: D  192 MET cc_start: 0.8013 (mmm) cc_final: 0.7601 (mmm)
REVERT: D  193 LYS cc_start: 0.8923 (tttp) cc_final: 0.8657 (mtpt)
REVERT: D  220 LYS cc_start: 0.9298 (tttp) cc_final: 0.8866 (tppt)
REVERT: D  245 GLN cc_start: 0.9005 (mt0) cc_final: 0.8362 (mt0)
REVERT: E  120 SER cc_start: 0.8487 (p) cc_final: 0.7576 (p)
REVERT: E  124 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8301 (mtmm)
REVERT: E  191 ASP cc_start: 0.8457 (t0) cc_final: 0.8233 (t0)
REVERT: E  242 GLN cc_start: 0.8265 (mt0) cc_final: 0.7849 (mt0)
REVERT: E  247 ARG cc_start: 0.7724 (tpt90) cc_final: 0.5608 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8236 (tt0) cc_final: 0.7738 (mt-10)
REVERT: F  168 GLN cc_start: 0.8819 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: F  181 LEU cc_start: 0.8819 (mt) cc_final: 0.8569 (mt)
REVERT: F  190 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8962 (mt)
REVERT: F  239 HIS cc_start: 0.7915 (t70) cc_final: 0.7329 (t-170)
  outliers start: 25
  outliers final: 13
  residues processed: 219
  average time/residue: 0.0861
  time to fit residues: 24.2130
Evaluate side-chains
  212 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  153 THR
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
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  241 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.2164

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.119064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.109685 restraints weight = 15930.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.111897 restraints weight = 6522.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.113285 restraints weight = 3478.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.114152 restraints weight = 2194.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.114802 restraints weight = 1592.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6630  Z= 0.134
  Angle     :  0.664   8.125   9018  Z= 0.356
  Chirality :  0.055   0.170   1086
  Planarity :  0.003   0.035   1116
  Dihedral  :  6.270  25.711    894
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.46 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 247 
 TYR   0.018   0.001   TYR E 143 
 PHE   0.009   0.001   PHE D 237 
 HIS   0.008   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6624)
  covalent geometry    : angle       0.66427 ( 9006)
  SS BOND              : bond        0.00113 (    6)
  SS BOND              : angle       0.24146 (   12)
  hydrogen bonds       : bond        0.02412 (  151)
  hydrogen bonds       : angle       4.87922 (  453)

*********************** 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
  239 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 216
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8909 (ttmm)
REVERT: A  181 LEU cc_start: 0.8836 (mt) cc_final: 0.8612 (mt)
REVERT: A  190 LEU cc_start: 0.9381 (mm) cc_final: 0.9097 (mt)
REVERT: A  240 SER cc_start: 0.9010 (m) cc_final: 0.8771 (p)
REVERT: B  124 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8507 (mmmt)
REVERT: B  134 SER cc_start: 0.9269 (t) cc_final: 0.8932 (t)
REVERT: B  136 ASP cc_start: 0.8146 (p0) cc_final: 0.7938 (p0)
REVERT: B  150 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8436 (mt)
REVERT: B  161 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8013 (tp30)
REVERT: B  180 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7182 (mpt180)
REVERT: B  205 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6462 (mm-30)
REVERT: B  210 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7188 (mtp)
REVERT: B  228 MET cc_start: 0.8757 (ttp) cc_final: 0.7175 (ttp)
REVERT: B  229 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7567 (mp10)
REVERT: C  192 MET cc_start: 0.7366 (mmt) cc_final: 0.6789 (ppp)
REVERT: C  228 MET cc_start: 0.8611 (ttp) cc_final: 0.8181 (ttp)
REVERT: C  245 GLN cc_start: 0.7911 (mt0) cc_final: 0.7447 (mt0)
REVERT: C  247 ARG cc_start: 0.7604 (tpt90) cc_final: 0.6274 (pmt-80)
REVERT: D  122 ASP cc_start: 0.7929 (t0) cc_final: 0.7193 (t0)
REVERT: D  161 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8007 (tp30)
REVERT: D  180 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7030 (mpt180)
REVERT: D  220 LYS cc_start: 0.9318 (tttp) cc_final: 0.8880 (tppt)
REVERT: D  228 MET cc_start: 0.8390 (ttp) cc_final: 0.8008 (ttp)
REVERT: D  229 GLN cc_start: 0.8345 (mp10) cc_final: 0.7426 (mp10)
REVERT: E  120 SER cc_start: 0.8458 (p) cc_final: 0.7490 (p)
REVERT: E  124 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8273 (mtmm)
REVERT: E  171 PHE cc_start: 0.8317 (t80) cc_final: 0.7935 (t80)
REVERT: E  192 MET cc_start: 0.7194 (mmp) cc_final: 0.6415 (ppp)
REVERT: E  216 LEU cc_start: 0.9289 (pp) cc_final: 0.7929 (mt)
REVERT: E  236 TYR cc_start: 0.8132 (t80) cc_final: 0.7819 (t80)
REVERT: E  242 GLN cc_start: 0.8328 (mt0) cc_final: 0.7526 (mt0)
REVERT: E  247 ARG cc_start: 0.7538 (tpt90) cc_final: 0.5444 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8020 (tt0) cc_final: 0.7574 (mt-10)
REVERT: F  168 GLN cc_start: 0.8844 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: F  181 LEU cc_start: 0.8720 (mt) cc_final: 0.8501 (mt)
REVERT: F  239 HIS cc_start: 0.7917 (t70) cc_final: 0.7588 (t-170)
  outliers start: 23
  outliers final: 14
  residues processed: 223
  average time/residue: 0.0903
  time to fit residues: 25.7083
Evaluate side-chains
  212 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  210 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  241 GLU
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  216 LEU
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  245 GLN
Chi-restraints excluded: chain F residue  210 MET
Chi-restraints excluded: chain F residue  218 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
B 194 GLN
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.117743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.108336 restraints weight = 15820.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.110524 restraints weight = 6559.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.111898 restraints weight = 3526.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.112841 restraints weight = 2233.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.113396 restraints weight = 1590.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6630  Z= 0.176
  Angle     :  0.681  10.578   9018  Z= 0.364
  Chirality :  0.055   0.163   1086
  Planarity :  0.003   0.036   1116
  Dihedral  :  6.173  26.069    894
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.99 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 247 
 TYR   0.017   0.002   TYR D 143 
 PHE   0.011   0.001   PHE D 237 
 HIS   0.015   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6624)
  covalent geometry    : angle       0.68091 ( 9006)
  SS BOND              : bond        0.00073 (    6)
  SS BOND              : angle       0.25193 (   12)
  hydrogen bonds       : bond        0.02452 (  151)
  hydrogen bonds       : angle       4.80333 (  453)

*********************** 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
  229 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 201
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: A  163 GLU cc_start: 0.7974 (mp0) cc_final: 0.7135 (mp0)
REVERT: A  181 LEU cc_start: 0.8836 (mt) cc_final: 0.8593 (mt)
REVERT: A  190 LEU cc_start: 0.9334 (mm) cc_final: 0.9036 (mt)
REVERT: B  134 SER cc_start: 0.9234 (t) cc_final: 0.8901 (t)
REVERT: B  150 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: B  161 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8048 (tp30)
REVERT: B  180 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7062 (mpt180)
REVERT: B  194 GLN cc_start: 0.8664 (pt0) cc_final: 0.8381 (pm20)
REVERT: B  205 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6876 (mm-30)
REVERT: B  210 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7280 (mtp)
REVERT: B  228 MET cc_start: 0.8743 (ttp) cc_final: 0.7437 (ttm)
REVERT: B  229 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: C  192 MET cc_start: 0.7608 (mmt) cc_final: 0.6845 (ppp)
REVERT: C  213 PHE cc_start: 0.8081 (t80) cc_final: 0.7835 (t80)
REVERT: C  228 MET cc_start: 0.8662 (ttp) cc_final: 0.8447 (ttm)
REVERT: C  229 GLN cc_start: 0.8127 (mp10) cc_final: 0.7880 (mp10)
REVERT: C  245 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7445 (mt0)
REVERT: C  247 ARG cc_start: 0.7636 (tpt90) cc_final: 0.6369 (pmt-80)
REVERT: D  161 GLU cc_start: 0.8685 (mt-10) cc_final: 0.7919 (tp30)
REVERT: D  163 GLU cc_start: 0.7528 (mp0) cc_final: 0.7068 (mp0)
REVERT: D  180 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7131 (mpt180)
REVERT: D  193 LYS cc_start: 0.9213 (mtpt) cc_final: 0.8728 (mmtm)
REVERT: D  220 LYS cc_start: 0.9309 (tttp) cc_final: 0.8882 (tppt)
REVERT: E  120 SER cc_start: 0.8481 (p) cc_final: 0.7544 (p)
REVERT: E  145 ASN cc_start: 0.7553 (m-40) cc_final: 0.6726 (t0)
REVERT: E  171 PHE cc_start: 0.8385 (t80) cc_final: 0.7957 (t80)
REVERT: E  182 ASN cc_start: 0.8629 (t0) cc_final: 0.8362 (t0)
REVERT: E  192 MET cc_start: 0.7726 (mmp) cc_final: 0.6580 (ppp)
REVERT: E  216 LEU cc_start: 0.9272 (pp) cc_final: 0.7874 (mt)
REVERT: E  242 GLN cc_start: 0.8181 (mt0) cc_final: 0.7906 (mt0)
REVERT: E  247 ARG cc_start: 0.7541 (tpt90) cc_final: 0.5578 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8085 (tt0) cc_final: 0.7526 (mt-10)
REVERT: F  168 GLN cc_start: 0.8908 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: F  181 LEU cc_start: 0.8847 (mt) cc_final: 0.8552 (mt)
REVERT: F  239 HIS cc_start: 0.8114 (t70) cc_final: 0.7276 (t-170)
  outliers start: 28
  outliers final: 17
  residues processed: 212
  average time/residue: 0.0932
  time to fit residues: 25.2299
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  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  241 GLU
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  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  216 LEU
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  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0270
   chunk 65 optimal weight:    0.0770
   chunk 23 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.118336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.108972 restraints weight = 15753.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.111179 restraints weight = 6578.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.112577 restraints weight = 3534.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.113505 restraints weight = 2235.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.114074 restraints weight = 1591.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.6277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6630  Z= 0.155
  Angle     :  0.689  11.434   9018  Z= 0.365
  Chirality :  0.055   0.155   1086
  Planarity :  0.003   0.034   1116
  Dihedral  :  6.101  25.892    894
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.31 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 247 
 TYR   0.019   0.002   TYR B 143 
 PHE   0.010   0.001   PHE D 237 
 HIS   0.013   0.001   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6624)
  covalent geometry    : angle       0.68970 ( 9006)
  SS BOND              : bond        0.00077 (    6)
  SS BOND              : angle       0.23389 (   12)
  hydrogen bonds       : bond        0.02382 (  151)
  hydrogen bonds       : angle       4.86085 (  453)

*********************** 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
  228 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8852 (ttmm)
REVERT: A  161 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: A  163 GLU cc_start: 0.8083 (mp0) cc_final: 0.7246 (mp0)
REVERT: A  181 LEU cc_start: 0.8839 (mt) cc_final: 0.8537 (mt)
REVERT: A  190 LEU cc_start: 0.9348 (mm) cc_final: 0.9146 (mt)
REVERT: B  134 SER cc_start: 0.9246 (t) cc_final: 0.8930 (t)
REVERT: B  145 ASN cc_start: 0.7233 (m-40) cc_final: 0.6924 (t0)
REVERT: B  150 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8471 (mt)
REVERT: B  180 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7124 (mpt180)
REVERT: B  191 ASP cc_start: 0.7936 (t0) cc_final: 0.7711 (t0)
REVERT: B  193 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8687 (tttp)
REVERT: B  205 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6833 (mm-30)
REVERT: B  210 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7247 (mtp)
REVERT: B  228 MET cc_start: 0.8751 (ttp) cc_final: 0.7213 (ttp)
REVERT: B  229 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7648 (mp10)
REVERT: C  192 MET cc_start: 0.7602 (mmt) cc_final: 0.6661 (ppp)
REVERT: C  213 PHE cc_start: 0.8079 (t80) cc_final: 0.7841 (t80)
REVERT: C  228 MET cc_start: 0.8647 (ttp) cc_final: 0.7378 (ttp)
REVERT: C  229 GLN cc_start: 0.8016 (mp10) cc_final: 0.7285 (mp10)
REVERT: C  245 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7510 (mt0)
REVERT: C  247 ARG cc_start: 0.7613 (tpt90) cc_final: 0.6369 (pmt-80)
REVERT: D  124 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8353 (mttp)
REVERT: D  145 ASN cc_start: 0.7324 (m-40) cc_final: 0.6802 (t0)
REVERT: D  180 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7080 (mpt180)
REVERT: D  220 LYS cc_start: 0.9313 (tttp) cc_final: 0.8884 (tppt)
REVERT: D  229 GLN cc_start: 0.8344 (mp10) cc_final: 0.7779 (mp10)
REVERT: E  120 SER cc_start: 0.8455 (p) cc_final: 0.7651 (p)
REVERT: E  145 ASN cc_start: 0.7377 (m-40) cc_final: 0.6778 (t0)
REVERT: E  171 PHE cc_start: 0.8408 (t80) cc_final: 0.7947 (t80)
REVERT: E  182 ASN cc_start: 0.8703 (t0) cc_final: 0.8466 (t0)
REVERT: E  192 MET cc_start: 0.6903 (mmp) cc_final: 0.6240 (ppp)
REVERT: E  216 LEU cc_start: 0.9241 (pp) cc_final: 0.7857 (mt)
REVERT: E  242 GLN cc_start: 0.8204 (mt0) cc_final: 0.7628 (mt0)
REVERT: E  247 ARG cc_start: 0.7464 (tpt90) cc_final: 0.5643 (pmt-80)
REVERT: F  168 GLN cc_start: 0.8930 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: F  181 LEU cc_start: 0.8787 (mt) cc_final: 0.8531 (mt)
REVERT: F  193 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4043 (pttm)
REVERT: F  239 HIS cc_start: 0.8040 (t70) cc_final: 0.7484 (t70)
REVERT: F  252 ASP cc_start: 0.8179 (t0) cc_final: 0.7768 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 213
  average time/residue: 0.0979
  time to fit residues: 26.7315
Evaluate side-chains
  210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  210 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  216 LEU
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  245 GLN
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4235 r_free = 0.4235 target = 0.113044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.103765 restraints weight = 16334.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.105923 restraints weight = 6800.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.107285 restraints weight = 3654.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.108045 restraints weight = 2317.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.108735 restraints weight = 1709.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.6452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   6630  Z= 0.298
  Angle     :  0.802  13.075   9018  Z= 0.423
  Chirality :  0.057   0.150   1086
  Planarity :  0.004   0.038   1116
  Dihedral  :  6.426  27.362    894
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.78 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 180 
 TYR   0.025   0.002   TYR B 143 
 PHE   0.015   0.002   PHE B 237 
 HIS   0.012   0.003   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00693 ( 6624)
  covalent geometry    : angle       0.80243 ( 9006)
  SS BOND              : bond        0.00053 (    6)
  SS BOND              : angle       0.48247 (   12)
  hydrogen bonds       : bond        0.02766 (  151)
  hydrogen bonds       : angle       4.92992 (  453)

*********************** 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
  220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 189
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 GLU cc_start: 0.8048 (mp0) cc_final: 0.7383 (mp0)
REVERT: A  190 LEU cc_start: 0.9338 (mm) cc_final: 0.9094 (mt)
REVERT: B  124 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8368 (mmmt)
REVERT: B  134 SER cc_start: 0.9219 (t) cc_final: 0.8890 (t)
REVERT: B  150 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: B  180 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7339 (mpt180)
REVERT: B  205 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6786 (mm-30)
REVERT: B  228 MET cc_start: 0.8831 (ttp) cc_final: 0.7531 (ttm)
REVERT: B  229 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7686 (mp10)
REVERT: B  245 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9031 (mt0)
REVERT: C  213 PHE cc_start: 0.8050 (t80) cc_final: 0.7827 (t80)
REVERT: C  228 MET cc_start: 0.8655 (ttp) cc_final: 0.8358 (ttm)
REVERT: C  245 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7809 (mt0)
REVERT: C  247 ARG cc_start: 0.7718 (tpt90) cc_final: 0.6477 (pmt-80)
REVERT: D  180 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7179 (mpt180)
REVERT: D  193 LYS cc_start: 0.9229 (mmtp) cc_final: 0.8773 (mmtm)
REVERT: D  220 LYS cc_start: 0.9334 (tttp) cc_final: 0.8940 (tppt)
REVERT: E  145 ASN cc_start: 0.7401 (m-40) cc_final: 0.6777 (t0)
REVERT: E  171 PHE cc_start: 0.8457 (t80) cc_final: 0.8019 (t80)
REVERT: E  181 LEU cc_start: 0.8824 (mm) cc_final: 0.8074 (pt)
REVERT: E  192 MET cc_start: 0.7711 (mmp) cc_final: 0.6481 (ppp)
REVERT: E  247 ARG cc_start: 0.7683 (tpt90) cc_final: 0.6317 (pmt-80)
REVERT: F  181 LEU cc_start: 0.8840 (mt) cc_final: 0.8563 (mt)
REVERT: F  193 LYS cc_start: 0.5022 (OUTLIER) cc_final: 0.3814 (pttm)
REVERT: F  239 HIS cc_start: 0.7638 (t70) cc_final: 0.7209 (t-170)
REVERT: F  246 GLU cc_start: 0.3565 (OUTLIER) cc_final: 0.2565 (pm20)
  outliers start: 31
  outliers final: 20
  residues processed: 205
  average time/residue: 0.1013
  time to fit residues: 26.4027
Evaluate side-chains
  202 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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 A residue  216 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  241 GLU
Chi-restraints excluded: chain B residue  245 GLN
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  216 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  216 LEU
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  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 60 optimal weight:    0.1980
   chunk 67 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 222 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.116405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.107281 restraints weight = 16034.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.109525 restraints weight = 6548.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.110899 restraints weight = 3472.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.111825 restraints weight = 2171.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.112379 restraints weight = 1533.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.6691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6630  Z= 0.175
  Angle     :  0.764  13.829   9018  Z= 0.391
  Chirality :  0.056   0.159   1086
  Planarity :  0.003   0.042   1116
  Dihedral  :  6.243  26.942    894
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.63 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 247 
 TYR   0.022   0.002   TYR A 143 
 PHE   0.010   0.001   PHE D 237 
 HIS   0.011   0.001   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6624)
  covalent geometry    : angle       0.76419 ( 9006)
  SS BOND              : bond        0.00059 (    6)
  SS BOND              : angle       0.29574 (   12)
  hydrogen bonds       : bond        0.02619 (  151)
  hydrogen bonds       : angle       5.03885 (  453)

*********************** 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
  225 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8491 (tttm)
REVERT: A  161 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: A  163 GLU cc_start: 0.8090 (mp0) cc_final: 0.7434 (mp0)
REVERT: A  181 LEU cc_start: 0.8881 (mt) cc_final: 0.8651 (mt)
REVERT: A  190 LEU cc_start: 0.9337 (mm) cc_final: 0.9097 (mt)
REVERT: A  252 ASP cc_start: 0.8160 (t0) cc_final: 0.7628 (t0)
REVERT: B  124 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8129 (mtmm)
REVERT: B  134 SER cc_start: 0.9202 (t) cc_final: 0.8878 (t)
REVERT: B  145 ASN cc_start: 0.7955 (m-40) cc_final: 0.7262 (t0)
REVERT: B  150 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8577 (mt)
REVERT: B  180 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7331 (mpt180)
REVERT: B  205 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6716 (mm-30)
REVERT: B  228 MET cc_start: 0.8645 (ttp) cc_final: 0.7382 (ttp)
REVERT: B  229 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7624 (mp10)
REVERT: C  213 PHE cc_start: 0.8051 (t80) cc_final: 0.7825 (t80)
REVERT: C  228 MET cc_start: 0.8469 (ttp) cc_final: 0.7137 (ttp)
REVERT: C  229 GLN cc_start: 0.7794 (mp10) cc_final: 0.6333 (mp10)
REVERT: C  240 SER cc_start: 0.9209 (m) cc_final: 0.8781 (p)
REVERT: C  245 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7842 (mt0)
REVERT: C  247 ARG cc_start: 0.7590 (tpt90) cc_final: 0.6373 (pmt-80)
REVERT: D  124 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8362 (mttp)
REVERT: D  180 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7177 (mpt180)
REVERT: D  220 LYS cc_start: 0.9363 (tttp) cc_final: 0.9104 (ttmt)
REVERT: D  229 GLN cc_start: 0.8072 (mp10) cc_final: 0.7101 (mp10)
REVERT: E  120 SER cc_start: 0.8145 (p) cc_final: 0.7570 (p)
REVERT: E  145 ASN cc_start: 0.7428 (m-40) cc_final: 0.6739 (t0)
REVERT: E  161 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8215 (mt-10)
REVERT: E  181 LEU cc_start: 0.8818 (mm) cc_final: 0.8026 (pt)
REVERT: E  182 ASN cc_start: 0.8735 (t0) cc_final: 0.8486 (t0)
REVERT: E  216 LEU cc_start: 0.9258 (pp) cc_final: 0.7897 (mt)
REVERT: E  236 TYR cc_start: 0.8205 (t80) cc_final: 0.7778 (t80)
REVERT: E  247 ARG cc_start: 0.7436 (tpt90) cc_final: 0.5743 (pmt-80)
REVERT: F  161 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8320 (mm-30)
REVERT: F  168 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: F  181 LEU cc_start: 0.8786 (mt) cc_final: 0.8528 (mt)
REVERT: F  193 LYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4009 (pttm)
REVERT: F  246 GLU cc_start: 0.3374 (OUTLIER) cc_final: 0.2371 (pm20)
REVERT: F  252 ASP cc_start: 0.8123 (t0) cc_final: 0.7743 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 209
  average time/residue: 0.0964
  time to fit residues: 25.8175
Evaluate side-chains
  208 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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 A residue  216 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  241 GLU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  216 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  216 LEU
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Chi-restraints excluded: chain F residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.118073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.108963 restraints weight = 15688.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.111189 restraints weight = 6573.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.112502 restraints weight = 3519.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.113455 restraints weight = 2240.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.114089 restraints weight = 1585.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.6830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6630  Z= 0.159
  Angle     :  0.762  15.629   9018  Z= 0.390
  Chirality :  0.056   0.254   1086
  Planarity :  0.003   0.037   1116
  Dihedral  :  6.147  25.821    894
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.56 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG F 247 
 TYR   0.018   0.002   TYR B 143 
 PHE   0.010   0.001   PHE D 237 
 HIS   0.016   0.003   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6624)
  covalent geometry    : angle       0.76204 ( 9006)
  SS BOND              : bond        0.00076 (    6)
  SS BOND              : angle       0.25868 (   12)
  hydrogen bonds       : bond        0.02567 (  151)
  hydrogen bonds       : angle       5.12396 (  453)

********************** 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
  221 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 196
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9244 (ttmm) cc_final: 0.8483 (tttm)
REVERT: A  145 ASN cc_start: 0.8000 (m-40) cc_final: 0.7350 (t0)
REVERT: A  161 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8014 (mt-10)
REVERT: A  163 GLU cc_start: 0.8107 (mp0) cc_final: 0.7287 (mp0)
REVERT: A  240 SER cc_start: 0.9087 (m) cc_final: 0.8705 (p)
REVERT: A  252 ASP cc_start: 0.8152 (t0) cc_final: 0.7618 (t0)
REVERT: B  134 SER cc_start: 0.9154 (t) cc_final: 0.8809 (t)
REVERT: B  145 ASN cc_start: 0.7896 (m-40) cc_final: 0.7347 (t0)
REVERT: B  150 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8563 (mt)
REVERT: B  180 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7334 (mpt180)
REVERT: B  210 MET cc_start: 0.6491 (mpp) cc_final: 0.6212 (mpp)
REVERT: B  228 MET cc_start: 0.8545 (ttp) cc_final: 0.7585 (ttp)
REVERT: B  229 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7699 (mp10)
REVERT: C  213 PHE cc_start: 0.8059 (t80) cc_final: 0.7818 (t80)
REVERT: C  228 MET cc_start: 0.8289 (ttp) cc_final: 0.7347 (ttp)
REVERT: C  229 GLN cc_start: 0.7711 (mp10) cc_final: 0.6797 (mp10)
REVERT: C  240 SER cc_start: 0.9171 (m) cc_final: 0.8810 (p)
REVERT: C  247 ARG cc_start: 0.7546 (tpt90) cc_final: 0.6253 (pmt-80)
REVERT: D  129 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8258 (tttp)
REVERT: D  180 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7121 (mpt180)
REVERT: D  220 LYS cc_start: 0.9332 (tttp) cc_final: 0.9065 (ttmt)
REVERT: D  229 GLN cc_start: 0.7813 (mp10) cc_final: 0.7439 (mp10)
REVERT: E  120 SER cc_start: 0.8195 (p) cc_final: 0.7595 (p)
REVERT: E  145 ASN cc_start: 0.7389 (m-40) cc_final: 0.6650 (t0)
REVERT: E  181 LEU cc_start: 0.8842 (mm) cc_final: 0.8036 (pt)
REVERT: E  182 ASN cc_start: 0.8731 (t0) cc_final: 0.8479 (t0)
REVERT: E  192 MET cc_start: 0.6978 (mmp) cc_final: 0.5932 (ppp)
REVERT: E  216 LEU cc_start: 0.9204 (pp) cc_final: 0.7867 (mt)
REVERT: E  247 ARG cc_start: 0.7357 (tpt90) cc_final: 0.5684 (pmt-80)
REVERT: F  168 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8526 (tm-30)
REVERT: F  181 LEU cc_start: 0.8816 (mt) cc_final: 0.8602 (mt)
REVERT: F  193 LYS cc_start: 0.5104 (OUTLIER) cc_final: 0.3886 (pttm)
REVERT: F  252 ASP cc_start: 0.8140 (t0) cc_final: 0.7726 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 209
  average time/residue: 0.0920
  time to fit residues: 24.6953
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  : 0.276 
-------------------------------------------------------------------------------
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 A residue  216 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain B residue  241 GLU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  180 ARG
Chi-restraints excluded: chain E residue  245 GLN
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  214 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 148 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.118948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.109900 restraints weight = 15803.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.112032 restraints weight = 6641.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.113410 restraints weight = 3612.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.114329 restraints weight = 2276.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.114958 restraints weight = 1609.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.6922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6630  Z= 0.156
  Angle     :  0.731  12.641   9018  Z= 0.381
  Chirality :  0.055   0.159   1086
  Planarity :  0.003   0.036   1116
  Dihedral  :  6.079  25.417    894
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.26), residues: 798
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 247 
 TYR   0.018   0.002   TYR A 143 
 PHE   0.009   0.001   PHE B 171 
 HIS   0.015   0.003   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6624)
  covalent geometry    : angle       0.73151 ( 9006)
  SS BOND              : bond        0.00081 (    6)
  SS BOND              : angle       0.24766 (   12)
  hydrogen bonds       : bond        0.02624 (  151)
  hydrogen bonds       : angle       5.26198 (  453)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1447.71 seconds
wall clock time: 25 minutes 45.06 seconds (1545.06 seconds total)