Starting phenix.real_space_refine
on Wed Sep 17 11:54:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b65_44247/09_2025/9b65_44247.map"
  }
  resolution = 3.03
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5416      2.51       5
     N    1448      2.21       5
     O    1538      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8463
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1659
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "B"
      Number of atoms: 2573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2573
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2013
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 256}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1751
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Classifications: {'peptide': 1}
  Time building chain proxies: 2.20, per 1000 atoms: 0.26
  Number of scatterers: 8463
  At special positions: 0
  Unit cell: (103.96, 119.6, 104.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     F       1      9.00
     O    1538      8.00
     N    1448      7.00
     C    5416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.02

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 479.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      32.3% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 29
      removed outlier: 3.510A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.626A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.032A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.566A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 3.531A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.596A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.892A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 8
      removed outlier: 3.619A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 4 through 8'
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 4.044A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 8 through 22
      removed outlier: 3.743A  pdb=" N   VAL C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU C  17 " --> pdb=" O   ARG C  13 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 42
      removed outlier: 3.921A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   TYR C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 114
      No H-bonds generated for 'chain 'R' and resid 112 through 114'
    Processing helix  chain 'R' and resid 115 through 121
      removed outlier: 3.538A  pdb=" N   ALA R 120 " --> pdb=" O   GLN R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 121 through 127
      removed outlier: 3.753A  pdb=" N   THR R 125 " --> pdb=" O   VAL R 121 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 138
      removed outlier: 3.794A  pdb=" N   LEU R 138 " --> pdb=" O   ASN R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 142
    Processing helix  chain 'R' and resid 154 through 172
      removed outlier: 3.809A  pdb=" N   LEU R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL R 171 " --> pdb=" O   SER R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 177
    Processing helix  chain 'R' and resid 189 through 220
      removed outlier: 3.514A  pdb=" N   VAL R 204 " --> pdb=" O   PHE R 200 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG R 214 " --> pdb=" O   THR R 210 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR R 215 " --> pdb=" O   ALA R 211 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE R 216 " --> pdb=" O   ILE R 212 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE R 218 " --> pdb=" O   ARG R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 247
      removed outlier: 4.151A  pdb=" N   ILE R 245 " --> pdb=" O   TRP R 241 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 287
      removed outlier: 3.755A  pdb=" N   ILE R 280 " --> pdb=" O   LEU R 276 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL R 285 " --> pdb=" O   GLY R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 290 through 311
      removed outlier: 3.675A  pdb=" N   TYR R 294 " --> pdb=" O   ILE R 290 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 341 through 357
      removed outlier: 5.321A  pdb=" N   LEU R 347 " --> pdb=" O   LYS R 343 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE R 348 " --> pdb=" O   THR R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 357 through 366
      removed outlier: 3.874A  pdb=" N   ASP R 366 " --> pdb=" O   ILE R 362 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 383
    Processing helix  chain 'R' and resid 384 through 397
      removed outlier: 3.994A  pdb=" N   SER R 390 " --> pdb=" O   CYS R 386 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR R 391 " --> pdb=" O   LEU R 387 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      Proline residue:  R 394  - end of helix
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.097A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.777A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 5.888A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.840A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.400A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.892A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.574A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.172A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.562A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.624A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.587A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.754A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.962A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.594A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183
      removed outlier: 3.663A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183
      removed outlier: 3.663A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    963 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: 1.38

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1340
        1.31 -     1.43: 2408
        1.43 -     1.56: 4805
        1.56 -     1.68: 0
        1.68 -     1.81: 87
  Bond restraints: 8640
  Sorted by residual:
  bond pdb=" N   KCA R 501 "
       pdb=" CAB KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.345  1.462 -0.117 2.00e-02 2.50e+03 3.41e+01
  bond pdb=" C   KCA R 501 "
       pdb=" OAF KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.320  1.391 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" CAB KCA R 501 "
       pdb=" CAM KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.476  1.526 -0.050 2.00e-02 2.50e+03 6.26e+00
  bond pdb=" CAG KCA R 501 "
       pdb=" OAF KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.430  1.392  0.038 2.00e-02 2.50e+03 3.68e+00
  bond pdb=" CAB KCA R 501 "
       pdb=" OAA KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.223  1.185  0.038 2.00e-02 2.50e+03 3.61e+00
  ... (remaining 8635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 11687
        4.03 -     8.06: 43
        8.06 -    12.09: 1
       12.09 -    16.13: 0
       16.13 -    20.16: 1
  Bond angle restraints: 11732
  Sorted by residual:
  angle pdb=" C   SER R 146 "
        pdb=" N   LEU R 147 "
        pdb=" CA  LEU R 147 "
      ideal   model   delta    sigma   weight residual
     121.70  129.32   -7.62 1.80e+00 3.09e-01 1.79e+01
  angle pdb=" C   HIS R 178 "
        pdb=" N   VAL R 179 "
        pdb=" CA  VAL R 179 "
      ideal   model   delta    sigma   weight residual
     122.77  118.51    4.26 1.05e+00 9.07e-01 1.65e+01
  angle pdb=" N   THR R 130 "
        pdb=" CA  THR R 130 "
        pdb=" C   THR R 130 "
      ideal   model   delta    sigma   weight residual
     113.56  108.27    5.29 1.39e+00 5.18e-01 1.45e+01
  angle pdb=" C   ILE R 271 "
        pdb=" N   ASP R 272 "
        pdb=" CA  ASP R 272 "
      ideal   model   delta    sigma   weight residual
     120.82  126.25   -5.43 1.47e+00 4.63e-01 1.36e+01
  angle pdb=" C   GLU C  58 "
        pdb=" N   ASN C  59 "
        pdb=" CA  ASN C  59 "
      ideal   model   delta    sigma   weight residual
     121.41  101.25   20.16 5.58e+00 3.21e-02 1.30e+01
  ... (remaining 11727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.30: 4997
       25.30 -    50.60: 82
       50.60 -    75.90: 4
       75.90 -   101.20: 1
      101.20 -   126.49: 1
  Dihedral angle restraints: 5085
    sinusoidal: 1861
      harmonic: 3224
  Sorted by residual:
  dihedral pdb=" CA  TYR S 178 "
           pdb=" C   TYR S 178 "
           pdb=" N   ARG S 179 "
           pdb=" CA  ARG S 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.91  -43.09     0      5.00e+00 4.00e-02 7.43e+01
  dihedral pdb=" CA  HIS R 270 "
           pdb=" C   HIS R 270 "
           pdb=" N   ILE R 271 "
           pdb=" CA  ILE R 271 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.89  -26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE R 174 "
           pdb=" C   PHE R 174 "
           pdb=" N   ILE R 175 "
           pdb=" CA  ILE R 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.74   24.26     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 5082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 796
       0.038 -    0.075: 407
       0.075 -    0.113: 133
       0.113 -    0.151: 24
       0.151 -    0.188: 3
  Chirality restraints: 1363
  Sorted by residual:
  chirality pdb=" CA  ASP B   5 "
            pdb=" N   ASP B   5 "
            pdb=" C   ASP B   5 "
            pdb=" CB  ASP B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CG  LEU S 162 "
            pdb=" CB  LEU S 162 "
            pdb=" CD1 LEU S 162 "
            pdb=" CD2 LEU S 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.98e-01
  chirality pdb=" CA  KCA R 501 "
            pdb=" N   KCA R 501 "
            pdb=" C   KCA R 501 "
            pdb=" CB  KCA R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 1360 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "   -0.019 2.00e-02 2.50e+03   1.84e-02 8.49e+00
        pdb=" CG  TRP S 111 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.016 2.00e-02 2.50e+03   1.85e-02 6.83e+00
        pdb=" CG  TYR B  59 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S  94 "   -0.010 2.00e-02 2.50e+03   1.39e-02 3.84e+00
        pdb=" CG  TYR S  94 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR S  94 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR S  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR S  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR S  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR S  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR S  94 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 101
        2.58 -     3.16: 7596
        3.16 -     3.74: 12648
        3.74 -     4.32: 19767
        4.32 -     4.90: 31492
  Nonbonded interactions: 71604
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.000 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.008 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.130 3.040
  ... (remaining 71599 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.740
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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      :  0.007   0.117   8642  Z= 0.332
  Angle     :  0.824  20.157  11734  Z= 0.464
  Chirality :  0.048   0.188   1363
  Planarity :  0.004   0.047   1470
  Dihedral  :  9.879 126.494   2998
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 29.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.61 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -4.23 (0.22), residues: 1091
  helix: -4.13 (0.17), residues: 314
  sheet: -2.01 (0.29), residues: 262
  loop : -2.22 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 314 
 TYR   0.045   0.003   TYR B  59 
 PHE   0.029   0.003   PHE A 354 
 TRP   0.048   0.003   TRP S 111 
 HIS   0.014   0.002   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 ( 8640)
  covalent geometry    : angle       0.82369 (11732)
  SS BOND              : bond        0.00801 (    1)
  SS BOND              : angle       1.14394 (    2)
  hydrogen bonds       : bond        0.26462 (  325)
  hydrogen bonds       : angle      11.14333 (  963)
  Misc. bond           : bond        0.00184 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8113 (mttt) cc_final: 0.7686 (mtpt)
REVERT: A   29 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8065 (ttmt)
REVERT: A  200 ASP cc_start: 0.8185 (t70) cc_final: 0.7883 (t0)
REVERT: A  231 ASP cc_start: 0.7871 (t70) cc_final: 0.7558 (t0)
REVERT: A  242 ARG cc_start: 0.4932 (mpt180) cc_final: 0.3685 (ttm-80)
REVERT: A  251 ASP cc_start: 0.8222 (t0) cc_final: 0.7930 (t0)
REVERT: B  155 ASN cc_start: 0.8204 (t0) cc_final: 0.8001 (t0)
REVERT: B  337 LYS cc_start: 0.8526 (mttm) cc_final: 0.8321 (mttt)
REVERT: C   20 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7371 (mtmm)
REVERT: R  226 ARG cc_start: 0.5958 (mtm110) cc_final: 0.5318 (ttp-110)
REVERT: R  240 MET cc_start: 0.5162 (mmp) cc_final: 0.4225 (mmp)
REVERT: S   23 SER cc_start: 0.8653 (m) cc_final: 0.8361 (t)
REVERT: S  142 SER cc_start: 0.8281 (t) cc_final: 0.7843 (p)
REVERT: S  194 SER cc_start: 0.8140 (t) cc_final: 0.7863 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1338
  time to fit residues: 33.1705
Evaluate side-chains
  159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  62 HIS
B  91 HIS
B 110 ASN
B 225 HIS
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 295 ASN
S  39 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.169991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.114279 restraints weight = 9251.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.33
r_work: 0.3051 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8642  Z= 0.185
  Angle     :  0.699  15.647  11734  Z= 0.367
  Chirality :  0.047   0.164   1363
  Planarity :  0.005   0.051   1470
  Dihedral  :  7.267 122.907   1211
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.13 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  7.31 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.36 (0.23), residues: 1091
  helix: -3.15 (0.21), residues: 337
  sheet: -1.67 (0.28), residues: 274
  loop : -1.66 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 197 
 TYR   0.026   0.002   TYR B  59 
 PHE   0.023   0.002   PHE A 189 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 8640)
  covalent geometry    : angle       0.69916 (11732)
  SS BOND              : bond        0.00584 (    1)
  SS BOND              : angle       1.12670 (    2)
  hydrogen bonds       : bond        0.04956 (  325)
  hydrogen bonds       : angle       6.26341 (  963)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8159 (mttt) cc_final: 0.7641 (mtpt)
REVERT: A   18 MET cc_start: 0.8711 (ttm) cc_final: 0.8405 (ttm)
REVERT: A   29 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7805 (ttmt)
REVERT: A   48 THR cc_start: 0.6913 (t) cc_final: 0.6629 (p)
REVERT: A  231 ASP cc_start: 0.7994 (t70) cc_final: 0.7607 (t0)
REVERT: A  242 ARG cc_start: 0.4601 (mpt180) cc_final: 0.3235 (ttm-80)
REVERT: A  243 MET cc_start: 0.7946 (tpp) cc_final: 0.7257 (tpp)
REVERT: A  244 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7221 (m170)
REVERT: A  247 MET cc_start: 0.8152 (mtp) cc_final: 0.7718 (mtp)
REVERT: A  251 ASP cc_start: 0.8427 (t0) cc_final: 0.7872 (t0)
REVERT: A  306 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7489 (mm-40)
REVERT: A  308 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7119 (mp0)
REVERT: B   14 LEU cc_start: 0.7289 (tp) cc_final: 0.7072 (tp)
REVERT: B   17 GLN cc_start: 0.8007 (tt0) cc_final: 0.7790 (tt0)
REVERT: B  155 ASN cc_start: 0.8325 (t0) cc_final: 0.7894 (t0)
REVERT: B  197 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7453 (mtt90)
REVERT: C   20 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7455 (mtmm)
REVERT: C   48 ASP cc_start: 0.7890 (p0) cc_final: 0.7677 (p0)
REVERT: R  109 MET cc_start: 0.3729 (pmt) cc_final: 0.3504 (pmm)
REVERT: R  278 PHE cc_start: 0.6027 (t80) cc_final: 0.5802 (t80)
REVERT: R  356 TRP cc_start: 0.7295 (m100) cc_final: 0.6352 (m100)
REVERT: S   23 SER cc_start: 0.8616 (m) cc_final: 0.8276 (t)
REVERT: S  146 SER cc_start: 0.8830 (p) cc_final: 0.8620 (t)
REVERT: S  171 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7982 (mt0)
  outliers start: 17
  outliers final: 7
  residues processed: 184
  average time/residue: 0.1221
  time to fit residues: 29.1954
Evaluate side-chains
  171 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 162
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 331 ASN
** B 259 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 = 0.3827 r_free = 0.3827 target = 0.166933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.111777 restraints weight = 9396.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.25
r_work: 0.3022 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8642  Z= 0.181
  Angle     :  0.657  11.823  11734  Z= 0.341
  Chirality :  0.045   0.164   1363
  Planarity :  0.004   0.045   1470
  Dihedral  :  6.928 117.116   1211
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.77 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.96 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.69 (0.24), residues: 1091
  helix: -2.41 (0.24), residues: 333
  sheet: -1.30 (0.28), residues: 277
  loop : -1.41 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.026   0.002   TYR S 178 
 PHE   0.017   0.002   PHE A 354 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8640)
  covalent geometry    : angle       0.65702 (11732)
  SS BOND              : bond        0.00485 (    1)
  SS BOND              : angle       1.08271 (    2)
  hydrogen bonds       : bond        0.04274 (  325)
  hydrogen bonds       : angle       5.66556 (  963)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8249 (mttt) cc_final: 0.7791 (mtpt)
REVERT: A   18 MET cc_start: 0.8724 (ttm) cc_final: 0.8386 (ttm)
REVERT: A  231 ASP cc_start: 0.8087 (t70) cc_final: 0.7728 (t0)
REVERT: A  243 MET cc_start: 0.8017 (tpp) cc_final: 0.7397 (tpp)
REVERT: A  244 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7302 (m170)
REVERT: A  247 MET cc_start: 0.8124 (mtp) cc_final: 0.7790 (mtt)
REVERT: A  251 ASP cc_start: 0.8366 (t0) cc_final: 0.7901 (t0)
REVERT: A  306 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7343 (mm110)
REVERT: A  308 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6836 (mp0)
REVERT: B  155 ASN cc_start: 0.8382 (t0) cc_final: 0.7897 (t0)
REVERT: B  197 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7690 (mmt-90)
REVERT: B  219 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7512 (mtp85)
REVERT: B  337 LYS cc_start: 0.8546 (mttt) cc_final: 0.8109 (mttt)
REVERT: C   20 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7558 (mtmm)
REVERT: C   36 ASP cc_start: 0.8756 (t70) cc_final: 0.8493 (m-30)
REVERT: C   42 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7351 (mp0)
REVERT: R  109 MET cc_start: 0.3831 (pmt) cc_final: 0.3593 (pmm)
REVERT: R  278 PHE cc_start: 0.5852 (t80) cc_final: 0.5591 (t80)
REVERT: R  356 TRP cc_start: 0.7241 (m100) cc_final: 0.6302 (m100)
REVERT: S   23 SER cc_start: 0.8625 (m) cc_final: 0.8299 (t)
REVERT: S  113 GLN cc_start: 0.8117 (mm110) cc_final: 0.7892 (mm-40)
REVERT: S  171 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8043 (mt0)
  outliers start: 19
  outliers final: 13
  residues processed: 171
  average time/residue: 0.1159
  time to fit residues: 26.0776
Evaluate side-chains
  167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0470
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.168818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.113829 restraints weight = 9435.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.27
r_work: 0.3053 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8642  Z= 0.135
  Angle     :  0.612  11.250  11734  Z= 0.317
  Chirality :  0.044   0.153   1363
  Planarity :  0.004   0.054   1470
  Dihedral  :  6.610 115.192   1211
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.13 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: 1091
  helix: -1.90 (0.26), residues: 336
  sheet: -1.05 (0.28), residues: 274
  loop : -1.22 (0.30), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 129 
 TYR   0.026   0.001   TYR S 178 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8640)
  covalent geometry    : angle       0.61172 (11732)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       1.05740 (    2)
  hydrogen bonds       : bond        0.03830 (  325)
  hydrogen bonds       : angle       5.31944 (  963)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8191 (mttt) cc_final: 0.7817 (mtpt)
REVERT: A   18 MET cc_start: 0.8690 (ttm) cc_final: 0.8333 (ttm)
REVERT: A  232 LEU cc_start: 0.7268 (mt) cc_final: 0.6954 (mp)
REVERT: A  243 MET cc_start: 0.8041 (tpp) cc_final: 0.7492 (tpp)
REVERT: A  244 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7360 (m170)
REVERT: A  251 ASP cc_start: 0.8121 (t0) cc_final: 0.7690 (t0)
REVERT: A  306 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7285 (mm110)
REVERT: A  308 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6858 (mp0)
REVERT: B   13 GLN cc_start: 0.6722 (pp30) cc_final: 0.6423 (pp30)
REVERT: B  130 GLU cc_start: 0.8635 (mp0) cc_final: 0.8429 (mt-10)
REVERT: B  197 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7633 (mpt180)
REVERT: B  219 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7537 (mtp85)
REVERT: B  325 MET cc_start: 0.8606 (tpp) cc_final: 0.8219 (mmt)
REVERT: B  337 LYS cc_start: 0.8552 (mttt) cc_final: 0.8188 (mttt)
REVERT: C   14 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7695 (ttpp)
REVERT: C   17 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7907 (mm-30)
REVERT: C   20 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7466 (mtmm)
REVERT: C   36 ASP cc_start: 0.8485 (t70) cc_final: 0.8279 (m-30)
REVERT: R  109 MET cc_start: 0.3674 (pmt) cc_final: 0.3441 (pmm)
REVERT: R  164 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6102 (tt)
REVERT: R  353 ILE cc_start: 0.7408 (mm) cc_final: 0.7064 (mt)
REVERT: R  356 TRP cc_start: 0.7182 (m100) cc_final: 0.6267 (m100)
REVERT: R  404 LEU cc_start: 0.5124 (mm) cc_final: 0.4919 (mm)
REVERT: S   18 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.7546 (tpt170)
REVERT: S   23 SER cc_start: 0.8644 (m) cc_final: 0.8327 (t)
REVERT: S  113 GLN cc_start: 0.8050 (mm110) cc_final: 0.7844 (mm-40)
REVERT: S  171 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8145 (mt0)
  outliers start: 24
  outliers final: 13
  residues processed: 175
  average time/residue: 0.1190
  time to fit residues: 27.4144
Evaluate side-chains
  171 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  349 LEU
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 100 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 GLN
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.167254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.111817 restraints weight = 9459.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.28
r_work: 0.3024 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8642  Z= 0.175
  Angle     :  0.633  11.670  11734  Z= 0.327
  Chirality :  0.044   0.156   1363
  Planarity :  0.004   0.058   1470
  Dihedral  :  6.564 111.075   1211
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.95 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.92 (0.25), residues: 1091
  helix: -1.55 (0.27), residues: 331
  sheet: -0.91 (0.28), residues: 291
  loop : -1.09 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  27 
 TYR   0.024   0.002   TYR S 178 
 PHE   0.016   0.002   PHE S  80 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8640)
  covalent geometry    : angle       0.63308 (11732)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       1.22085 (    2)
  hydrogen bonds       : bond        0.03847 (  325)
  hydrogen bonds       : angle       5.25469 (  963)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8157 (mttt) cc_final: 0.7761 (mtpt)
REVERT: A  231 ASP cc_start: 0.8098 (t70) cc_final: 0.7718 (t0)
REVERT: A  232 LEU cc_start: 0.7283 (mt) cc_final: 0.6823 (mp)
REVERT: A  251 ASP cc_start: 0.8046 (t0) cc_final: 0.7837 (t0)
REVERT: A  308 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6749 (mp0)
REVERT: B   13 GLN cc_start: 0.6924 (pp30) cc_final: 0.6609 (pp30)
REVERT: B  130 GLU cc_start: 0.8654 (mp0) cc_final: 0.8382 (mt-10)
REVERT: B  197 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7604 (mpt180)
REVERT: B  219 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7506 (mtp85)
REVERT: B  325 MET cc_start: 0.8602 (tpp) cc_final: 0.7987 (mmp)
REVERT: B  337 LYS cc_start: 0.8592 (mttt) cc_final: 0.8223 (mttt)
REVERT: C   14 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7622 (ttpp)
REVERT: C   36 ASP cc_start: 0.8487 (t70) cc_final: 0.8232 (m-30)
REVERT: R  109 MET cc_start: 0.3728 (pmt) cc_final: 0.3475 (pmm)
REVERT: R  150 ARG cc_start: 0.6369 (ptp-110) cc_final: 0.5827 (ptp-110)
REVERT: R  164 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6144 (tm)
REVERT: R  278 PHE cc_start: 0.5982 (t80) cc_final: 0.5714 (t80)
REVERT: R  356 TRP cc_start: 0.7205 (m100) cc_final: 0.6205 (m100)
REVERT: R  404 LEU cc_start: 0.5157 (mm) cc_final: 0.4945 (mm)
REVERT: S   23 SER cc_start: 0.8750 (m) cc_final: 0.8409 (t)
REVERT: S  113 GLN cc_start: 0.8130 (mm110) cc_final: 0.7908 (mm-40)
REVERT: S  171 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8107 (mt0)
REVERT: S  194 SER cc_start: 0.8683 (t) cc_final: 0.8389 (m)
  outliers start: 25
  outliers final: 17
  residues processed: 180
  average time/residue: 0.1295
  time to fit residues: 30.0496
Evaluate side-chains
  183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.166482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.110930 restraints weight = 9455.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.28
r_work: 0.3013 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8642  Z= 0.197
  Angle     :  0.649  12.650  11734  Z= 0.335
  Chirality :  0.045   0.172   1363
  Planarity :  0.004   0.071   1470
  Dihedral  :  6.480 102.907   1211
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.86 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.75 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.82 (0.25), residues: 1091
  helix: -1.47 (0.27), residues: 335
  sheet: -0.80 (0.28), residues: 290
  loop : -1.08 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 220 
 TYR   0.024   0.002   TYR S 178 
 PHE   0.015   0.002   PHE A 354 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8640)
  covalent geometry    : angle       0.64916 (11732)
  SS BOND              : bond        0.00317 (    1)
  SS BOND              : angle       1.39114 (    2)
  hydrogen bonds       : bond        0.03909 (  325)
  hydrogen bonds       : angle       5.25836 (  963)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 167
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8141 (mttt) cc_final: 0.7831 (mmtp)
REVERT: A  231 ASP cc_start: 0.8161 (t70) cc_final: 0.7738 (t0)
REVERT: A  251 ASP cc_start: 0.8025 (t0) cc_final: 0.7748 (t0)
REVERT: A  306 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6904 (mm110)
REVERT: A  308 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6813 (mp0)
REVERT: B   13 GLN cc_start: 0.6822 (pp30) cc_final: 0.6554 (pp30)
REVERT: B  197 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7577 (mpt180)
REVERT: B  219 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7522 (mtp85)
REVERT: B  337 LYS cc_start: 0.8572 (mttt) cc_final: 0.8219 (mttt)
REVERT: C   14 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7662 (ttpp)
REVERT: C   27 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8148 (mtt90)
REVERT: C   48 ASP cc_start: 0.7705 (p0) cc_final: 0.7503 (p0)
REVERT: R  109 MET cc_start: 0.3800 (pmt) cc_final: 0.3523 (pmm)
REVERT: R  150 ARG cc_start: 0.6410 (ptp-110) cc_final: 0.5862 (ptp-110)
REVERT: R  220 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6555 (mmp80)
REVERT: R  278 PHE cc_start: 0.5962 (t80) cc_final: 0.5698 (t80)
REVERT: R  336 ARG cc_start: 0.5626 (tpm-80) cc_final: 0.3287 (mmt-90)
REVERT: R  340 ARG cc_start: 0.6666 (ttm110) cc_final: 0.6418 (ptm160)
REVERT: R  384 MET cc_start: 0.6694 (mmp) cc_final: 0.6441 (mmp)
REVERT: R  405 ARG cc_start: 0.5835 (mtm-85) cc_final: 0.5204 (mtm-85)
REVERT: S   23 SER cc_start: 0.8747 (m) cc_final: 0.8409 (t)
REVERT: S  113 GLN cc_start: 0.8146 (mm110) cc_final: 0.7875 (mm-40)
REVERT: S  171 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8080 (mt0)
REVERT: S  194 SER cc_start: 0.8698 (t) cc_final: 0.8407 (m)
  outliers start: 30
  outliers final: 20
  residues processed: 184
  average time/residue: 0.1287
  time to fit residues: 30.5600
Evaluate side-chains
  185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0470
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 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 = 0.3835 r_free = 0.3835 target = 0.167773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.112339 restraints weight = 9529.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.31
r_work: 0.3029 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8642  Z= 0.161
  Angle     :  0.633  12.308  11734  Z= 0.321
  Chirality :  0.044   0.154   1363
  Planarity :  0.004   0.072   1470
  Dihedral  :  6.230  97.485   1211
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.95 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.01 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.69 (0.25), residues: 1091
  helix: -1.30 (0.27), residues: 333
  sheet: -0.75 (0.29), residues: 282
  loop : -1.04 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 220 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.014   0.001   PHE R 237 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8640)
  covalent geometry    : angle       0.63248 (11732)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       1.26870 (    2)
  hydrogen bonds       : bond        0.03682 (  325)
  hydrogen bonds       : angle       5.10998 (  963)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8142 (mttt) cc_final: 0.7854 (mmtp)
REVERT: A  243 MET cc_start: 0.7391 (tpp) cc_final: 0.7029 (ttm)
REVERT: A  251 ASP cc_start: 0.8009 (t0) cc_final: 0.7730 (t0)
REVERT: A  308 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6814 (mp0)
REVERT: B  197 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7575 (mpt180)
REVERT: B  219 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7526 (mtp85)
REVERT: B  325 MET cc_start: 0.8601 (tpp) cc_final: 0.8206 (mmt)
REVERT: C   14 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7619 (ttpp)
REVERT: R  109 MET cc_start: 0.3812 (pmt) cc_final: 0.3538 (pmm)
REVERT: R  220 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6616 (mmp80)
REVERT: R  336 ARG cc_start: 0.5508 (tpm-80) cc_final: 0.3171 (mmt-90)
REVERT: R  339 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7072 (pt)
REVERT: R  340 ARG cc_start: 0.6610 (ttm110) cc_final: 0.6303 (ptm160)
REVERT: R  405 ARG cc_start: 0.5797 (mtm-85) cc_final: 0.5193 (mtm-85)
REVERT: S   23 SER cc_start: 0.8669 (m) cc_final: 0.8339 (t)
REVERT: S  113 GLN cc_start: 0.8081 (mm110) cc_final: 0.7827 (mm-40)
REVERT: S  171 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8071 (mt0)
REVERT: S  194 SER cc_start: 0.8685 (t) cc_final: 0.8396 (m)
  outliers start: 25
  outliers final: 20
  residues processed: 180
  average time/residue: 0.1268
  time to fit residues: 29.0962
Evaluate side-chains
  188 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  306 VAL
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  339 ILE
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0980
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.167842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.112802 restraints weight = 9514.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.30
r_work: 0.3036 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8642  Z= 0.150
  Angle     :  0.623  11.925  11734  Z= 0.318
  Chirality :  0.044   0.153   1363
  Planarity :  0.004   0.070   1470
  Dihedral  :  6.072  93.131   1211
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 17.24 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.64 (0.25), residues: 1091
  helix: -1.15 (0.27), residues: 342
  sheet: -0.73 (0.28), residues: 290
  loop : -1.09 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  27 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.014   0.001   PHE R 237 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8640)
  covalent geometry    : angle       0.62248 (11732)
  SS BOND              : bond        0.00287 (    1)
  SS BOND              : angle       1.26403 (    2)
  hydrogen bonds       : bond        0.03620 (  325)
  hydrogen bonds       : angle       4.99175 (  963)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8129 (mttt) cc_final: 0.7855 (mmtp)
REVERT: A  251 ASP cc_start: 0.8000 (t0) cc_final: 0.7727 (t0)
REVERT: A  308 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6871 (mp0)
REVERT: A  337 ASP cc_start: 0.8127 (m-30) cc_final: 0.7926 (m-30)
REVERT: B   52 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7861 (mtp85)
REVERT: B  181 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7561 (p)
REVERT: B  197 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7576 (mpt180)
REVERT: B  219 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7510 (mtp85)
REVERT: B  325 MET cc_start: 0.8627 (tpp) cc_final: 0.8170 (mmt)
REVERT: B  337 LYS cc_start: 0.8559 (mttt) cc_final: 0.8239 (mttt)
REVERT: C   14 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7598 (ttpp)
REVERT: R  109 MET cc_start: 0.3830 (pmt) cc_final: 0.3339 (pmm)
REVERT: R  336 ARG cc_start: 0.5484 (tpm-80) cc_final: 0.3119 (mmt-90)
REVERT: R  340 ARG cc_start: 0.6565 (ttm110) cc_final: 0.6166 (ptm-80)
REVERT: R  405 ARG cc_start: 0.5759 (mtm-85) cc_final: 0.5147 (mtm-85)
REVERT: S   23 SER cc_start: 0.8668 (m) cc_final: 0.8334 (t)
REVERT: S  113 GLN cc_start: 0.8026 (mm110) cc_final: 0.7756 (mm-40)
REVERT: S  171 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8056 (mt0)
REVERT: S  194 SER cc_start: 0.8688 (t) cc_final: 0.8400 (m)
  outliers start: 32
  outliers final: 21
  residues processed: 183
  average time/residue: 0.1323
  time to fit residues: 30.9787
Evaluate side-chains
  189 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  306 VAL
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.166854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.111355 restraints weight = 9406.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.28
r_work: 0.3014 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8642  Z= 0.190
  Angle     :  0.663  12.781  11734  Z= 0.337
  Chirality :  0.045   0.158   1363
  Planarity :  0.005   0.076   1470
  Dihedral  :  6.127  88.971   1211
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.86 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.92 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.63 (0.25), residues: 1091
  helix: -1.17 (0.27), residues: 343
  sheet: -0.68 (0.29), residues: 290
  loop : -1.07 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 220 
 TYR   0.024   0.002   TYR S 178 
 PHE   0.014   0.002   PHE R 237 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 8640)
  covalent geometry    : angle       0.66279 (11732)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       1.49342 (    2)
  hydrogen bonds       : bond        0.03770 (  325)
  hydrogen bonds       : angle       5.09157 (  963)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8124 (mttt) cc_final: 0.7847 (mmtp)
REVERT: A  251 ASP cc_start: 0.8037 (t0) cc_final: 0.7767 (t0)
REVERT: A  308 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6856 (mp0)
REVERT: B   52 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7864 (mtp85)
REVERT: B  197 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7597 (mpt180)
REVERT: B  219 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7534 (mtp85)
REVERT: B  337 LYS cc_start: 0.8568 (mttt) cc_final: 0.8302 (mttt)
REVERT: C   20 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7808 (mtpt)
REVERT: R  109 MET cc_start: 0.3869 (pmt) cc_final: 0.3579 (pmm)
REVERT: R  220 ARG cc_start: 0.7215 (mmm160) cc_final: 0.6688 (mmp80)
REVERT: R  336 ARG cc_start: 0.5548 (tpm-80) cc_final: 0.3234 (mmt-90)
REVERT: R  340 ARG cc_start: 0.6555 (ttm110) cc_final: 0.6118 (ptm-80)
REVERT: R  405 ARG cc_start: 0.5601 (mtm-85) cc_final: 0.4936 (mtm-85)
REVERT: S   23 SER cc_start: 0.8761 (m) cc_final: 0.8424 (t)
REVERT: S  113 GLN cc_start: 0.8107 (mm110) cc_final: 0.7861 (mm-40)
REVERT: S  171 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8054 (mt0)
  outliers start: 27
  outliers final: 22
  residues processed: 174
  average time/residue: 0.1347
  time to fit residues: 29.9245
Evaluate side-chains
  178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  306 VAL
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 107 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.169796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.114846 restraints weight = 9428.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.30
r_work: 0.3063 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8642  Z= 0.124
  Angle     :  0.607  11.071  11734  Z= 0.309
  Chirality :  0.043   0.146   1363
  Planarity :  0.004   0.079   1470
  Dihedral  :  5.780  85.349   1211
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.69 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.39 (0.26), residues: 1091
  helix: -0.90 (0.28), residues: 342
  sheet: -0.64 (0.29), residues: 291
  loop : -0.93 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 220 
 TYR   0.025   0.001   TYR S 178 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8640)
  covalent geometry    : angle       0.60698 (11732)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       1.10294 (    2)
  hydrogen bonds       : bond        0.03459 (  325)
  hydrogen bonds       : angle       4.83859 (  963)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8070 (mttt) cc_final: 0.7795 (mmtp)
REVERT: A   22 ASN cc_start: 0.8133 (m-40) cc_final: 0.7665 (m110)
REVERT: A  251 ASP cc_start: 0.7957 (t0) cc_final: 0.7702 (t0)
REVERT: A  308 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: B   52 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7795 (mtp85)
REVERT: B  134 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7551 (ptm-80)
REVERT: B  197 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7557 (mpt180)
REVERT: B  219 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7513 (mtp85)
REVERT: B  227 SER cc_start: 0.9015 (t) cc_final: 0.8779 (m)
REVERT: B  325 MET cc_start: 0.8538 (tpp) cc_final: 0.8227 (mmt)
REVERT: B  337 LYS cc_start: 0.8533 (mttt) cc_final: 0.8203 (mttt)
REVERT: C   20 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7851 (mtpt)
REVERT: R  109 MET cc_start: 0.3811 (pmt) cc_final: 0.3334 (pmm)
REVERT: S   23 SER cc_start: 0.8579 (m) cc_final: 0.8249 (t)
REVERT: S   39 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7954 (tt0)
REVERT: S  113 GLN cc_start: 0.7986 (mm110) cc_final: 0.7739 (mm-40)
  outliers start: 27
  outliers final: 19
  residues processed: 177
  average time/residue: 0.1151
  time to fit residues: 27.0814
Evaluate side-chains
  178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  306 VAL
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.167418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.112465 restraints weight = 9440.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.27
r_work: 0.3033 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8642  Z= 0.174
  Angle     :  0.645  12.167  11734  Z= 0.330
  Chirality :  0.044   0.160   1363
  Planarity :  0.005   0.080   1470
  Dihedral  :  5.887  83.464   1211
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.04 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.04 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.44 (0.25), residues: 1091
  helix: -0.97 (0.27), residues: 348
  sheet: -0.68 (0.29), residues: 289
  loop : -0.92 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 220 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.014   0.002   PHE R 237 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8640)
  covalent geometry    : angle       0.64494 (11732)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       1.45625 (    2)
  hydrogen bonds       : bond        0.03675 (  325)
  hydrogen bonds       : angle       4.94974 (  963)
  Misc. bond           : bond        0.00002 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3166.68 seconds
wall clock time: 54 minutes 52.18 seconds (3292.18 seconds total)