Starting phenix.real_space_refine
on Sat May 10 16:35:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z5h_39774/05_2025/8z5h_39774.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4265      2.51       5
     N    1153      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6645
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1748
          Classifications: {'peptide': 236}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 212
          Unresolved non-hydrogen angles: 259
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 15, 'GLU:plan': 12, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 154
    Chain: "B"
      Number of atoms: 2450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2450
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 150
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 113
    Chain: "G"
      Number of atoms: 317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 317
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 2130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2130
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 8, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 203
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 124
  Time building chain proxies: 4.92, per 1000 atoms: 0.74
  Number of scatterers: 6645
  At special positions: 0
  Unit cell: (74, 100.64, 133.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1187      8.00
     N    1153      7.00
     C    4265      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  13 " - pdb=" SG  CYS R 258 " distance=2.23

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 997.3 milliseconds
  

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1730

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      44.9% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
      removed outlier: 3.779A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 4.138A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 248
      removed outlier: 3.655A  pdb=" N   GLN A 246 " --> pdb=" O   LYS A 243 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS A 247 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.787A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.878A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.258A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.536A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.785A  pdb=" N   LYS A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.852A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.677A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 18 through 22
    Processing helix  chain 'R' and resid 23 through 52
      Proline residue:  R  37  - end of helix
      removed outlier: 3.712A  pdb=" N   ALA R  52 " --> pdb=" O   LEU R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 83
      removed outlier: 4.228A  pdb=" N   TYR R  59 " --> pdb=" O   GLU R  55 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   SER R  73 " --> pdb=" O   PHE R  69 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      Proline residue:  R  75  - end of helix
    Processing helix  chain 'R' and resid 93 through 103
      removed outlier: 4.399A  pdb=" N   ILE R  99 " --> pdb=" O   GLN R  95 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 124
      removed outlier: 4.347A  pdb=" N   SER R 108 " --> pdb=" O   ASN R 104 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL R 109 " --> pdb=" O   ILE R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 155
    Processing helix  chain 'R' and resid 179 through 195
      removed outlier: 3.658A  pdb=" N   ARG R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA R 184 " --> pdb=" O   ALA R 180 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE R 185 " --> pdb=" O   TRP R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 214
      removed outlier: 3.888A  pdb=" N   GLY R 207 " --> pdb=" O   ALA R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 255
      removed outlier: 3.719A  pdb=" N   LYS R 223 " --> pdb=" O   GLN R 219 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP R 224 " --> pdb=" O   LYS R 220 " (cutoff:3.500A)
      Proline residue:  R 243  - end of helix
      removed outlier: 4.016A  pdb=" N   TRP R 254 " --> pdb=" O   VAL R 250 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU R 255 " --> pdb=" O   ARG R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 264
    Processing helix  chain 'R' and resid 264 through 275
    Processing helix  chain 'R' and resid 277 through 288
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 295
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224
      removed outlier: 4.716A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 253 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   VAL A 258 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.685A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.358A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP B  83 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.739A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.709A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.750A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.652A  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: 6.545A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 4.084A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    966 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: 1.87

  Time building geometry restraints manager: 1.99 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: 1060
        1.31 -     1.44: 1957
        1.44 -     1.56: 3733
        1.56 -     1.69: 0
        1.69 -     1.82: 49
  Bond restraints: 6799
  Sorted by residual:
  bond pdb=" CA  HIS R  17 "
       pdb=" C   HIS R  17 "
    ideal  model  delta    sigma   weight residual
    1.528  1.471  0.058 1.07e-02 8.73e+03 2.91e+01
  bond pdb=" CA  GLU A 392 "
       pdb=" C   GLU A 392 "
    ideal  model  delta    sigma   weight residual
    1.528  1.465  0.063 1.25e-02 6.40e+03 2.56e+01
  bond pdb=" CA  HIS R  17 "
       pdb=" CB  HIS R  17 "
    ideal  model  delta    sigma   weight residual
    1.527  1.490  0.038 7.60e-03 1.73e+04 2.46e+01
  bond pdb=" CA  THR R  14 "
       pdb=" C   THR R  14 "
    ideal  model  delta    sigma   weight residual
    1.523  1.461  0.062 1.34e-02 5.57e+03 2.12e+01
  bond pdb=" C   ASP A 225 "
       pdb=" O   ASP A 225 "
    ideal  model  delta    sigma   weight residual
    1.233  1.183  0.050 1.22e-02 6.72e+03 1.67e+01
  ... (remaining 6794 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 9093
        2.14 -     4.27: 170
        4.27 -     6.41: 23
        6.41 -     8.55: 7
        8.55 -    10.68: 7
  Bond angle restraints: 9300
  Sorted by residual:
  angle pdb=" N   GLY R 263 "
        pdb=" CA  GLY R 263 "
        pdb=" C   GLY R 263 "
      ideal   model   delta    sigma   weight residual
     112.50  121.93   -9.43 1.16e+00 7.43e-01 6.61e+01
  angle pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
        pdb=" C   GLU A 392 "
      ideal   model   delta    sigma   weight residual
     111.52  120.45   -8.93 1.40e+00 5.10e-01 4.07e+01
  angle pdb=" N   HIS R 175 "
        pdb=" CA  HIS R 175 "
        pdb=" C   HIS R 175 "
      ideal   model   delta    sigma   weight residual
     108.69   98.01   10.68 1.77e+00 3.19e-01 3.64e+01
  angle pdb=" C   TYR R 176 "
        pdb=" N   PRO R 177 "
        pdb=" CA  PRO R 177 "
      ideal   model   delta    sigma   weight residual
     119.84  112.30    7.54 1.25e+00 6.40e-01 3.63e+01
  angle pdb=" N   ILE R 178 "
        pdb=" CA  ILE R 178 "
        pdb=" C   ILE R 178 "
      ideal   model   delta    sigma   weight residual
     109.30  116.16   -6.86 1.31e+00 5.83e-01 2.74e+01
  ... (remaining 9295 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 3556
       15.05 -    30.09: 277
       30.09 -    45.14: 72
       45.14 -    60.19: 14
       60.19 -    75.23: 9
  Dihedral angle restraints: 3928
    sinusoidal: 1259
      harmonic: 2669
  Sorted by residual:
  dihedral pdb=" CB  CYS R  13 "
           pdb=" SG  CYS R  13 "
           pdb=" SG  CYS R 258 "
           pdb=" CB  CYS R 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.56   56.56     1      1.00e+01 1.00e-02 4.31e+01
  dihedral pdb=" CA  HIS R  89 "
           pdb=" C   HIS R  89 "
           pdb=" N   GLY R  90 "
           pdb=" CA  GLY R  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.43   23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  GLN A  59 "
           pdb=" C   GLN A  59 "
           pdb=" N   MET A  60 "
           pdb=" CA  MET A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.98   23.02     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 3925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1078
       0.124 -    0.249: 19
       0.249 -    0.373: 1
       0.373 -    0.497: 1
       0.497 -    0.622: 1
  Chirality restraints: 1100
  Sorted by residual:
  chirality pdb=" CA  GLU A 392 "
            pdb=" N   GLU A 392 "
            pdb=" C   GLU A 392 "
            pdb=" CB  GLU A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" CA  ILE R 178 "
            pdb=" N   ILE R 178 "
            pdb=" C   ILE R 178 "
            pdb=" CB  ILE R 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.01    0.43 2.00e-01 2.50e+01 4.55e+00
  chirality pdb=" CA  ASP A 225 "
            pdb=" N   ASP A 225 "
            pdb=" C   ASP A 225 "
            pdb=" CB  ASP A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 1097 not shown)

  Planarity restraints: 1182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 174 "    0.026 2.00e-02 2.50e+03   5.32e-02 2.83e+01
        pdb=" C   GLU R 174 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   GLU R 174 "    0.035 2.00e-02 2.50e+03
        pdb=" N   HIS R 175 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 262 "    0.016 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C   LYS R 262 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   LYS R 262 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLY R 263 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS R  17 "   -0.028 2.00e-02 2.50e+03   2.35e-02 8.29e+00
        pdb=" CG  HIS R  17 "    0.044 2.00e-02 2.50e+03
        pdb=" ND1 HIS R  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS R  17 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 HIS R  17 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS R  17 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1179 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2335
        2.85 -     3.36: 6014
        3.36 -     3.87: 10260
        3.87 -     4.39: 10849
        4.39 -     4.90: 19812
  Nonbonded interactions: 49270
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG  SER B  84 "
            pdb=" CE1 PHE G  61 "
     model   vdw
     2.359 3.340
  nonbonded pdb=" O   THR B 274 "
            pdb=" OG  SER B 275 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" OE2 GLU A 344 "
            pdb=" NH2 ARG A 347 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" O   THR B 164 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.375 3.040
  ... (remaining 49265 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:             2.300
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.830
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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      :  0.006   0.197   6800  Z= 0.328
  Angle     :  0.765  10.682   9302  Z= 0.450
  Chirality :  0.054   0.622   1100
  Planarity :  0.004   0.053   1182
  Dihedral  : 12.978  75.233   2195
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.29), residues: 901
  helix:  1.13 (0.28), residues: 386
  sheet:  0.05 (0.43), residues: 159
  loop : -2.14 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 244 
 HIS   0.016   0.002   HIS R  17 
 PHE   0.022   0.002   PHE R 173 
 TYR   0.016   0.001   TYR R  80 
 ARG   0.012   0.001   ARG R 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17531 (  332)
  hydrogen bonds       : angle       6.37917 (  966)
  SS BOND              : bond        0.19744 (    1)
  SS BOND              : angle       2.75052 (    2)
  covalent geometry    : bond        0.00515 ( 6799)
  covalent geometry    : angle       0.76412 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  272 ASP cc_start: 0.8247 (t0) cc_final: 0.7976 (t0)
REVERT: A  346 LEU cc_start: 0.8415 (mt) cc_final: 0.8091 (mp)
REVERT: B   58 ILE cc_start: 0.7712 (pt) cc_final: 0.7455 (mt)
REVERT: B  247 ASP cc_start: 0.6704 (t70) cc_final: 0.6420 (t0)
REVERT: B  291 ASP cc_start: 0.7199 (p0) cc_final: 0.6977 (p0)
REVERT: R   32 LEU cc_start: 0.8056 (tp) cc_final: 0.7684 (tp)
REVERT: R  204 SER cc_start: 0.8547 (p) cc_final: 0.8305 (p)
REVERT: R  242 LEU cc_start: 0.8652 (tt) cc_final: 0.8342 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 213
  average time/residue: 0.2012
  time to fit residues: 54.9033
Evaluate side-chains
  194 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   85 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
R  49 GLN
R  83 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.114598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.099578 restraints weight = 10488.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.29
r_work: 0.3084 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6800  Z= 0.147
  Angle     :  0.560   5.850   9302  Z= 0.301
  Chirality :  0.043   0.147   1100
  Planarity :  0.004   0.049   1182
  Dihedral  :  4.741  33.188    976
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.58 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.29), residues: 901
  helix:  1.45 (0.28), residues: 392
  sheet:  0.69 (0.45), residues: 150
  loop : -1.90 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.006   0.001   HIS A 230 
 PHE   0.015   0.002   PHE A 222 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.005   0.001   ARG R 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  332)
  hydrogen bonds       : angle       4.31136 (  966)
  SS BOND              : bond        0.00453 (    1)
  SS BOND              : angle       0.55913 (    2)
  covalent geometry    : bond        0.00332 ( 6799)
  covalent geometry    : angle       0.56003 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.798 
Fit side-chains
REVERT: B   83 ASP cc_start: 0.8324 (t0) cc_final: 0.8099 (t0)
REVERT: B  212 ASP cc_start: 0.7977 (t0) cc_final: 0.7775 (t0)
REVERT: B  237 ASN cc_start: 0.8731 (t0) cc_final: 0.8496 (t0)
REVERT: B  247 ASP cc_start: 0.7386 (t70) cc_final: 0.7074 (t0)
REVERT: B  338 ILE cc_start: 0.8571 (mm) cc_final: 0.8345 (mm)
REVERT: R  204 SER cc_start: 0.8492 (p) cc_final: 0.8262 (p)
REVERT: R  242 LEU cc_start: 0.8643 (tt) cc_final: 0.8351 (tp)
  outliers start: 18
  outliers final: 12
  residues processed: 202
  average time/residue: 0.2200
  time to fit residues: 56.4507
Evaluate side-chains
  198 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  185 ILE
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.0870
   chunk 72 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
** R  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.097211 restraints weight = 10511.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.24
r_work: 0.3053 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6800  Z= 0.146
  Angle     :  0.533   6.043   9302  Z= 0.287
  Chirality :  0.042   0.131   1100
  Planarity :  0.004   0.047   1182
  Dihedral  :  4.631  36.003    976
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.92 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.29), residues: 901
  helix:  1.68 (0.28), residues: 392
  sheet:  0.84 (0.42), residues: 168
  loop : -1.81 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 244 
 HIS   0.006   0.001   HIS R  17 
 PHE   0.020   0.001   PHE A 222 
 TYR   0.015   0.001   TYR R 268 
 ARG   0.005   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04389 (  332)
  hydrogen bonds       : angle       4.05692 (  966)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.50692 (    2)
  covalent geometry    : bond        0.00334 ( 6799)
  covalent geometry    : angle       0.53326 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 201
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.8440 (mt) cc_final: 0.8199 (mp)
REVERT: B  125 ASN cc_start: 0.8429 (t0) cc_final: 0.8194 (t0)
REVERT: B  161 SER cc_start: 0.8368 (t) cc_final: 0.8109 (t)
REVERT: B  219 ARG cc_start: 0.8222 (mmt90) cc_final: 0.8006 (mtt-85)
REVERT: B  228 ASP cc_start: 0.7986 (p0) cc_final: 0.7552 (p0)
REVERT: B  230 ASN cc_start: 0.8444 (m-40) cc_final: 0.8081 (m110)
REVERT: B  237 ASN cc_start: 0.8719 (t0) cc_final: 0.8434 (t0)
REVERT: B  258 ASP cc_start: 0.7850 (t0) cc_final: 0.7649 (t0)
REVERT: B  314 ARG cc_start: 0.8157 (ttt180) cc_final: 0.7946 (ttt180)
REVERT: R  204 SER cc_start: 0.8501 (p) cc_final: 0.8264 (p)
REVERT: R  242 LEU cc_start: 0.8710 (tt) cc_final: 0.8448 (tp)
  outliers start: 18
  outliers final: 13
  residues processed: 209
  average time/residue: 0.2174
  time to fit residues: 57.9345
Evaluate side-chains
  202 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 189
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.110574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095594 restraints weight = 10683.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.26
r_work: 0.3039 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6800  Z= 0.157
  Angle     :  0.539   8.979   9302  Z= 0.288
  Chirality :  0.042   0.160   1100
  Planarity :  0.003   0.047   1182
  Dihedral  :  4.605  35.814    976
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.65 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.29), residues: 901
  helix:  1.78 (0.28), residues: 392
  sheet:  1.03 (0.41), residues: 172
  loop : -1.74 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 244 
 HIS   0.004   0.001   HIS R 269 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.020   0.001   TYR R 268 
 ARG   0.004   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  332)
  hydrogen bonds       : angle       3.99660 (  966)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.27598 (    2)
  covalent geometry    : bond        0.00363 ( 6799)
  covalent geometry    : angle       0.53872 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  346 LEU cc_start: 0.8454 (mt) cc_final: 0.8244 (mp)
REVERT: B   67 SER cc_start: 0.8715 (m) cc_final: 0.8197 (t)
REVERT: B   70 LEU cc_start: 0.8416 (tt) cc_final: 0.8188 (tp)
REVERT: B  125 ASN cc_start: 0.8448 (t0) cc_final: 0.8199 (t0)
REVERT: B  161 SER cc_start: 0.8507 (t) cc_final: 0.8207 (t)
REVERT: B  219 ARG cc_start: 0.8300 (mmt90) cc_final: 0.7998 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8404 (m-40) cc_final: 0.8133 (m110)
REVERT: B  237 ASN cc_start: 0.8702 (t0) cc_final: 0.8451 (t0)
REVERT: R  204 SER cc_start: 0.8502 (p) cc_final: 0.8271 (p)
REVERT: R  242 LEU cc_start: 0.8728 (tt) cc_final: 0.8456 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 200
  average time/residue: 0.2087
  time to fit residues: 53.3255
Evaluate side-chains
  200 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0020
   chunk 73 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0030
   chunk 7 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
R 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.097532 restraints weight = 10488.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.25
r_work: 0.3084 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6800  Z= 0.105
  Angle     :  0.493   7.007   9302  Z= 0.262
  Chirality :  0.040   0.133   1100
  Planarity :  0.003   0.045   1182
  Dihedral  :  4.348  31.746    976
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.94 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 901
  helix:  1.92 (0.28), residues: 393
  sheet:  0.94 (0.42), residues: 173
  loop : -1.65 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 244 
 HIS   0.004   0.001   HIS R 269 
 PHE   0.021   0.001   PHE A 222 
 TYR   0.021   0.001   TYR R 268 
 ARG   0.003   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  332)
  hydrogen bonds       : angle       3.78684 (  966)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.25483 (    2)
  covalent geometry    : bond        0.00236 ( 6799)
  covalent geometry    : angle       0.49318 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.704 
Fit side-chains
REVERT: B  125 ASN cc_start: 0.8373 (t0) cc_final: 0.8169 (t0)
REVERT: B  160 SER cc_start: 0.8183 (m) cc_final: 0.7838 (p)
REVERT: B  161 SER cc_start: 0.8384 (t) cc_final: 0.8052 (p)
REVERT: B  187 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (m)
REVERT: B  219 ARG cc_start: 0.8299 (mmt90) cc_final: 0.7995 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8354 (m-40) cc_final: 0.7961 (m-40)
REVERT: B  237 ASN cc_start: 0.8717 (t0) cc_final: 0.8508 (t0)
REVERT: R  204 SER cc_start: 0.8490 (p) cc_final: 0.8284 (p)
REVERT: R  242 LEU cc_start: 0.8714 (tt) cc_final: 0.8473 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 200
  average time/residue: 0.2047
  time to fit residues: 52.5934
Evaluate side-chains
  203 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0020
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
R 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.095306 restraints weight = 10309.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.34
r_work: 0.3058 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6800  Z= 0.119
  Angle     :  0.500   6.000   9302  Z= 0.267
  Chirality :  0.041   0.138   1100
  Planarity :  0.003   0.045   1182
  Dihedral  :  4.340  31.106    976
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.70 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.29), residues: 901
  helix:  1.94 (0.28), residues: 393
  sheet:  0.94 (0.42), residues: 167
  loop : -1.58 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 269 
 PHE   0.019   0.001   PHE R 190 
 TYR   0.021   0.001   TYR R 268 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  332)
  hydrogen bonds       : angle       3.78496 (  966)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.23945 (    2)
  covalent geometry    : bond        0.00274 ( 6799)
  covalent geometry    : angle       0.49975 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.793 
Fit side-chains
REVERT: B  119 ASN cc_start: 0.8215 (m-40) cc_final: 0.8011 (m110)
REVERT: B  125 ASN cc_start: 0.8395 (t0) cc_final: 0.8137 (t0)
REVERT: B  161 SER cc_start: 0.8443 (t) cc_final: 0.8102 (p)
REVERT: B  187 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8513 (m)
REVERT: B  219 ARG cc_start: 0.8309 (mmt90) cc_final: 0.7964 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8330 (m-40) cc_final: 0.7961 (m-40)
REVERT: B  237 ASN cc_start: 0.8679 (t0) cc_final: 0.8442 (t0)
REVERT: B  258 ASP cc_start: 0.8030 (t0) cc_final: 0.7708 (t0)
REVERT: R  204 SER cc_start: 0.8522 (p) cc_final: 0.8315 (p)
REVERT: R  242 LEU cc_start: 0.8677 (tt) cc_final: 0.8430 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 195
  average time/residue: 0.2176
  time to fit residues: 54.0204
Evaluate side-chains
  201 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   48 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 63 optimal weight:    0.0980
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
R  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.107392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.091553 restraints weight = 10389.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.41
r_work: 0.2989 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6800  Z= 0.170
  Angle     :  0.542   7.215   9302  Z= 0.290
  Chirality :  0.042   0.133   1100
  Planarity :  0.004   0.046   1182
  Dihedral  :  4.545  33.485    976
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.35 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 901
  helix:  1.87 (0.28), residues: 393
  sheet:  0.97 (0.41), residues: 169
  loop : -1.58 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.022   0.002   PHE A 222 
 TYR   0.021   0.001   TYR R 268 
 ARG   0.004   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  332)
  hydrogen bonds       : angle       3.96178 (  966)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.16112 (    2)
  covalent geometry    : bond        0.00397 ( 6799)
  covalent geometry    : angle       0.54252 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.761 
Fit side-chains
REVERT: B  125 ASN cc_start: 0.8460 (t0) cc_final: 0.8142 (t0)
REVERT: B  160 SER cc_start: 0.8428 (m) cc_final: 0.8123 (p)
REVERT: B  161 SER cc_start: 0.8601 (t) cc_final: 0.8251 (p)
REVERT: B  187 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8494 (m)
REVERT: B  219 ARG cc_start: 0.8397 (mmt90) cc_final: 0.8015 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8382 (m-40) cc_final: 0.8030 (m110)
REVERT: B  237 ASN cc_start: 0.8683 (t0) cc_final: 0.8317 (t0)
REVERT: B  258 ASP cc_start: 0.8063 (t0) cc_final: 0.7692 (t0)
REVERT: R  204 SER cc_start: 0.8519 (p) cc_final: 0.8303 (p)
REVERT: R  242 LEU cc_start: 0.8693 (tt) cc_final: 0.8407 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 212
  average time/residue: 0.2118
  time to fit residues: 57.9019
Evaluate side-chains
  217 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    0.0980
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 82 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.107588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.091707 restraints weight = 10527.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.44
r_work: 0.3023 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6800  Z= 0.156
  Angle     :  0.542   7.524   9302  Z= 0.287
  Chirality :  0.042   0.132   1100
  Planarity :  0.003   0.046   1182
  Dihedral  :  4.432  27.315    976
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.67 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.29), residues: 901
  helix:  1.89 (0.28), residues: 391
  sheet:  0.97 (0.41), residues: 165
  loop : -1.55 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 222 
 TYR   0.022   0.001   TYR R 268 
 ARG   0.004   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  332)
  hydrogen bonds       : angle       3.95096 (  966)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.16754 (    2)
  covalent geometry    : bond        0.00366 ( 6799)
  covalent geometry    : angle       0.54194 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A  350 THR cc_start: 0.8434 (t) cc_final: 0.8150 (p)
REVERT: B   71 VAL cc_start: 0.8536 (t) cc_final: 0.8274 (p)
REVERT: B  125 ASN cc_start: 0.8457 (t0) cc_final: 0.8143 (t0)
REVERT: B  160 SER cc_start: 0.8391 (m) cc_final: 0.8060 (p)
REVERT: B  161 SER cc_start: 0.8532 (t) cc_final: 0.8245 (p)
REVERT: B  187 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8507 (m)
REVERT: B  219 ARG cc_start: 0.8408 (mmt90) cc_final: 0.8029 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8374 (m-40) cc_final: 0.8024 (m110)
REVERT: B  237 ASN cc_start: 0.8672 (t0) cc_final: 0.8322 (t0)
REVERT: B  258 ASP cc_start: 0.8037 (t0) cc_final: 0.7692 (t0)
REVERT: R  242 LEU cc_start: 0.8678 (tt) cc_final: 0.8396 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 209
  average time/residue: 0.2050
  time to fit residues: 54.8521
Evaluate side-chains
  211 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   85 ASP
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
R 225 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.111049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.095284 restraints weight = 10301.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.32
r_work: 0.3034 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6800  Z= 0.127
  Angle     :  0.525   7.265   9302  Z= 0.279
  Chirality :  0.041   0.139   1100
  Planarity :  0.003   0.046   1182
  Dihedral  :  4.303  24.672    976
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.79 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 901
  helix:  2.01 (0.28), residues: 387
  sheet:  1.05 (0.41), residues: 165
  loop : -1.49 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 244 
 HIS   0.004   0.001   HIS R  17 
 PHE   0.021   0.001   PHE A 222 
 TYR   0.022   0.001   TYR R 268 
 ARG   0.006   0.000   ARG A 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  332)
  hydrogen bonds       : angle       3.86402 (  966)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.21745 (    2)
  covalent geometry    : bond        0.00296 ( 6799)
  covalent geometry    : angle       0.52552 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  350 THR cc_start: 0.8460 (t) cc_final: 0.8174 (p)
REVERT: B   71 VAL cc_start: 0.8534 (t) cc_final: 0.8278 (p)
REVERT: B  125 ASN cc_start: 0.8427 (t0) cc_final: 0.8177 (t0)
REVERT: B  160 SER cc_start: 0.8340 (m) cc_final: 0.8040 (p)
REVERT: B  161 SER cc_start: 0.8510 (t) cc_final: 0.8255 (p)
REVERT: B  187 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8521 (m)
REVERT: B  219 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7975 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8341 (m-40) cc_final: 0.8014 (m110)
REVERT: B  237 ASN cc_start: 0.8694 (t0) cc_final: 0.8340 (t0)
REVERT: B  258 ASP cc_start: 0.8061 (t0) cc_final: 0.7641 (t0)
REVERT: R  242 LEU cc_start: 0.8684 (tt) cc_final: 0.8427 (tp)
  outliers start: 18
  outliers final: 17
  residues processed: 205
  average time/residue: 0.1999
  time to fit residues: 53.4544
Evaluate side-chains
  215 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 12 optimal weight:    0.3980
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 225 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.111143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.095416 restraints weight = 10499.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.30
r_work: 0.3024 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6800  Z= 0.132
  Angle     :  0.531   7.775   9302  Z= 0.281
  Chirality :  0.041   0.141   1100
  Planarity :  0.003   0.046   1182
  Dihedral  :  4.203  19.272    974
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 24.12 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 901
  helix:  1.98 (0.28), residues: 387
  sheet:  1.03 (0.40), residues: 167
  loop : -1.46 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE A 222 
 TYR   0.022   0.001   TYR R 268 
 ARG   0.004   0.000   ARG A 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  332)
  hydrogen bonds       : angle       3.85865 (  966)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.22749 (    2)
  covalent geometry    : bond        0.00306 ( 6799)
  covalent geometry    : angle       0.53097 ( 9300)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A  243 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7923 (mptt)
REVERT: A  350 THR cc_start: 0.8407 (t) cc_final: 0.8148 (p)
REVERT: B   71 VAL cc_start: 0.8533 (t) cc_final: 0.8284 (p)
REVERT: B  160 SER cc_start: 0.8341 (m) cc_final: 0.8013 (p)
REVERT: B  161 SER cc_start: 0.8512 (t) cc_final: 0.8280 (p)
REVERT: B  187 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8475 (m)
REVERT: B  219 ARG cc_start: 0.8374 (mmt90) cc_final: 0.7983 (mtt-85)
REVERT: B  230 ASN cc_start: 0.8319 (m-40) cc_final: 0.8003 (m110)
REVERT: B  237 ASN cc_start: 0.8711 (t0) cc_final: 0.8351 (t0)
REVERT: B  258 ASP cc_start: 0.7971 (t0) cc_final: 0.7555 (t0)
REVERT: R  242 LEU cc_start: 0.8679 (tt) cc_final: 0.8418 (tp)
  outliers start: 18
  outliers final: 17
  residues processed: 208
  average time/residue: 0.2094
  time to fit residues: 55.8407
Evaluate side-chains
  217 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   99 ILE
Chi-restraints excluded: chain R residue  117 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  240 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
R 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.093855 restraints weight = 10393.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.36
r_work: 0.3001 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6800  Z= 0.159
  Angle     :  0.554   8.134   9302  Z= 0.293
  Chirality :  0.042   0.143   1100
  Planarity :  0.003   0.047   1182
  Dihedral  :  4.315  19.691    974
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.28 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.29), residues: 901
  helix:  1.87 (0.28), residues: 391
  sheet:  1.00 (0.40), residues: 165
  loop : -1.52 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.020   0.002   PHE R 190 
 TYR   0.022   0.001   TYR R 268 
 ARG   0.006   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  332)
  hydrogen bonds       : angle       3.95979 (  966)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.15953 (    2)
  covalent geometry    : bond        0.00373 ( 6799)
  covalent geometry    : angle       0.55398 ( 9300)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3799.67 seconds
wall clock time: 66 minutes 26.26 seconds (3986.26 seconds total)