Starting phenix.real_space_refine
on Sat Aug 23 16:32:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rc1_19042/08_2025/8rc1_19042.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.007 sd=   0.046
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: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      2      5.21       5
     S      82      5.16       5
     C    8417      2.51       5
     N    2314      2.21       5
     O    2410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13235
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3144
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 20, 'TRANS': 410}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 235
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 177
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 9, 'ASP:plan': 16, 'ASN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 189
    Chain: "B"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3192
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 20, 'TRANS': 409}
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 227
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 149
    Chain: "C"
      Number of atoms: 3144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3144
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 20, 'TRANS': 410}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 235
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 177
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 21, 'GLN:plan1': 9, 'ASP:plan': 16, 'ASN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 189
    Chain: "D"
      Number of atoms: 3188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3188
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 20, 'TRANS': 409}
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 232
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 153
    Chain: "E"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 445
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'TRANS': 88}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 267
          Unresolved non-hydrogen dihedrals: 89
          Planarities with less than four sites: {'UNK:plan-1': 89}
          Unresolved non-hydrogen planarities: 89
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.88, per 1000 atoms: 0.22
  Number of scatterers: 13235
  At special positions: 0
  Unit cell: (76.824, 76.824, 190.993, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      82     16.00
     P      10     15.00
     Mg      2     11.99
     O    2410      8.00
     N    2314      7.00
     C    8417      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.04
  Conformation dependent library (CDL) restraints added in 608.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3370

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 11 sheets defined
      59.3% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 48 through 51
      removed outlier: 3.585A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 51'
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 128
      removed outlier: 3.692A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 4.268A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 3.852A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.622A  pdb=" N   VAL A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.114A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 4.212A  pdb=" N   GLN A 301 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 337
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.279A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 3.692A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
      removed outlier: 3.707A  pdb=" N   LYS B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 46
      removed outlier: 4.201A  pdb=" N   LEU B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 55 through 57
      No H-bonds generated for 'chain 'B' and resid 55 through 57'
    Processing helix  chain 'B' and resid 69 through 78
      removed outlier: 4.490A  pdb=" N   MET B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 107 through 126
      removed outlier: 4.090A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
      removed outlier: 3.623A  pdb=" N   SER B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   THR B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.943A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 3.759A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
      removed outlier: 3.934A  pdb=" N   MET B 299 " --> pdb=" O   ALA B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.702A  pdb=" N   PHE B 341 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 373 through 391
      removed outlier: 4.093A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ARG B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 4.053A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 428
      removed outlier: 3.725A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 29
    Processing helix  chain 'C' and resid 47 through 51
      removed outlier: 3.514A  pdb=" N   THR C  51 " --> pdb=" O   SER C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 88 through 90
      No H-bonds generated for 'chain 'C' and resid 88 through 90'
    Processing helix  chain 'C' and resid 102 through 108
    Processing helix  chain 'C' and resid 109 through 129
      removed outlier: 4.164A  pdb=" N   GLU C 113 " --> pdb=" O   THR C 109 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE C 114 " --> pdb=" O   ILE C 110 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ASP C 116 " --> pdb=" O   LYS C 112 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   LEU C 117 " --> pdb=" O   GLU C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 161
      removed outlier: 4.162A  pdb=" N   THR C 150 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C 159 " --> pdb=" O   GLU C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 195
    Processing helix  chain 'C' and resid 206 through 216
    Processing helix  chain 'C' and resid 223 through 239
    Processing helix  chain 'C' and resid 239 through 244
    Processing helix  chain 'C' and resid 251 through 260
    Processing helix  chain 'C' and resid 277 through 282
      removed outlier: 4.085A  pdb=" N   TYR C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 296
      removed outlier: 3.633A  pdb=" N   PHE C 296 " --> pdb=" O   THR C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 301
      removed outlier: 3.909A  pdb=" N   GLN C 301 " --> pdb=" O   PRO C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 310
    Processing helix  chain 'C' and resid 324 through 338
    Processing helix  chain 'C' and resid 383 through 401
      removed outlier: 4.033A  pdb=" N   ALA C 387 " --> pdb=" O   ALA C 383 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LYS C 401 " --> pdb=" O   LEU C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 410
      removed outlier: 3.999A  pdb=" N   TYR C 408 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 437
      removed outlier: 3.931A  pdb=" N   PHE C 418 " --> pdb=" O   GLU C 414 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER C 419 " --> pdb=" O   GLU C 415 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 29
      removed outlier: 3.668A  pdb=" N   LYS D  19 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 45
    Processing helix  chain 'D' and resid 46 through 49
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 69 through 78
      removed outlier: 4.569A  pdb=" N   MET D  73 " --> pdb=" O   GLU D  69 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER D  75 " --> pdb=" O   GLY D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 100 through 106
    Processing helix  chain 'D' and resid 107 through 126
      removed outlier: 3.940A  pdb=" N   GLU D 111 " --> pdb=" O   THR D 107 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ASP D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER D 115 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER D 126 " --> pdb=" O   LYS D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 159
    Processing helix  chain 'D' and resid 180 through 196
      removed outlier: 3.917A  pdb=" N   GLN D 191 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   GLU D 194 " --> pdb=" O   HIS D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 214
    Processing helix  chain 'D' and resid 221 through 242
      removed outlier: 3.578A  pdb=" N   THR D 237 " --> pdb=" O   MET D 233 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   CYS D 239 " --> pdb=" O   GLY D 235 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   LEU D 240 " --> pdb=" O   VAL D 236 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 258
      removed outlier: 3.670A  pdb=" N   ASN D 256 " --> pdb=" O   LYS D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 285 through 294
    Processing helix  chain 'D' and resid 295 through 299
      removed outlier: 3.835A  pdb=" N   MET D 299 " --> pdb=" O   ALA D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 308
    Processing helix  chain 'D' and resid 322 through 337
    Processing helix  chain 'D' and resid 338 through 341
    Processing helix  chain 'D' and resid 373 through 391
      removed outlier: 4.247A  pdb=" N   LEU D 377 " --> pdb=" O   ALA D 373 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ARG D 391 " --> pdb=" O   ALA D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 401
      removed outlier: 4.017A  pdb=" N   TYR D 398 " --> pdb=" O   PHE D 394 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU D 401 " --> pdb=" O   TRP D 397 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 428
      removed outlier: 3.602A  pdb=" N   PHE D 408 " --> pdb=" O   ASP D 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 87
      removed outlier: 3.537A  pdb=" N   UNK E  18 " --> pdb=" O   UNK E  14 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   UNK E  23 " --> pdb=" O   UNK E  19 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   UNK E  24 " --> pdb=" O   UNK E  20 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   UNK E  25 " --> pdb=" O   UNK E  21 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.900A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272
      removed outlier: 3.625A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92
      removed outlier: 8.253A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE B 163 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   HIS B 137 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 198 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.360A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.894A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR B 312 " --> pdb=" O   ASN B 370 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53
    Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94
      removed outlier: 8.004A  pdb=" N   ILE C  93 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   PHE C  67 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   SER C 140 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   PHE C 135 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   PHE C 169 " --> pdb=" O   PHE C 135 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   VAL C 137 " --> pdb=" O   PHE C 169 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ILE C 171 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   HIS C 139 " --> pdb=" O   ILE C 171 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LYS C 166 " --> pdb=" O   CYS C 200 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   PHE C 202 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLU C 168 " --> pdb=" O   PHE C 202 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   VAL C 204 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   SER C 170 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 272
      removed outlier: 8.433A  pdb=" N   LYS C 352 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   CYS C 315 " --> pdb=" O   LYS C 352 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   GLY C 354 " --> pdb=" O   CYS C 315 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   LEU C 317 " --> pdb=" O   GLY C 354 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92
      removed outlier: 8.176A  pdb=" N   VAL D  91 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU D  65 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   ILE D  64 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   HIS D   6 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL D  66 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLN D   8 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   GLU D   3 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY D 132 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   SER D 138 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ILE D 163 " --> pdb=" O   GLN D 131 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 92
      removed outlier: 8.176A  pdb=" N   VAL D  91 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU D  65 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   ILE D  64 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   HIS D   6 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL D  66 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLN D   8 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   GLU D   3 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY D 132 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   SER D 138 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ILE D 163 " --> pdb=" O   GLN D 131 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   MET D 164 " --> pdb=" O   GLU D 198 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   TYR D 200 " --> pdb=" O   MET D 164 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   THR D 166 " --> pdb=" O   TYR D 200 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   THR D 199 " --> pdb=" O   PHE D 266 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   PHE D 265 " --> pdb=" O   SER D 371 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   SER D 371 " --> pdb=" O   PHE D 265 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR D 312 " --> pdb=" O   ASN D 370 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 51 through 53

    758 hydrogen bonds defined for protein.
    2190 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4323
        1.34 -     1.46: 3049
        1.46 -     1.58: 6024
        1.58 -     1.69: 16
        1.69 -     1.81: 132
  Bond restraints: 13544
  Sorted by residual:
  bond pdb=" C5  GDP D 501 "
       pdb=" C4  GDP D 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.466  0.024 2.00e-02 2.50e+03 1.48e+00
  bond pdb=" C5  GDP B 501 "
       pdb=" C4  GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.466  0.024 2.00e-02 2.50e+03 1.40e+00
  bond pdb=" C   ILE B 356 "
       pdb=" O   ILE B 356 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.009 1.01e-02 9.80e+03 7.11e-01
  bond pdb=" CA  ILE A 171 "
       pdb=" CB  ILE A 171 "
    ideal  model  delta    sigma   weight residual
    1.527  1.538 -0.011 1.31e-02 5.83e+03 6.80e-01
  bond pdb=" CA  ILE C 171 "
       pdb=" CB  ILE C 171 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.62e-01
  ... (remaining 13539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 18128
        1.30 -     2.60: 289
        2.60 -     3.90: 74
        3.90 -     5.21: 15
        5.21 -     6.51: 7
  Bond angle restraints: 18513
  Sorted by residual:
  angle pdb=" N   ALA D 271 "
        pdb=" CA  ALA D 271 "
        pdb=" C   ALA D 271 "
      ideal   model   delta    sigma   weight residual
     109.81  114.97   -5.16 2.21e+00 2.05e-01 5.45e+00
  angle pdb=" C2' GTP A 501 "
        pdb=" C3' GTP A 501 "
        pdb=" C4' GTP A 501 "
      ideal   model   delta    sigma   weight residual
     111.00  104.58    6.42 3.00e+00 1.11e-01 4.59e+00
  angle pdb=" C2' GTP C 501 "
        pdb=" C3' GTP C 501 "
        pdb=" C4' GTP C 501 "
      ideal   model   delta    sigma   weight residual
     111.00  104.71    6.29 3.00e+00 1.11e-01 4.39e+00
  angle pdb=" N   ASP C  33 "
        pdb=" CA  ASP C  33 "
        pdb=" C   ASP C  33 "
      ideal   model   delta    sigma   weight residual
     113.20  110.68    2.52 1.21e+00 6.83e-01 4.35e+00
  angle pdb=" C   GLY A 436 "
        pdb=" N   VAL A 437 "
        pdb=" CA  VAL A 437 "
      ideal   model   delta    sigma   weight residual
     120.50  123.24   -2.74 1.34e+00 5.57e-01 4.18e+00
  ... (remaining 18508 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.96: 7868
       34.96 -    69.93: 41
       69.93 -   104.89: 3
      104.89 -   139.85: 7
      139.85 -   174.82: 2
  Dihedral angle restraints: 7921
    sinusoidal: 2679
      harmonic: 5242
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -115.92 -174.82     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C8  GTP C 501 "
           pdb=" C1' GTP C 501 "
           pdb=" N9  GTP C 501 "
           pdb=" O4' GTP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -67.13  171.72     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" O3B GTP C 501 "
           pdb=" O3A GTP C 501 "
           pdb=" PB  GTP C 501 "
           pdb=" PA  GTP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  153.68  137.40     1      2.00e+01 2.50e-03 4.17e+01
  ... (remaining 7918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1227
       0.026 -    0.052: 532
       0.052 -    0.078: 229
       0.078 -    0.104: 107
       0.104 -    0.130: 46
  Chirality restraints: 2141
  Sorted by residual:
  chirality pdb=" CA  VAL C 363 "
            pdb=" N   VAL C 363 "
            pdb=" C   VAL C 363 "
            pdb=" CB  VAL C 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  VAL A 363 "
            pdb=" N   VAL A 363 "
            pdb=" C   VAL A 363 "
            pdb=" CB  VAL A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE D   4 "
            pdb=" N   ILE D   4 "
            pdb=" C   ILE D   4 "
            pdb=" CB  ILE D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  ... (remaining 2138 not shown)

  Planarity restraints: 2371
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 267 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO C 268 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 268 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 268 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 357 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO D 358 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 358 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 358 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 170 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO D 171 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO D 171 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 171 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 2368 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 111
        2.58 -     3.16: 11051
        3.16 -     3.74: 21199
        3.74 -     4.32: 28039
        4.32 -     4.90: 48268
  Nonbonded interactions: 108668
  Sorted by model distance:
  nonbonded pdb=" O1B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.994 2.170
  nonbonded pdb=" O1G GTP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     1.994 2.170
  nonbonded pdb=" O1G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.026 2.170
  nonbonded pdb=" O1B GTP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     2.053 2.170
  nonbonded pdb=" OD2 ASP B  67 "
            pdb=" OG1 THR B  72 "
     model   vdw
     2.255 3.040
  ... (remaining 108663 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 333 or (resid 334 through 336 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 337 through 501))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.630
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.720
  Find NCS groups from input model:        0.200
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
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      :  0.002   0.024  13544  Z= 0.107
  Angle     :  0.475   6.507  18513  Z= 0.245
  Chirality :  0.039   0.130   2141
  Planarity :  0.003   0.029   2371
  Dihedral  : 11.146 174.815   4551
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  3.91 %
    Favored  : 94.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.21), residues: 1710
  helix:  2.42 (0.19), residues: 762
  sheet:  0.38 (0.34), residues: 268
  loop : -0.15 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 123 
 TYR   0.008   0.001   TYR B 310 
 PHE   0.008   0.001   PHE B 260 
 TRP   0.009   0.001   TRP B  21 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (13544)
  covalent geometry    : angle       0.47477 (18513)
  hydrogen bonds       : bond        0.19451 (  747)
  hydrogen bonds       : angle       6.60376 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9195 (m) cc_final: 0.8846 (m)
REVERT: A   69 ASP cc_start: 0.8098 (t0) cc_final: 0.7733 (t0)
REVERT: A  183 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8088 (mt-10)
REVERT: A  302 MET cc_start: 0.8704 (mmt) cc_final: 0.8424 (mpp)
REVERT: A  377 MET cc_start: 0.8880 (ttp) cc_final: 0.8658 (ttm)
REVERT: A  378 LEU cc_start: 0.9426 (mt) cc_final: 0.9225 (mt)
REVERT: A  411 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7989 (mm-30)
REVERT: B   19 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8655 (mmmm)
REVERT: B  252 LYS cc_start: 0.9366 (tttt) cc_final: 0.8708 (tttm)
REVERT: B  289 LEU cc_start: 0.9548 (mt) cc_final: 0.9155 (mp)
REVERT: B  321 MET cc_start: 0.8463 (pmm) cc_final: 0.7943 (pmm)
REVERT: B  363 MET cc_start: 0.8800 (ptp) cc_final: 0.8394 (ptp)
REVERT: C   69 ASP cc_start: 0.8659 (t0) cc_final: 0.8331 (t0)
REVERT: C  133 GLN cc_start: 0.9016 (mm110) cc_final: 0.8192 (mm110)
REVERT: C  183 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8376 (mt-10)
REVERT: C  213 CYS cc_start: 0.8714 (t) cc_final: 0.8503 (t)
REVERT: C  301 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7751 (pm20)
REVERT: C  304 LYS cc_start: 0.8904 (tppt) cc_final: 0.8409 (tppt)
REVERT: C  377 MET cc_start: 0.8785 (ttp) cc_final: 0.7928 (tmm)
REVERT: C  392 ASP cc_start: 0.8541 (t70) cc_final: 0.8074 (t0)
REVERT: C  417 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8600 (tm-30)
REVERT: D    6 HIS cc_start: 0.8802 (t-90) cc_final: 0.8322 (t-170)
REVERT: D   19 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9079 (mmmm)
REVERT: D   58 LYS cc_start: 0.8440 (mmtp) cc_final: 0.7980 (pttt)
REVERT: D  103 LYS cc_start: 0.8865 (tttp) cc_final: 0.8509 (ttmm)
REVERT: D  129 CYS cc_start: 0.8932 (t) cc_final: 0.8660 (m)
REVERT: D  162 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8239 (mpp80)
REVERT: D  257 MET cc_start: 0.7730 (mmm) cc_final: 0.6554 (mmm)
REVERT: D  312 THR cc_start: 0.9141 (p) cc_final: 0.7782 (p)
REVERT: D  350 LYS cc_start: 0.8880 (tptt) cc_final: 0.7942 (tppt)
REVERT: D  403 MET cc_start: 0.8918 (mmm) cc_final: 0.7962 (mmm)
REVERT: D  407 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8370 (mt-10)
  outliers start: 21
  outliers final: 7
  residues processed: 216
  average time/residue: 0.0986
  time to fit residues: 30.9089
Evaluate side-chains
  139 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  327 ASP
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  162 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  48 ASN
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 300 ASN
D 292 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.059927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.050132 restraints weight = 43459.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.052136 restraints weight = 20601.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.053532 restraints weight = 12042.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.054420 restraints weight = 8005.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.055092 restraints weight = 5871.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13544  Z= 0.182
  Angle     :  0.554   6.730  18513  Z= 0.280
  Chirality :  0.042   0.161   2141
  Planarity :  0.004   0.036   2371
  Dihedral  : 10.650 173.100   2009
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  7.57 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.21), residues: 1710
  helix:  2.16 (0.19), residues: 782
  sheet:  0.12 (0.33), residues: 276
  loop : -0.19 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 282 
 TYR   0.011   0.001   TYR C 272 
 PHE   0.016   0.001   PHE D 367 
 TRP   0.011   0.001   TRP C  21 
 HIS   0.007   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (13544)
  covalent geometry    : angle       0.55380 (18513)
  hydrogen bonds       : bond        0.04524 (  747)
  hydrogen bonds       : angle       4.58526 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9196 (m) cc_final: 0.8869 (m)
REVERT: A   69 ASP cc_start: 0.8076 (t0) cc_final: 0.7733 (t0)
REVERT: A  183 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: A  203 MET cc_start: 0.8499 (mtm) cc_final: 0.8251 (mtm)
REVERT: A  205 ASP cc_start: 0.7779 (t0) cc_final: 0.7550 (m-30)
REVERT: A  301 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8255 (mp10)
REVERT: A  302 MET cc_start: 0.8665 (mmt) cc_final: 0.8351 (mpp)
REVERT: A  327 ASP cc_start: 0.9258 (m-30) cc_final: 0.9041 (m-30)
REVERT: A  377 MET cc_start: 0.8959 (ttp) cc_final: 0.8683 (ttm)
REVERT: A  411 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8155 (mm-30)
REVERT: B    1 MET cc_start: 0.8263 (mmt) cc_final: 0.7985 (mmt)
REVERT: B  321 MET cc_start: 0.8536 (pmm) cc_final: 0.8084 (pmm)
REVERT: B  363 MET cc_start: 0.8746 (ptp) cc_final: 0.8365 (ptp)
REVERT: C   36 MET cc_start: 0.8982 (tpp) cc_final: 0.8634 (tmm)
REVERT: C   69 ASP cc_start: 0.8632 (t0) cc_final: 0.8263 (t0)
REVERT: C  133 GLN cc_start: 0.8959 (mm110) cc_final: 0.8149 (mm110)
REVERT: C  183 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: C  213 CYS cc_start: 0.8615 (t) cc_final: 0.8309 (t)
REVERT: C  301 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8246 (mm-40)
REVERT: C  304 LYS cc_start: 0.8469 (tppt) cc_final: 0.8237 (tppt)
REVERT: C  417 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8603 (tm-30)
REVERT: D    6 HIS cc_start: 0.8835 (t-90) cc_final: 0.8144 (t-170)
REVERT: D   19 LYS cc_start: 0.9322 (mmmt) cc_final: 0.9043 (mmmm)
REVERT: D   73 MET cc_start: 0.9166 (mmm) cc_final: 0.8966 (mmm)
REVERT: D  162 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8210 (mpp80)
REVERT: D  257 MET cc_start: 0.8048 (mmm) cc_final: 0.7330 (mmm)
REVERT: D  300 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8759 (mtm)
REVERT: D  312 THR cc_start: 0.9170 (p) cc_final: 0.7863 (p)
REVERT: D  321 MET cc_start: 0.8370 (ptp) cc_final: 0.8076 (ptp)
REVERT: D  363 MET cc_start: 0.8206 (ptp) cc_final: 0.7891 (ptp)
REVERT: D  403 MET cc_start: 0.8923 (mmm) cc_final: 0.8291 (mmm)
REVERT: D  407 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8417 (mt-10)
  outliers start: 31
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0840
  time to fit residues: 22.2731
Evaluate side-chains
  155 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  376 CYS
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  300 ASN
Chi-restraints excluded: chain C residue  327 ASP
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  233 MET
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain D residue  395 LEU
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 140 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 143 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 152 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 GLN
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.061057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.051209 restraints weight = 43782.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053283 restraints weight = 20307.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.054707 restraints weight = 11708.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.055624 restraints weight = 7684.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.056334 restraints weight = 5579.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13544  Z= 0.118
  Angle     :  0.500   7.041  18513  Z= 0.247
  Chirality :  0.041   0.149   2141
  Planarity :  0.004   0.034   2371
  Dihedral  : 10.396 171.060   2005
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.17 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.21), residues: 1710
  helix:  2.17 (0.19), residues: 784
  sheet:  0.06 (0.33), residues: 272
  loop : -0.18 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 390 
 TYR   0.008   0.001   TYR B 310 
 PHE   0.013   0.001   PHE D 367 
 TRP   0.011   0.001   TRP D 397 
 HIS   0.004   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (13544)
  covalent geometry    : angle       0.50015 (18513)
  hydrogen bonds       : bond        0.03814 (  747)
  hydrogen bonds       : angle       4.26466 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9163 (m) cc_final: 0.8812 (m)
REVERT: A   69 ASP cc_start: 0.7972 (t0) cc_final: 0.7647 (t0)
REVERT: A  183 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: A  203 MET cc_start: 0.8513 (mtm) cc_final: 0.8284 (mtm)
REVERT: A  205 ASP cc_start: 0.7704 (t0) cc_final: 0.7452 (m-30)
REVERT: A  301 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8206 (mp10)
REVERT: A  302 MET cc_start: 0.8635 (mmt) cc_final: 0.8315 (mpp)
REVERT: A  327 ASP cc_start: 0.9266 (m-30) cc_final: 0.9062 (m-30)
REVERT: A  377 MET cc_start: 0.9054 (ttp) cc_final: 0.8546 (ttm)
REVERT: B    1 MET cc_start: 0.8394 (mmt) cc_final: 0.8169 (mmt)
REVERT: B  321 MET cc_start: 0.8497 (pmm) cc_final: 0.8141 (pmm)
REVERT: B  363 MET cc_start: 0.8727 (ptp) cc_final: 0.8355 (ptt)
REVERT: C   36 MET cc_start: 0.8930 (tpp) cc_final: 0.8520 (tmm)
REVERT: C   69 ASP cc_start: 0.8541 (t0) cc_final: 0.8172 (t70)
REVERT: C  133 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8722 (mm-40)
REVERT: C  183 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8370 (mt-10)
REVERT: C  205 ASP cc_start: 0.7864 (t0) cc_final: 0.7569 (t0)
REVERT: C  213 CYS cc_start: 0.8563 (t) cc_final: 0.8158 (t)
REVERT: C  301 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8096 (mm-40)
REVERT: C  304 LYS cc_start: 0.8695 (tppt) cc_final: 0.8321 (tppt)
REVERT: C  377 MET cc_start: 0.8937 (ttp) cc_final: 0.8656 (ttm)
REVERT: C  413 MET cc_start: 0.8632 (mmm) cc_final: 0.8039 (tpp)
REVERT: C  417 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: D   19 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8879 (mmmm)
REVERT: D  162 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8188 (mpp80)
REVERT: D  257 MET cc_start: 0.7925 (mmm) cc_final: 0.6957 (mmm)
REVERT: D  300 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8572 (mtm)
REVERT: D  312 THR cc_start: 0.9079 (p) cc_final: 0.7511 (p)
REVERT: D  321 MET cc_start: 0.8382 (ptp) cc_final: 0.8027 (ptp)
REVERT: D  363 MET cc_start: 0.8159 (ptp) cc_final: 0.7819 (ptp)
REVERT: D  403 MET cc_start: 0.8867 (mmm) cc_final: 0.8308 (mmm)
REVERT: D  407 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8314 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 155
  average time/residue: 0.0936
  time to fit residues: 22.1490
Evaluate side-chains
  146 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue  327 ASP
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 167 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 162 optimal weight:    3.9990
   chunk 144 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   chunk 21 optimal weight:    0.4980
   chunk 109 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 HIS
** C   8 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 = 0.3250 r_free = 0.3250 target = 0.060299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.050626 restraints weight = 43616.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.052627 restraints weight = 20531.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.053972 restraints weight = 11919.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.054927 restraints weight = 7965.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.055605 restraints weight = 5745.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13544  Z= 0.153
  Angle     :  0.514   7.108  18513  Z= 0.253
  Chirality :  0.041   0.146   2141
  Planarity :  0.004   0.043   2371
  Dihedral  : 10.302 169.390   2005
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.85 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.21), residues: 1710
  helix:  2.22 (0.19), residues: 782
  sheet:  0.01 (0.33), residues: 272
  loop : -0.09 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 390 
 TYR   0.009   0.001   TYR B 425 
 PHE   0.014   0.001   PHE B 367 
 TRP   0.010   0.001   TRP D 397 
 HIS   0.005   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13544)
  covalent geometry    : angle       0.51389 (18513)
  hydrogen bonds       : bond        0.03718 (  747)
  hydrogen bonds       : angle       4.16220 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9176 (m) cc_final: 0.8829 (m)
REVERT: A   69 ASP cc_start: 0.7865 (t0) cc_final: 0.7511 (t0)
REVERT: A  183 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: A  203 MET cc_start: 0.8501 (mtm) cc_final: 0.8267 (mtm)
REVERT: A  205 ASP cc_start: 0.7761 (t0) cc_final: 0.7488 (m-30)
REVERT: A  302 MET cc_start: 0.8610 (mmt) cc_final: 0.8353 (mpp)
REVERT: A  377 MET cc_start: 0.9081 (ttp) cc_final: 0.8840 (ttm)
REVERT: B    1 MET cc_start: 0.8316 (mmt) cc_final: 0.8099 (mmp)
REVERT: B  321 MET cc_start: 0.8451 (pmm) cc_final: 0.8035 (pmm)
REVERT: B  363 MET cc_start: 0.8708 (ptp) cc_final: 0.8332 (ptt)
REVERT: C   36 MET cc_start: 0.8945 (tpp) cc_final: 0.8541 (tmm)
REVERT: C   69 ASP cc_start: 0.8557 (t0) cc_final: 0.8210 (t70)
REVERT: C  183 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8368 (mt-10)
REVERT: C  205 ASP cc_start: 0.7831 (t0) cc_final: 0.7562 (t0)
REVERT: C  213 CYS cc_start: 0.8595 (t) cc_final: 0.8143 (t)
REVERT: C  301 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8134 (mm-40)
REVERT: C  304 LYS cc_start: 0.8677 (tppt) cc_final: 0.8299 (tppt)
REVERT: C  377 MET cc_start: 0.8983 (ttp) cc_final: 0.8654 (ttm)
REVERT: C  413 MET cc_start: 0.8589 (mmm) cc_final: 0.8144 (tpp)
REVERT: C  417 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: C  432 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7548 (t80)
REVERT: D   19 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8911 (mmmm)
REVERT: D  162 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8183 (mpp80)
REVERT: D  257 MET cc_start: 0.7910 (mmm) cc_final: 0.6952 (mmm)
REVERT: D  300 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8597 (mtm)
REVERT: D  312 THR cc_start: 0.9063 (p) cc_final: 0.7465 (p)
REVERT: D  321 MET cc_start: 0.8412 (ptp) cc_final: 0.8099 (ptp)
REVERT: D  363 MET cc_start: 0.8168 (ptp) cc_final: 0.7618 (ptt)
REVERT: D  403 MET cc_start: 0.8858 (mmm) cc_final: 0.8090 (mmm)
REVERT: D  407 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8265 (mt-10)
  outliers start: 32
  outliers final: 21
  residues processed: 154
  average time/residue: 0.0933
  time to fit residues: 22.5091
Evaluate side-chains
  148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  395 LEU
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 178 optimal weight:   10.0000
   chunk 152 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.050601 restraints weight = 43949.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.052621 restraints weight = 20831.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054050 restraints weight = 12222.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.054943 restraints weight = 8128.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.055616 restraints weight = 5993.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13544  Z= 0.134
  Angle     :  0.506   8.607  18513  Z= 0.248
  Chirality :  0.041   0.141   2141
  Planarity :  0.004   0.041   2371
  Dihedral  : 10.170 166.411   2004
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 10.74 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.21), residues: 1710
  helix:  2.15 (0.19), residues: 786
  sheet:  0.03 (0.33), residues: 272
  loop : -0.09 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 390 
 TYR   0.009   0.001   TYR B 310 
 PHE   0.013   0.001   PHE D 367 
 TRP   0.011   0.001   TRP D 397 
 HIS   0.008   0.001   HIS D  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13544)
  covalent geometry    : angle       0.50578 (18513)
  hydrogen bonds       : bond        0.03533 (  747)
  hydrogen bonds       : angle       4.04037 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9172 (m) cc_final: 0.8808 (m)
REVERT: A   69 ASP cc_start: 0.7839 (t0) cc_final: 0.7483 (t0)
REVERT: A  183 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7986 (mt-10)
REVERT: A  203 MET cc_start: 0.8454 (mtm) cc_final: 0.8214 (mtm)
REVERT: A  205 ASP cc_start: 0.7753 (t0) cc_final: 0.7459 (m-30)
REVERT: A  302 MET cc_start: 0.8581 (mmt) cc_final: 0.8352 (mpp)
REVERT: B  293 MET cc_start: 0.8713 (mmm) cc_final: 0.8407 (mmm)
REVERT: B  321 MET cc_start: 0.8450 (pmm) cc_final: 0.8054 (pmm)
REVERT: B  363 MET cc_start: 0.8700 (ptp) cc_final: 0.8308 (ptt)
REVERT: B  374 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8878 (pt)
REVERT: C   36 MET cc_start: 0.8936 (tpp) cc_final: 0.8510 (tmm)
REVERT: C   69 ASP cc_start: 0.8608 (t0) cc_final: 0.8203 (t70)
REVERT: C  133 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8289 (mm-40)
REVERT: C  172 TYR cc_start: 0.7892 (t80) cc_final: 0.7467 (t80)
REVERT: C  183 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8360 (mt-10)
REVERT: C  213 CYS cc_start: 0.8554 (t) cc_final: 0.8090 (t)
REVERT: C  301 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7984 (mm-40)
REVERT: C  304 LYS cc_start: 0.8697 (tppt) cc_final: 0.8321 (tppt)
REVERT: C  377 MET cc_start: 0.8898 (ttp) cc_final: 0.7847 (tmm)
REVERT: C  392 ASP cc_start: 0.8023 (t0) cc_final: 0.7744 (t0)
REVERT: C  413 MET cc_start: 0.8613 (mmm) cc_final: 0.8216 (tpp)
REVERT: C  417 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: C  432 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7591 (t80)
REVERT: D  162 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8166 (mpp80)
REVERT: D  257 MET cc_start: 0.7839 (mmm) cc_final: 0.6889 (mmm)
REVERT: D  300 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8519 (mpp)
REVERT: D  312 THR cc_start: 0.9018 (p) cc_final: 0.7383 (p)
REVERT: D  321 MET cc_start: 0.8403 (ptp) cc_final: 0.8122 (ptp)
REVERT: D  363 MET cc_start: 0.8164 (ptp) cc_final: 0.7586 (ptt)
REVERT: D  403 MET cc_start: 0.8908 (mmm) cc_final: 0.8233 (mmm)
REVERT: D  407 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8236 (mt-10)
  outliers start: 34
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0806
  time to fit residues: 20.4151
Evaluate side-chains
  148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  133 GLN
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 177 optimal weight:   20.0000
   chunk 66 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0970
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.061350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.051366 restraints weight = 43050.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.053405 restraints weight = 20585.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.054784 restraints weight = 12100.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.055759 restraints weight = 8101.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.056460 restraints weight = 5883.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13544  Z= 0.113
  Angle     :  0.490   7.487  18513  Z= 0.240
  Chirality :  0.040   0.166   2141
  Planarity :  0.004   0.039   2371
  Dihedral  : 10.050 164.212   2004
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.47 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.21), residues: 1710
  helix:  2.23 (0.19), residues: 780
  sheet: -0.00 (0.33), residues: 282
  loop : -0.01 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 390 
 TYR   0.008   0.001   TYR B 310 
 PHE   0.011   0.001   PHE D 367 
 TRP   0.010   0.001   TRP D 397 
 HIS   0.005   0.001   HIS D  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (13544)
  covalent geometry    : angle       0.49044 (18513)
  hydrogen bonds       : bond        0.03341 (  747)
  hydrogen bonds       : angle       3.94331 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9168 (m) cc_final: 0.8797 (m)
REVERT: A   69 ASP cc_start: 0.7824 (t70) cc_final: 0.7462 (t0)
REVERT: A  183 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7966 (mt-10)
REVERT: A  203 MET cc_start: 0.8440 (mtm) cc_final: 0.8199 (mtm)
REVERT: A  205 ASP cc_start: 0.7580 (t0) cc_final: 0.7254 (m-30)
REVERT: A  302 MET cc_start: 0.8604 (mmt) cc_final: 0.8357 (mpp)
REVERT: B  293 MET cc_start: 0.8713 (mmm) cc_final: 0.8386 (mtp)
REVERT: B  363 MET cc_start: 0.8699 (ptp) cc_final: 0.8254 (ptt)
REVERT: B  374 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8846 (pt)
REVERT: C   36 MET cc_start: 0.8925 (tpp) cc_final: 0.8485 (tmm)
REVERT: C   69 ASP cc_start: 0.8567 (t0) cc_final: 0.8175 (t70)
REVERT: C  183 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8346 (mt-10)
REVERT: C  213 CYS cc_start: 0.8571 (t) cc_final: 0.8085 (t)
REVERT: C  301 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7913 (mm-40)
REVERT: C  327 ASP cc_start: 0.9192 (m-30) cc_final: 0.8915 (p0)
REVERT: C  377 MET cc_start: 0.8967 (ttp) cc_final: 0.7754 (tmm)
REVERT: C  413 MET cc_start: 0.8632 (mmm) cc_final: 0.8257 (tpp)
REVERT: C  417 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: C  432 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7608 (t80)
REVERT: D    6 HIS cc_start: 0.8846 (t-90) cc_final: 0.8215 (t-170)
REVERT: D  162 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8149 (mpp80)
REVERT: D  257 MET cc_start: 0.7795 (mmm) cc_final: 0.6833 (mmm)
REVERT: D  300 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8366 (mpp)
REVERT: D  312 THR cc_start: 0.8975 (p) cc_final: 0.7343 (p)
REVERT: D  363 MET cc_start: 0.8154 (ptp) cc_final: 0.7564 (ptt)
REVERT: D  403 MET cc_start: 0.8907 (mmm) cc_final: 0.8237 (mmm)
REVERT: D  407 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8318 (mt-10)
  outliers start: 29
  outliers final: 21
  residues processed: 155
  average time/residue: 0.0792
  time to fit residues: 19.7926
Evaluate side-chains
  150 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 156 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 33 optimal weight:    0.1980
   chunk 120 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.060888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.051143 restraints weight = 43556.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.053172 restraints weight = 20614.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.054562 restraints weight = 11996.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.055456 restraints weight = 7937.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.056104 restraints weight = 5789.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13544  Z= 0.134
  Angle     :  0.507   9.847  18513  Z= 0.248
  Chirality :  0.041   0.141   2141
  Planarity :  0.004   0.036   2371
  Dihedral  :  9.950 164.287   2004
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.80 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.21), residues: 1710
  helix:  2.23 (0.19), residues: 780
  sheet: -0.02 (0.32), residues: 282
  loop : -0.00 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 390 
 TYR   0.009   0.001   TYR B 310 
 PHE   0.011   0.001   PHE D 367 
 TRP   0.021   0.001   TRP D 397 
 HIS   0.004   0.001   HIS D  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13544)
  covalent geometry    : angle       0.50653 (18513)
  hydrogen bonds       : bond        0.03374 (  747)
  hydrogen bonds       : angle       3.91230 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9192 (m) cc_final: 0.8830 (m)
REVERT: A   69 ASP cc_start: 0.7861 (t70) cc_final: 0.7488 (t0)
REVERT: A  183 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: A  203 MET cc_start: 0.8439 (mtm) cc_final: 0.8172 (mtm)
REVERT: A  302 MET cc_start: 0.8593 (mmt) cc_final: 0.8355 (mpp)
REVERT: A  417 GLU cc_start: 0.7606 (mp0) cc_final: 0.7308 (mp0)
REVERT: B  321 MET cc_start: 0.8742 (ptp) cc_final: 0.8509 (pmm)
REVERT: B  363 MET cc_start: 0.8689 (ptp) cc_final: 0.8357 (ptt)
REVERT: B  374 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8855 (pt)
REVERT: B  407 GLU cc_start: 0.8876 (tt0) cc_final: 0.8412 (tt0)
REVERT: C   36 MET cc_start: 0.8849 (tpp) cc_final: 0.8390 (tmm)
REVERT: C   69 ASP cc_start: 0.8524 (t0) cc_final: 0.8141 (t70)
REVERT: C  172 TYR cc_start: 0.7890 (t80) cc_final: 0.7472 (t80)
REVERT: C  183 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8351 (mt-10)
REVERT: C  213 CYS cc_start: 0.8576 (t) cc_final: 0.8082 (t)
REVERT: C  301 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8116 (mm-40)
REVERT: C  327 ASP cc_start: 0.9187 (m-30) cc_final: 0.8926 (p0)
REVERT: C  377 MET cc_start: 0.9015 (ttp) cc_final: 0.8685 (ttm)
REVERT: C  413 MET cc_start: 0.8621 (mmm) cc_final: 0.6960 (tpp)
REVERT: C  432 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7599 (t80)
REVERT: D    6 HIS cc_start: 0.8854 (t-90) cc_final: 0.8227 (t-170)
REVERT: D  162 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8123 (mpp80)
REVERT: D  257 MET cc_start: 0.7820 (mmm) cc_final: 0.6845 (mmm)
REVERT: D  300 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8408 (mpp)
REVERT: D  312 THR cc_start: 0.8979 (p) cc_final: 0.7341 (p)
REVERT: D  363 MET cc_start: 0.8143 (ptp) cc_final: 0.7666 (ptt)
REVERT: D  403 MET cc_start: 0.8934 (mmm) cc_final: 0.8241 (mmm)
REVERT: D  407 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8328 (mt-10)
  outliers start: 31
  outliers final: 21
  residues processed: 156
  average time/residue: 0.0746
  time to fit residues: 18.8647
Evaluate side-chains
  148 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  395 LEU
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 161 optimal weight:    4.9990
   chunk 169 optimal weight:    0.7980
   chunk 99 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 168 optimal weight:    0.7980
   chunk 131 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.061703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.051871 restraints weight = 43069.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.053905 restraints weight = 20497.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.055345 restraints weight = 11961.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.056278 restraints weight = 7839.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.056989 restraints weight = 5686.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13544  Z= 0.112
  Angle     :  0.508  10.400  18513  Z= 0.246
  Chirality :  0.040   0.146   2141
  Planarity :  0.003   0.034   2371
  Dihedral  :  9.834 164.372   2004
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.37 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.21), residues: 1710
  helix:  2.20 (0.19), residues: 780
  sheet:  0.04 (0.33), residues: 270
  loop : -0.08 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 390 
 TYR   0.008   0.001   TYR B 310 
 PHE   0.011   0.001   PHE D 367 
 TRP   0.016   0.001   TRP D 397 
 HIS   0.004   0.001   HIS D 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13544)
  covalent geometry    : angle       0.50849 (18513)
  hydrogen bonds       : bond        0.03290 (  747)
  hydrogen bonds       : angle       3.89644 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9142 (m) cc_final: 0.8775 (m)
REVERT: A   69 ASP cc_start: 0.7814 (t70) cc_final: 0.7444 (t0)
REVERT: A  183 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: A  203 MET cc_start: 0.8393 (mtm) cc_final: 0.8167 (mtm)
REVERT: B  224 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8347 (p0)
REVERT: B  363 MET cc_start: 0.8696 (ptp) cc_final: 0.8352 (ptt)
REVERT: B  403 MET cc_start: 0.8812 (mmm) cc_final: 0.8457 (mmp)
REVERT: C   36 MET cc_start: 0.8861 (tpp) cc_final: 0.8416 (tmm)
REVERT: C   69 ASP cc_start: 0.8551 (t0) cc_final: 0.8169 (t70)
REVERT: C  133 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8331 (mm-40)
REVERT: C  172 TYR cc_start: 0.7802 (t80) cc_final: 0.7281 (t80)
REVERT: C  183 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8346 (mt-10)
REVERT: C  301 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8041 (mm-40)
REVERT: C  327 ASP cc_start: 0.9144 (m-30) cc_final: 0.8906 (p0)
REVERT: C  377 MET cc_start: 0.9011 (ttp) cc_final: 0.8693 (ttm)
REVERT: C  432 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7573 (t80)
REVERT: D    6 HIS cc_start: 0.8839 (t-90) cc_final: 0.8290 (t-170)
REVERT: D  162 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8162 (mpp80)
REVERT: D  257 MET cc_start: 0.7767 (mmm) cc_final: 0.6814 (mmm)
REVERT: D  300 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8438 (mpp)
REVERT: D  312 THR cc_start: 0.8951 (p) cc_final: 0.7317 (p)
REVERT: D  363 MET cc_start: 0.8149 (ptp) cc_final: 0.7782 (ptt)
REVERT: D  403 MET cc_start: 0.8894 (mmm) cc_final: 0.8229 (mmm)
REVERT: D  407 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8345 (mt-10)
  outliers start: 25
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0750
  time to fit residues: 18.0533
Evaluate side-chains
  149 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  133 GLN
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  395 LEU
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 177 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9990
   chunk 94 optimal weight:    0.3980
   chunk 70 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.051141 restraints weight = 43898.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.053189 restraints weight = 20906.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.054575 restraints weight = 12245.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.055505 restraints weight = 8157.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.056182 restraints weight = 5974.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13544  Z= 0.136
  Angle     :  0.525  10.788  18513  Z= 0.255
  Chirality :  0.041   0.141   2141
  Planarity :  0.004   0.035   2371
  Dihedral  :  9.738 164.433   2000
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.53 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.21), residues: 1710
  helix:  2.20 (0.19), residues: 780
  sheet:  0.03 (0.33), residues: 270
  loop : -0.07 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 390 
 TYR   0.008   0.001   TYR B 425 
 PHE   0.011   0.001   PHE D 367 
 TRP   0.012   0.001   TRP D 397 
 HIS   0.004   0.001   HIS D 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13544)
  covalent geometry    : angle       0.52535 (18513)
  hydrogen bonds       : bond        0.03325 (  747)
  hydrogen bonds       : angle       3.92804 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9179 (m) cc_final: 0.8813 (m)
REVERT: A   69 ASP cc_start: 0.7836 (t70) cc_final: 0.7466 (t0)
REVERT: A  183 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7989 (mt-10)
REVERT: A  203 MET cc_start: 0.8474 (mtm) cc_final: 0.8160 (mtm)
REVERT: A  302 MET cc_start: 0.8735 (mpp) cc_final: 0.8183 (mpp)
REVERT: B  363 MET cc_start: 0.8730 (ptp) cc_final: 0.7988 (ptt)
REVERT: B  374 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8850 (pt)
REVERT: B  403 MET cc_start: 0.8770 (mmm) cc_final: 0.8515 (mmp)
REVERT: C   36 MET cc_start: 0.8831 (tpp) cc_final: 0.8325 (tmm)
REVERT: C   69 ASP cc_start: 0.8574 (t0) cc_final: 0.8187 (t70)
REVERT: C  183 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8363 (mt-10)
REVERT: C  301 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8073 (mm-40)
REVERT: C  327 ASP cc_start: 0.9176 (m-30) cc_final: 0.8926 (p0)
REVERT: C  377 MET cc_start: 0.9032 (ttp) cc_final: 0.8728 (ttm)
REVERT: C  432 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7578 (t80)
REVERT: D    6 HIS cc_start: 0.8862 (t-90) cc_final: 0.8277 (t-170)
REVERT: D  162 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8169 (mpp80)
REVERT: D  257 MET cc_start: 0.7799 (mmm) cc_final: 0.6824 (mmm)
REVERT: D  300 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8455 (mpp)
REVERT: D  312 THR cc_start: 0.8970 (p) cc_final: 0.7331 (p)
REVERT: D  363 MET cc_start: 0.8200 (ptp) cc_final: 0.7728 (ptt)
REVERT: D  403 MET cc_start: 0.8933 (mmm) cc_final: 0.8229 (mmm)
REVERT: D  407 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8371 (mt-10)
  outliers start: 28
  outliers final: 21
  residues processed: 148
  average time/residue: 0.0809
  time to fit residues: 19.1913
Evaluate side-chains
  147 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0770
   chunk 140 optimal weight:    0.7980
   chunk 171 optimal weight:    0.9990
   chunk 176 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9990
   chunk 167 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.062105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.052129 restraints weight = 43015.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.054165 restraints weight = 20553.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.055604 restraints weight = 12148.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.056572 restraints weight = 8009.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.057258 restraints weight = 5802.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  13544  Z= 0.106
  Angle     :  0.517  10.521  18513  Z= 0.250
  Chirality :  0.040   0.168   2141
  Planarity :  0.003   0.042   2371
  Dihedral  :  9.583 164.573   2000
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.77 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.21), residues: 1710
  helix:  2.20 (0.19), residues: 786
  sheet:  0.03 (0.33), residues: 282
  loop : -0.00 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 390 
 TYR   0.008   0.001   TYR B 310 
 PHE   0.013   0.001   PHE B 367 
 TRP   0.012   0.001   TRP D 397 
 HIS   0.008   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (13544)
  covalent geometry    : angle       0.51675 (18513)
  hydrogen bonds       : bond        0.03134 (  747)
  hydrogen bonds       : angle       3.84669 ( 2190)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 CYS cc_start: 0.9145 (m) cc_final: 0.8767 (m)
REVERT: A   69 ASP cc_start: 0.7788 (t70) cc_final: 0.7424 (t0)
REVERT: A  183 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7957 (mt-10)
REVERT: A  203 MET cc_start: 0.8395 (mtm) cc_final: 0.8153 (mtm)
REVERT: A  302 MET cc_start: 0.8748 (mpp) cc_final: 0.8096 (mpp)
REVERT: B  224 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8337 (p0)
REVERT: B  363 MET cc_start: 0.8611 (ptp) cc_final: 0.8048 (ptt)
REVERT: B  374 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8833 (pt)
REVERT: B  403 MET cc_start: 0.8834 (mmm) cc_final: 0.8400 (mmm)
REVERT: C   36 MET cc_start: 0.8825 (tpp) cc_final: 0.8315 (tmm)
REVERT: C   69 ASP cc_start: 0.8523 (t0) cc_final: 0.8124 (t70)
REVERT: C  183 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: C  301 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8018 (mm-40)
REVERT: C  377 MET cc_start: 0.9030 (ttp) cc_final: 0.8724 (ttm)
REVERT: C  432 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7559 (t80)
REVERT: D    6 HIS cc_start: 0.8833 (t-90) cc_final: 0.8305 (t-170)
REVERT: D  162 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8135 (mpp80)
REVERT: D  257 MET cc_start: 0.7746 (mmm) cc_final: 0.6775 (mmm)
REVERT: D  300 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8513 (mpp)
REVERT: D  312 THR cc_start: 0.8918 (p) cc_final: 0.7300 (p)
REVERT: D  363 MET cc_start: 0.8124 (ptp) cc_final: 0.7727 (ptt)
REVERT: D  403 MET cc_start: 0.8918 (mmm) cc_final: 0.8239 (mmm)
REVERT: D  407 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8366 (mt-10)
  outliers start: 25
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0837
  time to fit residues: 19.6462
Evaluate side-chains
  145 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 ASP
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  422 TYR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  371 VAL
Chi-restraints excluded: chain C residue  375 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  162 ARG
Chi-restraints excluded: chain D residue  300 MET
Chi-restraints excluded: chain D residue  422 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 164 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0060
   chunk 89 optimal weight:    6.9990
   chunk 167 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0070
   overall best weight:    0.4814

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.061874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.051653 restraints weight = 43678.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.053779 restraints weight = 20571.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.055200 restraints weight = 11932.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.056172 restraints weight = 7930.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.056934 restraints weight = 5772.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  13544  Z= 0.096
  Angle     :  0.514  11.333  18513  Z= 0.247
  Chirality :  0.040   0.166   2141
  Planarity :  0.003   0.039   2371
  Dihedral  :  9.400 165.026   2000
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.86 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.21), residues: 1710
  helix:  2.22 (0.19), residues: 786
  sheet:  0.03 (0.33), residues: 282
  loop :  0.01 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 390 
 TYR   0.007   0.001   TYR B 310 
 PHE   0.012   0.001   PHE B 367 
 TRP   0.010   0.001   TRP D 397 
 HIS   0.008   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (13544)
  covalent geometry    : angle       0.51381 (18513)
  hydrogen bonds       : bond        0.03007 (  747)
  hydrogen bonds       : angle       3.79503 ( 2190)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1599.54 seconds
wall clock time: 28 minutes 37.57 seconds (1717.57 seconds total)