Starting phenix.real_space_refine
on Sat Sep 12 08:32:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u96_20694/09_2026/6u96_20694.map"
  }
  resolution = 3.8
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S     110      5.16       5
     C    9410      2.51       5
     N    2510      2.21       5
     O    2870      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14910
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Link IDs: {'CIS': 1, 'TRANS': 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'EEP:plan-1': 1, 'ALO:plan-1': 1, 'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, G, H, I, J
  Time building chain proxies: 3.05, per 1000 atoms: 0.20
  Number of scatterers: 14910
  At special positions: 0
  Unit cell: (87.74, 102.72, 204.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     110     16.00
     P      10     15.00
     O    2870      8.00
     N    2510      7.00
     C    9410      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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 729.9 milliseconds
  

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3500

  Finding SS restraints...
    Secondary structure from input PDB file:
      105 helices and 25 sheets defined
      42.8% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.568A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 91
      removed outlier: 3.630A  pdb=" N   MET A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS A  84 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR A  91 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.801A  pdb=" N   GLU A 100 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS A 101 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 97 through 101'
    Processing helix  chain 'A' and resid 114 through 125
      removed outlier: 4.212A  pdb=" N   MET A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE A 122 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 123 " --> pdb=" O   MET A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 140
      No H-bonds generated for 'chain 'A' and resid 138 through 140'
    Processing helix  chain 'A' and resid 141 through 146
      removed outlier: 3.652A  pdb=" N   SER A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 175
      removed outlier: 4.172A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 175'
    Processing helix  chain 'A' and resid 182 through 193
      removed outlier: 3.725A  pdb=" N   LYS A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 206 through 216
      removed outlier: 3.989A  pdb=" N   ILE A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 233
      removed outlier: 3.550A  pdb=" N   MET A 227 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 231 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 262
      removed outlier: 3.658A  pdb=" N   THR A 260 " --> pdb=" O   CYS A 257 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 261 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 4.009A  pdb=" N   THR A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 3.977A  pdb=" N   ALA A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.947A  pdb=" N   MET A 305 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR A 306 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 302 through 306'
    Processing helix  chain 'A' and resid 309 through 318
      removed outlier: 3.576A  pdb=" N   MET A 313 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS A 315 " --> pdb=" O   ASP A 311 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE A 317 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 348
      removed outlier: 3.566A  pdb=" N   GLY A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 347 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.616A  pdb=" N   GLN A 353 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 365
      removed outlier: 3.735A  pdb=" N   TYR A 362 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.770A  pdb=" N   CYS A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 61
      removed outlier: 3.567A  pdb=" N   LYS B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 92
      removed outlier: 3.631A  pdb=" N   MET B  82 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR B  91 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.801A  pdb=" N   GLU B 100 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   HIS B 101 " --> pdb=" O   PRO B  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 97 through 101'
    Processing helix  chain 'B' and resid 114 through 125
      removed outlier: 4.213A  pdb=" N   MET B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN B 121 " --> pdb=" O   GLU B 117 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET B 123 " --> pdb=" O   MET B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 140
      No H-bonds generated for 'chain 'B' and resid 138 through 140'
    Processing helix  chain 'B' and resid 141 through 146
      removed outlier: 3.653A  pdb=" N   SER B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 175
      removed outlier: 4.173A  pdb=" N   ILE B 175 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 175'
    Processing helix  chain 'B' and resid 182 through 193
      removed outlier: 3.724A  pdb=" N   LYS B 191 " --> pdb=" O   ASP B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 196
      No H-bonds generated for 'chain 'B' and resid 194 through 196'
    Processing helix  chain 'B' and resid 206 through 216
      removed outlier: 3.988A  pdb=" N   ILE B 212 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS B 215 " --> pdb=" O   ASP B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 233
      removed outlier: 3.551A  pdb=" N   MET B 227 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA B 231 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 262
      removed outlier: 3.658A  pdb=" N   THR B 260 " --> pdb=" O   CYS B 257 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 261 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
      removed outlier: 4.009A  pdb=" N   THR B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 295
      removed outlier: 3.977A  pdb=" N   ALA B 295 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.947A  pdb=" N   MET B 305 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TYR B 306 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 302 through 306'
    Processing helix  chain 'B' and resid 309 through 318
      removed outlier: 3.576A  pdb=" N   MET B 313 " --> pdb=" O   ILE B 309 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS B 315 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE B 317 " --> pdb=" O   MET B 313 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR B 318 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 348
      removed outlier: 3.566A  pdb=" N   GLY B 343 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B 345 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B 347 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER B 348 " --> pdb=" O   SER B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 3.616A  pdb=" N   GLN B 353 " --> pdb=" O   SER B 350 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN B 354 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 365
      removed outlier: 3.735A  pdb=" N   TYR B 362 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA B 365 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 368
      No H-bonds generated for 'chain 'B' and resid 366 through 368'
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.770A  pdb=" N   CYS B 374 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 61
      removed outlier: 3.567A  pdb=" N   LYS C  61 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 91
      removed outlier: 3.630A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR C  91 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.801A  pdb=" N   GLU C 100 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   HIS C 101 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 97 through 101'
    Processing helix  chain 'C' and resid 114 through 125
      removed outlier: 4.212A  pdb=" N   MET C 119 " --> pdb=" O   ASN C 115 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR C 120 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN C 121 " --> pdb=" O   GLU C 117 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE C 122 " --> pdb=" O   LYS C 118 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 140
      No H-bonds generated for 'chain 'C' and resid 138 through 140'
    Processing helix  chain 'C' and resid 141 through 146
      removed outlier: 3.653A  pdb=" N   SER C 145 " --> pdb=" O   SER C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
      removed outlier: 4.173A  pdb=" N   ILE C 175 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 172 through 175'
    Processing helix  chain 'C' and resid 182 through 193
      removed outlier: 3.725A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 196
      No H-bonds generated for 'chain 'C' and resid 194 through 196'
    Processing helix  chain 'C' and resid 206 through 216
      removed outlier: 3.989A  pdb=" N   ILE C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS C 215 " --> pdb=" O   ASP C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 233
      removed outlier: 3.550A  pdb=" N   MET C 227 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA C 228 " --> pdb=" O   GLU C 224 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA C 231 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER C 232 " --> pdb=" O   ALA C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 262
      removed outlier: 3.658A  pdb=" N   THR C 260 " --> pdb=" O   CYS C 257 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU C 261 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 284
      removed outlier: 4.010A  pdb=" N   THR C 278 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 295
      removed outlier: 3.976A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 306
      removed outlier: 3.947A  pdb=" N   MET C 305 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 302 through 306'
    Processing helix  chain 'C' and resid 309 through 318
      removed outlier: 3.576A  pdb=" N   MET C 313 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS C 315 " --> pdb=" O   ASP C 311 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE C 317 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR C 318 " --> pdb=" O   GLN C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 348
      removed outlier: 3.566A  pdb=" N   GLY C 343 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE C 345 " --> pdb=" O   ILE C 341 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA C 347 " --> pdb=" O   GLY C 343 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.616A  pdb=" N   GLN C 353 " --> pdb=" O   SER C 350 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 365
      removed outlier: 3.735A  pdb=" N   TYR C 362 " --> pdb=" O   THR C 358 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA C 365 " --> pdb=" O   GLU C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 368
      No H-bonds generated for 'chain 'C' and resid 366 through 368'
    Processing helix  chain 'C' and resid 369 through 374
      removed outlier: 3.770A  pdb=" N   CYS C 374 " --> pdb=" O   VAL C 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 61
      removed outlier: 3.567A  pdb=" N   LYS D  61 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 92
      removed outlier: 3.630A  pdb=" N   MET D  82 " --> pdb=" O   ASN D  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS D  84 " --> pdb=" O   ASP D  80 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE D  85 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR D  91 " --> pdb=" O   HIS D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.801A  pdb=" N   GLU D 100 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   HIS D 101 " --> pdb=" O   PRO D  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 97 through 101'
    Processing helix  chain 'D' and resid 114 through 125
      removed outlier: 4.212A  pdb=" N   MET D 119 " --> pdb=" O   ASN D 115 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   THR D 120 " --> pdb=" O   ARG D 116 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN D 121 " --> pdb=" O   GLU D 117 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE D 122 " --> pdb=" O   LYS D 118 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET D 123 " --> pdb=" O   MET D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 140
      No H-bonds generated for 'chain 'D' and resid 138 through 140'
    Processing helix  chain 'D' and resid 141 through 146
      removed outlier: 3.653A  pdb=" N   SER D 145 " --> pdb=" O   SER D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 175
      removed outlier: 4.174A  pdb=" N   ILE D 175 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 172 through 175'
    Processing helix  chain 'D' and resid 182 through 193
      removed outlier: 3.725A  pdb=" N   LYS D 191 " --> pdb=" O   ASP D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 196
      No H-bonds generated for 'chain 'D' and resid 194 through 196'
    Processing helix  chain 'D' and resid 206 through 216
      removed outlier: 3.989A  pdb=" N   ILE D 212 " --> pdb=" O   ILE D 208 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS D 215 " --> pdb=" O   ASP D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 233
      removed outlier: 3.550A  pdb=" N   MET D 227 " --> pdb=" O   PHE D 223 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA D 228 " --> pdb=" O   GLU D 224 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA D 231 " --> pdb=" O   MET D 227 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 257 through 262
      removed outlier: 3.658A  pdb=" N   THR D 260 " --> pdb=" O   CYS D 257 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU D 261 " --> pdb=" O   PRO D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 284
      removed outlier: 4.009A  pdb=" N   THR D 278 " --> pdb=" O   ILE D 274 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 290 through 295
      removed outlier: 3.976A  pdb=" N   ALA D 295 " --> pdb=" O   LYS D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 306
      removed outlier: 3.947A  pdb=" N   MET D 305 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR D 306 " --> pdb=" O   THR D 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 302 through 306'
    Processing helix  chain 'D' and resid 309 through 318
      removed outlier: 3.576A  pdb=" N   MET D 313 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS D 315 " --> pdb=" O   ASP D 311 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE D 317 " --> pdb=" O   MET D 313 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR D 318 " --> pdb=" O   GLN D 314 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 348
      removed outlier: 3.566A  pdb=" N   GLY D 343 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE D 345 " --> pdb=" O   ILE D 341 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA D 347 " --> pdb=" O   GLY D 343 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER D 348 " --> pdb=" O   SER D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 350 through 355
      removed outlier: 3.616A  pdb=" N   GLN D 353 " --> pdb=" O   SER D 350 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN D 354 " --> pdb=" O   THR D 351 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 358 through 365
      removed outlier: 3.735A  pdb=" N   TYR D 362 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA D 365 " --> pdb=" O   GLU D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 368
      No H-bonds generated for 'chain 'D' and resid 366 through 368'
    Processing helix  chain 'D' and resid 369 through 374
      removed outlier: 3.770A  pdb=" N   CYS D 374 " --> pdb=" O   VAL D 370 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 56 through 61
      removed outlier: 3.568A  pdb=" N   LYS E  61 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 92
      removed outlier: 3.630A  pdb=" N   MET E  82 " --> pdb=" O   ASN E  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS E  84 " --> pdb=" O   ASP E  80 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE E  85 " --> pdb=" O   ASP E  81 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR E  91 " --> pdb=" O   HIS E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.801A  pdb=" N   GLU E 100 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   HIS E 101 " --> pdb=" O   PRO E  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 97 through 101'
    Processing helix  chain 'E' and resid 114 through 125
      removed outlier: 4.212A  pdb=" N   MET E 119 " --> pdb=" O   ASN E 115 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR E 120 " --> pdb=" O   ARG E 116 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN E 121 " --> pdb=" O   GLU E 117 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE E 122 " --> pdb=" O   LYS E 118 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET E 123 " --> pdb=" O   MET E 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 140
      No H-bonds generated for 'chain 'E' and resid 138 through 140'
    Processing helix  chain 'E' and resid 141 through 146
      removed outlier: 3.653A  pdb=" N   SER E 145 " --> pdb=" O   SER E 141 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 172 through 175
      removed outlier: 4.173A  pdb=" N   ILE E 175 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 172 through 175'
    Processing helix  chain 'E' and resid 182 through 193
      removed outlier: 3.725A  pdb=" N   LYS E 191 " --> pdb=" O   ASP E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 194 through 196
      No H-bonds generated for 'chain 'E' and resid 194 through 196'
    Processing helix  chain 'E' and resid 206 through 216
      removed outlier: 3.988A  pdb=" N   ILE E 212 " --> pdb=" O   ILE E 208 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LYS E 215 " --> pdb=" O   ASP E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 223 through 233
      removed outlier: 3.551A  pdb=" N   MET E 227 " --> pdb=" O   PHE E 223 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA E 228 " --> pdb=" O   GLU E 224 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA E 231 " --> pdb=" O   MET E 227 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER E 232 " --> pdb=" O   ALA E 228 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 257 through 262
      removed outlier: 3.658A  pdb=" N   THR E 260 " --> pdb=" O   CYS E 257 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU E 261 " --> pdb=" O   PRO E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 273 through 284
      removed outlier: 4.009A  pdb=" N   THR E 278 " --> pdb=" O   ILE E 274 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 290 through 295
      removed outlier: 3.977A  pdb=" N   ALA E 295 " --> pdb=" O   LYS E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 306
      removed outlier: 3.946A  pdb=" N   MET E 305 " --> pdb=" O   GLY E 302 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR E 306 " --> pdb=" O   THR E 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 302 through 306'
    Processing helix  chain 'E' and resid 309 through 318
      removed outlier: 3.577A  pdb=" N   MET E 313 " --> pdb=" O   ILE E 309 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS E 315 " --> pdb=" O   ASP E 311 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE E 317 " --> pdb=" O   MET E 313 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR E 318 " --> pdb=" O   GLN E 314 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 337 through 348
      removed outlier: 3.567A  pdb=" N   GLY E 343 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE E 345 " --> pdb=" O   ILE E 341 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA E 347 " --> pdb=" O   GLY E 343 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER E 348 " --> pdb=" O   SER E 344 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 350 through 355
      removed outlier: 3.616A  pdb=" N   GLN E 353 " --> pdb=" O   SER E 350 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN E 354 " --> pdb=" O   THR E 351 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 358 through 365
      removed outlier: 3.736A  pdb=" N   TYR E 362 " --> pdb=" O   THR E 358 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA E 365 " --> pdb=" O   GLU E 361 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 368
      No H-bonds generated for 'chain 'E' and resid 366 through 368'
    Processing helix  chain 'E' and resid 369 through 374
      removed outlier: 3.770A  pdb=" N   CYS E 374 " --> pdb=" O   VAL E 370 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12
      removed outlier: 3.563A  pdb=" N   PHE A  31 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A  29 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42
      removed outlier: 4.421A  pdb=" N   GLN A  41 " --> pdb=" O   ALA D 170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107
      removed outlier: 7.119A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151
      removed outlier: 4.424A  pdb=" N   GLN E  41 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162
      removed outlier: 3.691A  pdb=" N   MET A 176 " --> pdb=" O   ASN A 162 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12
      removed outlier: 3.564A  pdb=" N   PHE B  31 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA B  29 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107
      removed outlier: 7.119A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 151
      removed outlier: 4.533A  pdb=" N   GLN C  41 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162
      removed outlier: 3.691A  pdb=" N   MET B 176 " --> pdb=" O   ASN B 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 12
      removed outlier: 3.562A  pdb=" N   PHE C  31 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA C  29 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 105 through 107
      removed outlier: 7.119A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 162
      removed outlier: 3.691A  pdb=" N   MET C 176 " --> pdb=" O   ASN C 162 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 12
      removed outlier: 3.563A  pdb=" N   PHE D  31 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA D  29 " --> pdb=" O   ALA D  19 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 105 through 107
      removed outlier: 7.119A  pdb=" N   LEU D 105 " --> pdb=" O   ALA D 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 162
      removed outlier: 3.691A  pdb=" N   MET D 176 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241
    Processing sheet with id=AC3, first strand: chain 'E' and resid 8 through 12
      removed outlier: 3.562A  pdb=" N   PHE E  31 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA E  29 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 105 through 107
      removed outlier: 7.119A  pdb=" N   LEU E 105 " --> pdb=" O   ALA E 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'E' and resid 150 through 151
    Processing sheet with id=AC6, first strand: chain 'E' and resid 160 through 162
      removed outlier: 3.692A  pdb=" N   MET E 176 " --> pdb=" O   ASN E 162 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241

    316 hydrogen bonds defined for protein.
    858 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: 2.26

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2486
        1.31 -     1.44: 3934
        1.44 -     1.57: 8615
        1.57 -     1.70: 20
        1.70 -     1.83: 190
  Bond restraints: 15245
  Sorted by residual:
  bond pdb=" C   CYS H   4 "
       pdb=" N   HYP H   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.488 -0.159 1.40e-02 5.10e+03 1.28e+02
  bond pdb=" C   CYS J   4 "
       pdb=" N   HYP J   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.487 -0.158 1.40e-02 5.10e+03 1.27e+02
  bond pdb=" C   CYS G   4 "
       pdb=" N   HYP G   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.487 -0.158 1.40e-02 5.10e+03 1.27e+02
  bond pdb=" C   CYS I   4 "
       pdb=" N   HYP I   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.487 -0.158 1.40e-02 5.10e+03 1.27e+02
  bond pdb=" C   CYS F   4 "
       pdb=" N   HYP F   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.486 -0.157 1.40e-02 5.10e+03 1.26e+02
  ... (remaining 15240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 19847
        2.49 -     4.98: 715
        4.98 -     7.46: 113
        7.46 -     9.95: 15
        9.95 -    12.44: 15
  Bond angle restraints: 20705
  Sorted by residual:
  angle pdb=" CD1 TRP F   7 "
        pdb=" NE1 TRP F   7 "
        pdb=" CE2 TRP F   7 "
      ideal   model   delta    sigma   weight residual
     108.90  120.67  -11.77 1.80e+00 3.09e-01 4.27e+01
  angle pdb=" CD1 TRP H   7 "
        pdb=" NE1 TRP H   7 "
        pdb=" CE2 TRP H   7 "
      ideal   model   delta    sigma   weight residual
     108.90  120.66  -11.76 1.80e+00 3.09e-01 4.27e+01
  angle pdb=" CD1 TRP J   7 "
        pdb=" NE1 TRP J   7 "
        pdb=" CE2 TRP J   7 "
      ideal   model   delta    sigma   weight residual
     108.90  120.66  -11.76 1.80e+00 3.09e-01 4.27e+01
  angle pdb=" CD1 TRP I   7 "
        pdb=" NE1 TRP I   7 "
        pdb=" CE2 TRP I   7 "
      ideal   model   delta    sigma   weight residual
     108.90  120.65  -11.75 1.80e+00 3.09e-01 4.26e+01
  angle pdb=" CD1 TRP G   7 "
        pdb=" NE1 TRP G   7 "
        pdb=" CE2 TRP G   7 "
      ideal   model   delta    sigma   weight residual
     108.90  120.62  -11.72 1.80e+00 3.09e-01 4.24e+01
  ... (remaining 20700 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.43: 8920
       24.43 -    48.87: 175
       48.87 -    73.30: 15
       73.30 -    97.74: 0
       97.74 -   122.17: 5
  Dihedral angle restraints: 9115
    sinusoidal: 3655
      harmonic: 5460
  Sorted by residual:
  dihedral pdb=" O1B ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PB  ADP A 801 "
           pdb=" PA  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  177.82  122.17     1      2.00e+01 2.50e-03 3.68e+01
  dihedral pdb=" O1B ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PB  ADP B 801 "
           pdb=" PA  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  177.83  122.17     1      2.00e+01 2.50e-03 3.68e+01
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  177.85  122.15     1      2.00e+01 2.50e-03 3.68e+01
  ... (remaining 9112 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.157: 2258
       0.157 -    0.313: 42
       0.313 -    0.470: 0
       0.470 -    0.626: 0
       0.626 -    0.783: 5
  Chirality restraints: 2305
  Sorted by residual:
  chirality pdb=" CA  HIC E  73 "
            pdb=" N   HIC E  73 "
            pdb=" C   HIC E  73 "
            pdb=" CB  HIC E  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.73    0.78 2.00e-01 2.50e+01 1.53e+01
  chirality pdb=" CA  HIC D  73 "
            pdb=" N   HIC D  73 "
            pdb=" C   HIC D  73 "
            pdb=" CB  HIC D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.73    0.78 2.00e-01 2.50e+01 1.52e+01
  chirality pdb=" CA  HIC A  73 "
            pdb=" N   HIC A  73 "
            pdb=" C   HIC A  73 "
            pdb=" CB  HIC A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.73    0.78 2.00e-01 2.50e+01 1.52e+01
  ... (remaining 2302 not shown)

  Planarity restraints: 2630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  69 "   -0.042 5.00e-02 4.00e+02   6.44e-02 6.63e+00
        pdb=" N   PRO A  70 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E  69 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO E  70 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E  70 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E  70 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  69 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO B  70 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2627 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 40
        2.45 -     3.06: 8363
        3.06 -     3.68: 19943
        3.68 -     4.29: 27494
        4.29 -     4.90: 46955
  Nonbonded interactions: 102795
  Sorted by model distance:
  nonbonded pdb=" SG  CYS I   4 "
            pdb=" CD1 TRP I   7 "
     model   vdw
     1.838 3.620
  nonbonded pdb=" SG  CYS J   4 "
            pdb=" CD1 TRP J   7 "
     model   vdw
     1.838 3.620
  nonbonded pdb=" SG  CYS G   4 "
            pdb=" CD1 TRP G   7 "
     model   vdw
     1.838 3.620
  nonbonded pdb=" SG  CYS H   4 "
            pdb=" CD1 TRP H   7 "
     model   vdw
     1.838 3.620
  nonbonded pdb=" SG  CYS F   4 "
            pdb=" CD1 TRP F   7 "
     model   vdw
     1.838 3.620
  ... (remaining 102790 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             0.590
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     13.720
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
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      :  0.014   0.219  15250  Z= 0.747
  Angle     :  1.120  12.440  20705  Z= 0.579
  Chirality :  0.071   0.783   2305
  Planarity :  0.007   0.064   2630
  Dihedral  : 10.699 122.172   5615
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.13 %
    Favored  : 95.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -4.97 (0.15), residues: 1830
  helix: -4.52 (0.09), residues: 580
  sheet: -1.96 (0.26), residues: 385
  loop : -2.97 (0.17), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 372 
 TYR   0.024   0.002   TYR D 294 
 PHE   0.016   0.003   PHE B 262 
 TRP   0.027   0.003   TRP C 340 
 HIS   0.004   0.002   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01379 /  0.74 (15245)
  covalent geometry    : angle       1.12018 /  0.58 (20705)
  hydrogen bonds       : bond        0.37798 / 26.60 (  316)
  hydrogen bonds       : angle       9.04257 /  6.13 (  858)
  Misc. bond           : bond        0.05523 /  2.89 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 230
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 THR cc_start: 0.9112 (p) cc_final: 0.8887 (t)
REVERT: E  216 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8524 (pp)
  outliers start: 10
  outliers final: 4
  residues processed: 240
  average time/residue: 0.1304
  time to fit residues: 45.6023
Evaluate side-chains
  122 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue  216 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 GLN
B 121 GLN
B 137 GLN
B 371 HIS
C 137 GLN
D 360 GLN
D 371 HIS
E 121 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.061120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.051212 restraints weight = 46275.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.052841 restraints weight = 24303.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.053959 restraints weight = 15514.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.054693 restraints weight = 11244.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.055234 restraints weight = 8966.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  15250  Z= 0.233
  Angle     :  0.776   6.984  20705  Z= 0.381
  Chirality :  0.052   0.178   2305
  Planarity :  0.006   0.052   2630
  Dihedral  :  9.096 112.387   2130
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  7.56 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -3.96 (0.17), residues: 1830
  helix: -3.24 (0.15), residues: 595
  sheet: -1.77 (0.27), residues: 385
  loop : -2.46 (0.18), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 372 
 TYR   0.015   0.001   TYR E 294 
 PHE   0.009   0.001   PHE C 200 
 TRP   0.014   0.001   TRP B 340 
 HIS   0.005   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.23 (15245)
  covalent geometry    : angle       0.77598 /  0.38 (20705)
  hydrogen bonds       : bond        0.06318 /  4.42 (  316)
  hydrogen bonds       : angle       5.90346 /  4.04 (  858)
  Misc. bond           : bond        0.00216 /  0.11 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 ASP cc_start: 0.7941 (t0) cc_final: 0.7570 (t0)
REVERT: A  283 MET cc_start: 0.9022 (tpp) cc_final: 0.8641 (tpp)
REVERT: A  325 MET cc_start: 0.8637 (mtt) cc_final: 0.8413 (mtt)
REVERT: B  355 MET cc_start: 0.8442 (mmm) cc_final: 0.8028 (mtp)
REVERT: E  236 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8716 (pt)
REVERT: E  283 MET cc_start: 0.8989 (tpp) cc_final: 0.8583 (tpp)
  outliers start: 22
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1180
  time to fit residues: 27.3616
Evaluate side-chains
  119 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  269 MET
Chi-restraints excluded: chain E residue  374 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 130 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 178 optimal weight:    5.9990
   chunk 167 optimal weight:    7.9990
   chunk 131 optimal weight:    9.9990
   chunk 163 optimal weight:    5.9990
   chunk 140 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0670
   chunk 176 optimal weight:    1.9990
   overall best weight:    3.8126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.062374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.052170 restraints weight = 46725.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.053896 restraints weight = 23623.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.055053 restraints weight = 14747.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.055864 restraints weight = 10575.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.056395 restraints weight = 8320.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15250  Z= 0.137
  Angle     :  0.651   6.361  20705  Z= 0.310
  Chirality :  0.047   0.158   2305
  Planarity :  0.004   0.040   2630
  Dihedral  :  8.415 105.762   2130
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  8.13 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -3.25 (0.18), residues: 1830
  helix: -2.28 (0.19), residues: 595
  sheet: -1.55 (0.27), residues: 355
  loop : -2.26 (0.18), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 210 
 TYR   0.010   0.001   TYR E 294 
 PHE   0.006   0.001   PHE C 200 
 TRP   0.009   0.001   TRP B 340 
 HIS   0.002   0.001   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 (15245)
  covalent geometry    : angle       0.65092 /  0.31 (20705)
  hydrogen bonds       : bond        0.04447 /  3.09 (  316)
  hydrogen bonds       : angle       5.20005 /  3.55 (  858)
  Misc. bond           : bond        0.00009 /  0.00 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8914 (mt)
REVERT: A  244 ASP cc_start: 0.7973 (t0) cc_final: 0.7729 (t0)
REVERT: A  283 MET cc_start: 0.8972 (tpp) cc_final: 0.8667 (tpp)
REVERT: B  283 MET cc_start: 0.8879 (tpp) cc_final: 0.8035 (tpp)
REVERT: B  349 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: B  355 MET cc_start: 0.8537 (mmm) cc_final: 0.8082 (mtp)
REVERT: C   72 GLU cc_start: 0.7864 (tp30) cc_final: 0.7420 (tp30)
REVERT: C  349 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8518 (mp)
REVERT: D   82 MET cc_start: 0.8647 (mmm) cc_final: 0.8253 (tpt)
REVERT: E  283 MET cc_start: 0.8935 (tpp) cc_final: 0.8509 (tpp)
  outliers start: 39
  outliers final: 17
  residues processed: 155
  average time/residue: 0.1018
  time to fit residues: 24.6643
Evaluate side-chains
  123 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  303 THR
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  374 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 120 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 155 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 109 optimal weight:   20.0000
   chunk 7 optimal weight:    0.6980
   chunk 154 optimal weight:    0.4980
   chunk 43 optimal weight:    9.9990
   overall best weight:    4.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.061438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.051405 restraints weight = 46445.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.053088 restraints weight = 23982.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.054230 restraints weight = 15145.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.055006 restraints weight = 10943.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.055533 restraints weight = 8669.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15250  Z= 0.146
  Angle     :  0.648   6.443  20705  Z= 0.307
  Chirality :  0.048   0.161   2305
  Planarity :  0.004   0.039   2630
  Dihedral  :  8.201 101.000   2130
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  8.51 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.86 (0.18), residues: 1830
  helix: -1.82 (0.20), residues: 595
  sheet: -1.58 (0.27), residues: 355
  loop : -2.00 (0.19), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 210 
 TYR   0.011   0.001   TYR A 294 
 PHE   0.013   0.001   PHE B 375 
 TRP   0.010   0.001   TRP A  79 
 HIS   0.003   0.001   HIS B 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (15245)
  covalent geometry    : angle       0.64821 /  0.31 (20705)
  hydrogen bonds       : bond        0.04105 /  2.87 (  316)
  hydrogen bonds       : angle       5.00918 /  3.41 (  858)
  Misc. bond           : bond        0.00018 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 110
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  208 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8961 (mt)
REVERT: A  244 ASP cc_start: 0.7947 (t0) cc_final: 0.7732 (t0)
REVERT: A  283 MET cc_start: 0.8904 (tpp) cc_final: 0.8554 (tpp)
REVERT: B  283 MET cc_start: 0.8894 (tpp) cc_final: 0.7980 (mpp)
REVERT: B  349 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8614 (mp)
REVERT: B  355 MET cc_start: 0.8487 (mmm) cc_final: 0.8047 (mtp)
REVERT: C  208 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9040 (mt)
REVERT: C  349 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8702 (mp)
REVERT: E  236 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8690 (pt)
REVERT: E  283 MET cc_start: 0.8920 (tpp) cc_final: 0.8622 (tpp)
REVERT: E  349 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8532 (mp)
  outliers start: 37
  outliers final: 22
  residues processed: 145
  average time/residue: 0.1055
  time to fit residues: 23.9845
Evaluate side-chains
  130 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  303 THR
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  349 LEU
Chi-restraints excluded: chain E residue  374 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 128 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 175 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 180 optimal weight:    0.0050
   chunk 177 optimal weight:    5.9990
   chunk 162 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    3.7400

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.061730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.051683 restraints weight = 46360.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.053364 restraints weight = 23948.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.054503 restraints weight = 15166.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.055284 restraints weight = 10973.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.055816 restraints weight = 8699.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15250  Z= 0.127
  Angle     :  0.619   6.489  20705  Z= 0.290
  Chirality :  0.047   0.163   2305
  Planarity :  0.004   0.035   2630
  Dihedral  :  7.973  96.010   2130
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  8.63 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.56 (0.19), residues: 1830
  helix: -1.48 (0.21), residues: 595
  sheet: -1.56 (0.27), residues: 355
  loop : -1.83 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 372 
 TYR   0.009   0.001   TYR C 294 
 PHE   0.010   0.001   PHE A 200 
 TRP   0.006   0.001   TRP D 340 
 HIS   0.002   0.001   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (15245)
  covalent geometry    : angle       0.61853 /  0.29 (20705)
  hydrogen bonds       : bond        0.03661 /  2.56 (  316)
  hydrogen bonds       : angle       4.75128 /  3.24 (  858)
  Misc. bond           : bond        0.00017 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A  124 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8416 (m-10)
REVERT: A  283 MET cc_start: 0.8850 (tpp) cc_final: 0.8524 (tpp)
REVERT: B  269 MET cc_start: 0.8850 (ttm) cc_final: 0.8565 (ttm)
REVERT: B  283 MET cc_start: 0.8849 (tpp) cc_final: 0.7957 (mpp)
REVERT: B  304 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8831 (m)
REVERT: B  349 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8701 (mp)
REVERT: B  355 MET cc_start: 0.8468 (mmm) cc_final: 0.8009 (mtp)
REVERT: C  124 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8611 (m-10)
REVERT: C  349 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8754 (mp)
REVERT: D   82 MET cc_start: 0.8581 (mmm) cc_final: 0.8212 (tpt)
REVERT: E  236 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8700 (pt)
REVERT: E  283 MET cc_start: 0.8860 (tpp) cc_final: 0.8584 (tpp)
  outliers start: 39
  outliers final: 25
  residues processed: 133
  average time/residue: 0.1077
  time to fit residues: 22.8719
Evaluate side-chains
  129 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  269 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  375 PHE
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 150 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 155 optimal weight:    0.0970
   chunk 160 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 115 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 173 optimal weight:    9.9990
   chunk 124 optimal weight:    8.9990
   overall best weight:    6.8186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.059584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.049732 restraints weight = 46806.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.051284 restraints weight = 24849.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.052365 restraints weight = 16057.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.053057 restraints weight = 11760.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.053581 restraints weight = 9486.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15250  Z= 0.207
  Angle     :  0.696   6.531  20705  Z= 0.332
  Chirality :  0.050   0.184   2305
  Planarity :  0.004   0.039   2630
  Dihedral  :  8.180  99.060   2130
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.02 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.56 (0.19), residues: 1830
  helix: -1.48 (0.21), residues: 595
  sheet: -1.63 (0.27), residues: 355
  loop : -1.79 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 183 
 TYR   0.011   0.001   TYR C 294 
 PHE   0.012   0.001   PHE D 200 
 TRP   0.007   0.001   TRP D 340 
 HIS   0.004   0.001   HIS B 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.21 (15245)
  covalent geometry    : angle       0.69634 /  0.33 (20705)
  hydrogen bonds       : bond        0.04868 /  3.39 (  316)
  hydrogen bonds       : angle       5.14533 /  3.51 (  858)
  Misc. bond           : bond        0.00012 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 100
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A  124 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8324 (m-10)
REVERT: B  269 MET cc_start: 0.8881 (ttm) cc_final: 0.8644 (ttm)
REVERT: B  304 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9026 (m)
REVERT: B  349 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (mp)
REVERT: C  124 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8667 (m-10)
REVERT: C  349 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8815 (mp)
REVERT: E  236 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8689 (pt)
REVERT: E  283 MET cc_start: 0.8848 (tpp) cc_final: 0.8630 (tpp)
  outliers start: 40
  outliers final: 24
  residues processed: 136
  average time/residue: 0.1057
  time to fit residues: 22.5073
Evaluate side-chains
  124 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  269 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 138 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 154 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 123 optimal weight:   20.0000
   chunk 160 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.060115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.050276 restraints weight = 46545.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.051852 restraints weight = 24716.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.052932 restraints weight = 15985.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.053662 restraints weight = 11717.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.054161 restraints weight = 9394.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15250  Z= 0.176
  Angle     :  0.660   6.897  20705  Z= 0.313
  Chirality :  0.049   0.161   2305
  Planarity :  0.004   0.039   2630
  Dihedral  :  8.000  97.846   2130
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.78 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.46 (0.19), residues: 1830
  helix: -1.33 (0.21), residues: 595
  sheet: -1.67 (0.27), residues: 355
  loop : -1.74 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 372 
 TYR   0.009   0.001   TYR C 294 
 PHE   0.009   0.001   PHE C 200 
 TRP   0.008   0.001   TRP D 340 
 HIS   0.003   0.001   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 (15245)
  covalent geometry    : angle       0.66047 /  0.31 (20705)
  hydrogen bonds       : bond        0.04243 /  2.96 (  316)
  hydrogen bonds       : angle       4.97008 /  3.38 (  858)
  Misc. bond           : bond        0.00012 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8406 (m-10)
REVERT: B  269 MET cc_start: 0.8879 (ttm) cc_final: 0.8638 (ttm)
REVERT: B  283 MET cc_start: 0.8735 (tpp) cc_final: 0.8122 (tpp)
REVERT: B  349 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8863 (mp)
REVERT: B  355 MET cc_start: 0.8419 (mmm) cc_final: 0.8101 (mtp)
REVERT: C  124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8647 (m-10)
REVERT: C  349 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8919 (mp)
REVERT: D   82 MET cc_start: 0.8650 (mmm) cc_final: 0.8290 (tpt)
REVERT: E  236 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8659 (pt)
REVERT: E  283 MET cc_start: 0.8824 (tpp) cc_final: 0.8619 (tpp)
REVERT: E  325 MET cc_start: 0.7807 (mmt) cc_final: 0.7532 (mmt)
  outliers start: 33
  outliers final: 23
  residues processed: 123
  average time/residue: 0.1019
  time to fit residues: 20.1494
Evaluate side-chains
  122 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  269 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue  119 MET
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 169 optimal weight:   10.0000
   chunk 162 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 39 optimal weight:    0.2980
   chunk 67 optimal weight:    4.9990
   chunk 148 optimal weight:   20.0000
   overall best weight:    3.6588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.061307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.051505 restraints weight = 46284.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.053116 restraints weight = 24447.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.054214 restraints weight = 15680.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.054941 restraints weight = 11443.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.055448 restraints weight = 9166.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  15250  Z= 0.121
  Angle     :  0.611   6.577  20705  Z= 0.284
  Chirality :  0.047   0.163   2305
  Planarity :  0.004   0.035   2630
  Dihedral  :  7.551  94.057   2130
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.29 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.21 (0.19), residues: 1830
  helix: -1.01 (0.22), residues: 595
  sheet: -1.59 (0.27), residues: 355
  loop : -1.65 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 183 
 TYR   0.008   0.001   TYR C 294 
 PHE   0.007   0.001   PHE E 200 
 TRP   0.007   0.001   TRP D 340 
 HIS   0.002   0.001   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 (15245)
  covalent geometry    : angle       0.61089 /  0.28 (20705)
  hydrogen bonds       : bond        0.03402 /  2.37 (  316)
  hydrogen bonds       : angle       4.63534 /  3.15 (  858)
  Misc. bond           : bond        0.00006 /  0.00 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8469 (m-10)
REVERT: A  283 MET cc_start: 0.8824 (tpp) cc_final: 0.8549 (tpp)
REVERT: B  269 MET cc_start: 0.8846 (ttm) cc_final: 0.8592 (ttm)
REVERT: B  283 MET cc_start: 0.8750 (tpp) cc_final: 0.8095 (tpp)
REVERT: B  355 MET cc_start: 0.8370 (mmm) cc_final: 0.7998 (mtt)
REVERT: C  124 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8590 (m-10)
REVERT: D   82 MET cc_start: 0.8573 (mmm) cc_final: 0.8217 (tpt)
REVERT: E  236 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8636 (pt)
REVERT: E  325 MET cc_start: 0.7675 (mmt) cc_final: 0.7466 (mmt)
  outliers start: 30
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1069
  time to fit residues: 20.6404
Evaluate side-chains
  117 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue  119 MET
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 128 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 99 optimal weight:    9.9990
   chunk 32 optimal weight:    0.2980
   chunk 75 optimal weight:   20.0000
   chunk 178 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 148 optimal weight:   30.0000
   chunk 133 optimal weight:    7.9990
   overall best weight:    7.4588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.059336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.049470 restraints weight = 47251.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.051032 restraints weight = 25156.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.052105 restraints weight = 16228.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.052815 restraints weight = 11895.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.053322 restraints weight = 9571.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15250  Z= 0.218
  Angle     :  0.703   6.967  20705  Z= 0.334
  Chirality :  0.051   0.175   2305
  Planarity :  0.004   0.040   2630
  Dihedral  :  7.848  98.584   2130
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.67 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.35 (0.19), residues: 1830
  helix: -1.19 (0.21), residues: 595
  sheet: -1.68 (0.27), residues: 355
  loop : -1.68 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 183 
 TYR   0.021   0.001   TYR E 279 
 PHE   0.012   0.001   PHE C 200 
 TRP   0.007   0.001   TRP D 340 
 HIS   0.004   0.001   HIS D 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00526 /  0.22 (15245)
  covalent geometry    : angle       0.70256 /  0.33 (20705)
  hydrogen bonds       : bond        0.04773 /  3.32 (  316)
  hydrogen bonds       : angle       5.15671 /  3.51 (  858)
  Misc. bond           : bond        0.00015 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8374 (m-10)
REVERT: A  349 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.9001 (mp)
REVERT: B  283 MET cc_start: 0.8804 (tpp) cc_final: 0.8147 (tpp)
REVERT: B  355 MET cc_start: 0.8462 (mmm) cc_final: 0.8040 (mtt)
REVERT: C  124 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8666 (m-10)
REVERT: C  349 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8882 (mp)
REVERT: D   82 MET cc_start: 0.8728 (mmm) cc_final: 0.8362 (tpt)
REVERT: E  236 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8681 (pt)
  outliers start: 26
  outliers final: 19
  residues processed: 120
  average time/residue: 0.1120
  time to fit residues: 20.6597
Evaluate side-chains
  120 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 150 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 120 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 147 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   overall best weight:    5.4388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.060034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.050211 restraints weight = 46898.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.051792 restraints weight = 24767.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.052868 restraints weight = 15941.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.053596 restraints weight = 11687.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.054062 restraints weight = 9371.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  15250  Z= 0.165
  Angle     :  0.652   6.597  20705  Z= 0.307
  Chirality :  0.049   0.160   2305
  Planarity :  0.004   0.039   2630
  Dihedral  :  7.763  97.192   2130
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.67 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -2.24 (0.19), residues: 1830
  helix: -1.06 (0.21), residues: 595
  sheet: -1.65 (0.27), residues: 355
  loop : -1.63 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 210 
 TYR   0.014   0.001   TYR E 279 
 PHE   0.012   0.001   PHE E 375 
 TRP   0.008   0.001   TRP B 340 
 HIS   0.003   0.001   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 (15245)
  covalent geometry    : angle       0.65233 /  0.31 (20705)
  hydrogen bonds       : bond        0.04049 /  2.81 (  316)
  hydrogen bonds       : angle       4.89798 /  3.33 (  858)
  Misc. bond           : bond        0.00012 /  0.01 (    5)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8431 (m-10)
REVERT: A  283 MET cc_start: 0.8847 (tpp) cc_final: 0.8570 (tpp)
REVERT: B  283 MET cc_start: 0.8786 (tpp) cc_final: 0.8176 (tpp)
REVERT: B  355 MET cc_start: 0.8428 (mmm) cc_final: 0.7989 (mtt)
REVERT: C  124 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8594 (m-10)
REVERT: C  190 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8386 (ptp)
REVERT: C  349 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8918 (mp)
REVERT: D   82 MET cc_start: 0.8672 (mmm) cc_final: 0.8299 (tpt)
REVERT: E  236 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8629 (pt)
REVERT: E  283 MET cc_start: 0.8712 (tpp) cc_final: 0.8287 (ttm)
  outliers start: 26
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1110
  time to fit residues: 20.9523
Evaluate side-chains
  121 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain C residue  124 PHE
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  190 MET
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  351 THR
Chi-restraints excluded: chain D residue  124 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   49 GLN
Chi-restraints excluded: chain E residue  119 MET
Chi-restraints excluded: chain E residue  202 THR
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  303 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 137 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   chunk 143 optimal weight:    0.0010
   chunk 63 optimal weight:    0.0270
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 147 optimal weight:    7.9990
   overall best weight:    1.9848

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.062284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.052273 restraints weight = 45759.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.053961 restraints weight = 23481.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.055093 restraints weight = 14814.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.055857 restraints weight = 10687.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.056331 restraints weight = 8480.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  15250  Z= 0.090
  Angle     :  0.587   6.698  20705  Z= 0.270
  Chirality :  0.046   0.168   2305
  Planarity :  0.004   0.033   2630
  Dihedral  :  7.196  90.037   2130
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.98 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.28 %
    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 are not related in a simple way.
  whole: -1.93 (0.20), residues: 1830
  helix: -0.69 (0.22), residues: 595
  sheet: -1.51 (0.27), residues: 355
  loop : -1.52 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 210 
 TYR   0.012   0.001   TYR E 279 
 PHE   0.007   0.001   PHE D 375 
 TRP   0.007   0.001   TRP B 340 
 HIS   0.002   0.000   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00207 /  0.09 (15245)
  covalent geometry    : angle       0.58659 /  0.27 (20705)
  hydrogen bonds       : bond        0.02684 /  1.85 (  316)
  hydrogen bonds       : angle       4.33359 /  2.93 (  858)
  Misc. bond           : bond        0.00009 /  0.00 (    5)

===============================================================================
Job complete
usr+sys time: 1821.52 seconds
wall clock time: 32 minutes 29.70 seconds (1949.70 seconds total)