Starting phenix.real_space_refine
on Mon Nov 17 21:24:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6avb_7008/11_2025/6avb_7008.cif"
  }
  resolution = 3.9
  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=   0.000 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       6      5.49       5
     S      60      5.16       5
     C    5469      2.51       5
     N    1458      2.21       5
     O    1680      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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8673
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 2864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2864
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 19, 'TRANS': 347}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      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:
    A, B
  Time building chain proxies: 2.15, per 1000 atoms: 0.25
  Number of scatterers: 8673
  At special positions: 0
  Unit cell: (86.403, 89.526, 135.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       6     15.00
     O    1680      8.00
     N    1458      7.00
     C    5469      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 336.7 milliseconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2034

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 15 sheets defined
      41.7% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'C' and resid 55 through 61
      removed outlier: 4.033A  pdb=" N   LYS C  61 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 92
      removed outlier: 3.670A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TRP C  86 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR C  91 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 123
      removed outlier: 4.358A  pdb=" N   LYS C 118 " --> pdb=" O   ALA C 114 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET C 119 " --> pdb=" O   ASN C 115 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   THR C 120 " --> pdb=" O   ARG C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 146
      removed outlier: 4.066A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 194
      removed outlier: 3.551A  pdb=" N   TYR C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU C 189 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR C 194 " --> pdb=" O   MET C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 205 through 216
      removed outlier: 3.882A  pdb=" N   ASP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 232
    Processing helix  chain 'C' and resid 257 through 263
    Processing helix  chain 'C' and resid 273 through 284
      removed outlier: 3.672A  pdb=" N   THR C 278 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR C 279 " --> pdb=" O   HIS C 275 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS C 284 " --> pdb=" O   ASN C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 297
      removed outlier: 4.249A  pdb=" N   LEU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR C 294 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 320
      removed outlier: 3.732A  pdb=" N   THR C 318 " --> pdb=" O   GLN C 314 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA C 319 " --> pdb=" O   LYS C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 347
      removed outlier: 4.070A  pdb=" N   GLY C 343 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 356
      removed outlier: 3.671A  pdb=" N   TRP C 356 " --> pdb=" O   GLN C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 365
      removed outlier: 3.570A  pdb=" N   ALA C 365 " --> pdb=" O   GLU C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 371
      removed outlier: 4.008A  pdb=" N   ILE C 369 " --> pdb=" O   GLY C 366 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   HIS C 371 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 4.033A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 92
      removed outlier: 3.670A  pdb=" N   LYS A  84 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ILE A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TRP A  86 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR A  91 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 123
      removed outlier: 4.358A  pdb=" N   LYS A 118 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   THR A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 146
      removed outlier: 4.066A  pdb=" N   LEU A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 175
    Processing helix  chain 'A' and resid 181 through 194
      removed outlier: 3.552A  pdb=" N   TYR A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   THR A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.882A  pdb=" N   ASP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
    Processing helix  chain 'A' and resid 257 through 263
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 3.671A  pdb=" N   THR A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   TYR A 279 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 284 " --> pdb=" O   ASN A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 4.249A  pdb=" N   LEU A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 320
      removed outlier: 3.732A  pdb=" N   THR A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 347
      removed outlier: 4.069A  pdb=" N   GLY A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 356
      removed outlier: 3.672A  pdb=" N   TRP A 356 " --> pdb=" O   GLN A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 365
      removed outlier: 3.570A  pdb=" N   ALA A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 4.008A  pdb=" N   ILE A 369 " --> pdb=" O   GLY A 366 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   HIS A 371 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 61
      removed outlier: 4.032A  pdb=" N   LYS B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 92
      removed outlier: 3.670A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TRP B  86 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR B  91 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 123
      removed outlier: 4.358A  pdb=" N   LYS B 118 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   THR B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 146
      removed outlier: 4.066A  pdb=" N   LEU B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 175
    Processing helix  chain 'B' and resid 181 through 194
      removed outlier: 3.552A  pdb=" N   TYR B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   THR B 194 " --> pdb=" O   MET B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 205 through 216
      removed outlier: 3.882A  pdb=" N   ASP B 211 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 232
    Processing helix  chain 'B' and resid 257 through 263
    Processing helix  chain 'B' and resid 273 through 284
      removed outlier: 3.672A  pdb=" N   THR B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR B 279 " --> pdb=" O   HIS B 275 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS B 284 " --> pdb=" O   ASN B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 4.249A  pdb=" N   LEU B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR B 294 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA B 295 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 320
      removed outlier: 3.733A  pdb=" N   THR B 318 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B 319 " --> pdb=" O   LYS B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 347
      removed outlier: 4.070A  pdb=" N   GLY B 343 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 356
      removed outlier: 3.672A  pdb=" N   TRP B 356 " --> pdb=" O   GLN B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 365
      removed outlier: 3.570A  pdb=" N   ALA B 365 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
      removed outlier: 4.008A  pdb=" N   ILE B 369 " --> pdb=" O   GLY B 366 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   HIS B 371 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.749A  pdb=" N   LYS C  18 " --> pdb=" O   ASP C  11 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU C 104 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AA5, first strand: chain 'C' and resid 240 through 242
      removed outlier: 3.631A  pdb=" N   LEU C 242 " --> pdb=" O   GLN C 246 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN C 246 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.748A  pdb=" N   LYS A  18 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 104 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA8, first strand: chain 'A' and resid 150 through 151
    Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AB1, first strand: chain 'A' and resid 240 through 242
      removed outlier: 3.630A  pdb=" N   LEU A 242 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 32
      removed outlier: 3.748A  pdb=" N   LYS B  18 " --> pdb=" O   ASP B  11 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU B 104 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AB4, first strand: chain 'B' and resid 150 through 151
    Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 242
      removed outlier: 3.632A  pdb=" N   LEU B 242 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN B 246 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)

    264 hydrogen bonds defined for protein.
    657 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1452
        1.30 -     1.42: 2208
        1.42 -     1.55: 5086
        1.55 -     1.68: 11
        1.68 -     1.81: 108
  Bond restraints: 8865
  Sorted by residual:
  bond pdb=" CG  HIC C  73 "
       pdb=" CD2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.307  0.062 2.00e-02 2.50e+03 9.66e+00
  bond pdb=" CG  HIC A  73 "
       pdb=" CD2 HIC A  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.307  0.062 2.00e-02 2.50e+03 9.64e+00
  bond pdb=" CG  HIC B  73 "
       pdb=" CD2 HIC B  73 "
    ideal  model  delta    sigma   weight residual
    1.369  1.307  0.062 2.00e-02 2.50e+03 9.55e+00
  bond pdb=" C   HIC B  73 "
       pdb=" O   HIC B  73 "
    ideal  model  delta    sigma   weight residual
    1.231  1.169  0.062 2.00e-02 2.50e+03 9.54e+00
  bond pdb=" C   HIC C  73 "
       pdb=" O   HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.231  1.169  0.062 2.00e-02 2.50e+03 9.54e+00
  ... (remaining 8860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 11235
        1.94 -     3.88: 607
        3.88 -     5.82: 149
        5.82 -     7.76: 39
        7.76 -     9.70: 12
  Bond angle restraints: 12042
  Sorted by residual:
  angle pdb=" C   CYS C 217 "
        pdb=" N   TYR C 218 "
        pdb=" CA  TYR C 218 "
      ideal   model   delta    sigma   weight residual
     121.76  130.12   -8.36 2.19e+00 2.09e-01 1.46e+01
  angle pdb=" C   CYS A 217 "
        pdb=" N   TYR A 218 "
        pdb=" CA  TYR A 218 "
      ideal   model   delta    sigma   weight residual
     121.76  130.11   -8.35 2.19e+00 2.09e-01 1.45e+01
  angle pdb=" C   CYS B 217 "
        pdb=" N   TYR B 218 "
        pdb=" CA  TYR B 218 "
      ideal   model   delta    sigma   weight residual
     121.76  130.11   -8.35 2.19e+00 2.09e-01 1.45e+01
  angle pdb=" N   GLU A 224 "
        pdb=" CA  GLU A 224 "
        pdb=" C   GLU A 224 "
      ideal   model   delta    sigma   weight residual
     110.80  103.60    7.20 2.13e+00 2.20e-01 1.14e+01
  angle pdb=" N   GLU C 224 "
        pdb=" CA  GLU C 224 "
        pdb=" C   GLU C 224 "
      ideal   model   delta    sigma   weight residual
     110.80  103.65    7.15 2.13e+00 2.20e-01 1.13e+01
  ... (remaining 12037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4929
       16.21 -    32.42: 309
       32.42 -    48.63: 60
       48.63 -    64.84: 9
       64.84 -    81.04: 9
  Dihedral angle restraints: 5316
    sinusoidal: 2136
      harmonic: 3180
  Sorted by residual:
  dihedral pdb=" CA  ARG B 116 "
           pdb=" C   ARG B 116 "
           pdb=" N   GLU B 117 "
           pdb=" CA  GLU B 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.29   29.71     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  ARG C 116 "
           pdb=" C   ARG C 116 "
           pdb=" N   GLU C 117 "
           pdb=" CA  GLU C 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.33   29.67     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  ARG A 116 "
           pdb=" C   ARG A 116 "
           pdb=" N   GLU A 117 "
           pdb=" CA  GLU A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.33   29.67     0      5.00e+00 4.00e-02 3.52e+01
  ... (remaining 5313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 743
       0.044 -    0.088: 406
       0.088 -    0.132: 139
       0.132 -    0.176: 44
       0.176 -    0.220: 9
  Chirality restraints: 1341
  Sorted by residual:
  chirality pdb=" CA  SME A  47 "
            pdb=" N   SME A  47 "
            pdb=" C   SME A  47 "
            pdb=" CB  SME A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.18    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  SME B  47 "
            pdb=" N   SME B  47 "
            pdb=" C   SME B  47 "
            pdb=" CB  SME B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.18    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  SME C  47 "
            pdb=" N   SME C  47 "
            pdb=" C   SME C  47 "
            pdb=" CB  SME C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.19    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1338 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 101 "   -0.041 5.00e-02 4.00e+02   6.11e-02 5.97e+00
        pdb=" N   PRO A 102 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 101 "   -0.040 5.00e-02 4.00e+02   6.10e-02 5.94e+00
        pdb=" N   PRO B 102 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 101 "    0.040 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO C 102 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 102 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 102 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 286
        2.64 -     3.20: 9676
        3.20 -     3.77: 13887
        3.77 -     4.33: 19536
        4.33 -     4.90: 29691
  Nonbonded interactions: 73076
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 358 "
            pdb=" OE1 GLU B 361 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OG1 THR C 358 "
            pdb=" OE1 GLU C 361 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OG1 THR A 358 "
            pdb=" OE1 GLU A 361 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OG  SER C 155 "
            pdb=" OG1 THR C 303 "
     model   vdw
     2.073 3.040
  nonbonded pdb=" OG  SER A 155 "
            pdb=" OG1 THR A 303 "
     model   vdw
     2.073 3.040
  ... (remaining 73071 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
}

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=0.00 max=1.00 mean=0.94
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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.500
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
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      :  0.009   0.062   8865  Z= 0.406
  Angle     :  1.130   9.701  12042  Z= 0.573
  Chirality :  0.061   0.220   1341
  Planarity :  0.006   0.061   1536
  Dihedral  : 11.850  81.044   3282
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 27.42
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 12.92 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.00 (0.19), residues: 1068
  helix: -4.19 (0.14), residues: 330
  sheet: -1.74 (0.34), residues: 210
  loop : -3.41 (0.20), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 254 
 TYR   0.028   0.003   TYR A 218 
 PHE   0.031   0.003   PHE B 262 
 TRP   0.018   0.003   TRP C  86 
 HIS   0.009   0.003   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00886 ( 8865)
  covalent geometry    : angle       1.13049 (12042)
  hydrogen bonds       : bond        0.28072 (  264)
  hydrogen bonds       : angle      11.17500 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  118 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7954 (tptp)
REVERT: C  148 THR cc_start: 0.8234 (t) cc_final: 0.7978 (m)
REVERT: C  153 LEU cc_start: 0.8606 (tt) cc_final: 0.8351 (tp)
REVERT: C  159 VAL cc_start: 0.8680 (p) cc_final: 0.8405 (m)
REVERT: C  325 MET cc_start: 0.8267 (ttp) cc_final: 0.8021 (mtt)
REVERT: C  356 TRP cc_start: 0.7797 (m100) cc_final: 0.7326 (m100)
REVERT: A  118 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7901 (mtpt)
REVERT: A  159 VAL cc_start: 0.8816 (p) cc_final: 0.8511 (m)
REVERT: A  299 MET cc_start: 0.8180 (ptm) cc_final: 0.7878 (ppp)
REVERT: A  315 LYS cc_start: 0.8382 (tttm) cc_final: 0.8171 (tppt)
REVERT: A  356 TRP cc_start: 0.7819 (m100) cc_final: 0.7490 (m100)
REVERT: B   79 TRP cc_start: 0.8017 (m100) cc_final: 0.6527 (m-90)
REVERT: B  123 MET cc_start: 0.9098 (mmt) cc_final: 0.8869 (mmt)
REVERT: B  159 VAL cc_start: 0.8789 (p) cc_final: 0.8456 (m)
REVERT: B  299 MET cc_start: 0.8018 (ptm) cc_final: 0.7754 (ppp)
REVERT: B  325 MET cc_start: 0.8277 (ttp) cc_final: 0.8072 (mtt)
REVERT: B  354 GLN cc_start: 0.8559 (pm20) cc_final: 0.8074 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1082
  time to fit residues: 36.2645
Evaluate side-chains
  152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 128 ASN
C 280 ASN
C 314 GLN
A 128 ASN
A 280 ASN
A 314 GLN
B 128 ASN
B 280 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.091492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.081907 restraints weight = 24737.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.083930 restraints weight = 12511.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.085338 restraints weight = 7528.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.086260 restraints weight = 5107.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.086882 restraints weight = 3834.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8865  Z= 0.220
  Angle     :  0.946   9.264  12042  Z= 0.467
  Chirality :  0.053   0.196   1341
  Planarity :  0.006   0.056   1536
  Dihedral  :  9.294  57.577   1245
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  :  9.88 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.43 (0.22), residues: 1068
  helix: -2.38 (0.24), residues: 315
  sheet: -1.54 (0.34), residues: 210
  loop : -2.51 (0.22), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.023   0.002   TYR B 218 
 PHE   0.019   0.002   PHE C 352 
 TRP   0.036   0.003   TRP A  79 
 HIS   0.010   0.002   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 8865)
  covalent geometry    : angle       0.94602 (12042)
  hydrogen bonds       : bond        0.04823 (  264)
  hydrogen bonds       : angle       7.02817 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 219
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 ASN cc_start: 0.7670 (m-40) cc_final: 0.7393 (m-40)
REVERT: C  159 VAL cc_start: 0.8686 (p) cc_final: 0.8392 (m)
REVERT: C  216 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: C  305 MET cc_start: 0.7680 (mpp) cc_final: 0.7440 (mpp)
REVERT: C  356 TRP cc_start: 0.7747 (m100) cc_final: 0.7220 (m-90)
REVERT: A  148 THR cc_start: 0.8381 (t) cc_final: 0.8047 (m)
REVERT: A  159 VAL cc_start: 0.8783 (p) cc_final: 0.8490 (m)
REVERT: A  216 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8483 (pp)
REVERT: A  356 TRP cc_start: 0.7724 (m100) cc_final: 0.7315 (m100)
REVERT: B   88 HIS cc_start: 0.7393 (m-70) cc_final: 0.7163 (m-70)
REVERT: B  107 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: B  137 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8243 (mm110)
REVERT: B  159 VAL cc_start: 0.8595 (p) cc_final: 0.8228 (m)
REVERT: B  216 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8308 (pp)
REVERT: B  305 MET cc_start: 0.7530 (mpp) cc_final: 0.7321 (mpp)
REVERT: B  355 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7470 (mtp)
  outliers start: 45
  outliers final: 25
  residues processed: 243
  average time/residue: 0.0742
  time to fit residues: 26.8454
Evaluate side-chains
  188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  355 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 83 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 15 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
C 121 GLN
A 128 ASN
A 280 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.092427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.082851 restraints weight = 24384.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.084897 restraints weight = 12315.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.086293 restraints weight = 7401.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.087213 restraints weight = 5023.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.087878 restraints weight = 3769.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8865  Z= 0.164
  Angle     :  0.880  11.968  12042  Z= 0.423
  Chirality :  0.050   0.198   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  8.282  57.963   1245
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 14.77 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.90 (0.23), residues: 1068
  helix: -1.73 (0.26), residues: 339
  sheet: -1.29 (0.35), residues: 210
  loop : -2.30 (0.23), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 183 
 TYR   0.020   0.002   TYR B 218 
 PHE   0.013   0.002   PHE B 262 
 TRP   0.020   0.003   TRP B  79 
 HIS   0.003   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8865)
  covalent geometry    : angle       0.88010 (12042)
  hydrogen bonds       : bond        0.04141 (  264)
  hydrogen bonds       : angle       6.20804 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 203
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: C  159 VAL cc_start: 0.8608 (p) cc_final: 0.8318 (m)
REVERT: C  221 LEU cc_start: 0.8150 (tp) cc_final: 0.7881 (tp)
REVERT: C  283 MET cc_start: 0.8410 (mmp) cc_final: 0.7933 (mmm)
REVERT: C  356 TRP cc_start: 0.7646 (m100) cc_final: 0.7149 (m100)
REVERT: A  148 THR cc_start: 0.8423 (t) cc_final: 0.8103 (m)
REVERT: A  159 VAL cc_start: 0.8742 (p) cc_final: 0.8473 (m)
REVERT: A  216 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8486 (pp)
REVERT: A  283 MET cc_start: 0.8385 (mmp) cc_final: 0.8020 (mmm)
REVERT: A  356 TRP cc_start: 0.7694 (m100) cc_final: 0.7286 (m100)
REVERT: B    8 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7428 (pp)
REVERT: B  137 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8174 (mm-40)
REVERT: B  159 VAL cc_start: 0.8555 (p) cc_final: 0.8202 (m)
REVERT: B  315 LYS cc_start: 0.8313 (tppt) cc_final: 0.7573 (ttmm)
REVERT: B  349 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8118 (pp)
  outliers start: 47
  outliers final: 29
  residues processed: 228
  average time/residue: 0.0643
  time to fit residues: 22.8141
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  179 ASP
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS
B  87 HIS
B 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.090837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.081159 restraints weight = 24818.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.083182 restraints weight = 12504.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.084554 restraints weight = 7525.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.085451 restraints weight = 5132.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.086104 restraints weight = 3879.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8865  Z= 0.203
  Angle     :  0.893  11.804  12042  Z= 0.431
  Chirality :  0.051   0.198   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  8.384  59.468   1245
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 16.29 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.61 (0.24), residues: 1068
  helix: -1.51 (0.27), residues: 330
  sheet: -1.32 (0.35), residues: 210
  loop : -2.00 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 290 
 TYR   0.024   0.002   TYR C 166 
 PHE   0.017   0.002   PHE A 200 
 TRP   0.020   0.002   TRP B  79 
 HIS   0.005   0.002   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 8865)
  covalent geometry    : angle       0.89328 (12042)
  hydrogen bonds       : bond        0.04029 (  264)
  hydrogen bonds       : angle       6.00691 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 170
  time to evaluate  : 0.317 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8658 (p) cc_final: 0.8362 (m)
REVERT: C  283 MET cc_start: 0.8421 (mmp) cc_final: 0.8022 (mmm)
REVERT: C  314 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7506 (mp10)
REVERT: C  356 TRP cc_start: 0.7622 (m100) cc_final: 0.7305 (m100)
REVERT: A  159 VAL cc_start: 0.8774 (p) cc_final: 0.8506 (m)
REVERT: A  171 LEU cc_start: 0.9346 (mp) cc_final: 0.9080 (mp)
REVERT: A  216 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8464 (pp)
REVERT: A  221 LEU cc_start: 0.7988 (tp) cc_final: 0.7651 (tp)
REVERT: A  283 MET cc_start: 0.8373 (mmp) cc_final: 0.8114 (mmm)
REVERT: B  137 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7986 (mm-40)
REVERT: B  140 LEU cc_start: 0.8675 (mp) cc_final: 0.8463 (mp)
REVERT: B  159 VAL cc_start: 0.8579 (p) cc_final: 0.8229 (m)
REVERT: B  315 LYS cc_start: 0.8352 (tppt) cc_final: 0.7594 (ttmm)
REVERT: B  354 GLN cc_start: 0.7881 (pm20) cc_final: 0.7628 (pm20)
  outliers start: 56
  outliers final: 32
  residues processed: 207
  average time/residue: 0.0652
  time to fit residues: 20.9562
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  223 PHE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 24 optimal weight:    0.1980
   chunk 20 optimal weight:   10.0000
   overall best weight:    4.8388

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** 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 = 0.3277 r_free = 0.3277 target = 0.090767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.081198 restraints weight = 24438.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083214 restraints weight = 12333.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.084612 restraints weight = 7394.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.085527 restraints weight = 5023.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.086084 restraints weight = 3779.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8865  Z= 0.198
  Angle     :  0.893   8.963  12042  Z= 0.430
  Chirality :  0.051   0.203   1341
  Planarity :  0.005   0.051   1536
  Dihedral  :  8.368  59.395   1245
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 18.46 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.47 (0.24), residues: 1068
  helix: -1.31 (0.27), residues: 330
  sheet: -1.27 (0.35), residues: 210
  loop : -1.97 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 290 
 TYR   0.023   0.002   TYR B 218 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.021   0.002   TRP B  79 
 HIS   0.005   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8865)
  covalent geometry    : angle       0.89254 (12042)
  hydrogen bonds       : bond        0.03843 (  264)
  hydrogen bonds       : angle       5.98048 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 174
  time to evaluate  : 0.352 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8603 (p) cc_final: 0.8334 (m)
REVERT: C  221 LEU cc_start: 0.8061 (tp) cc_final: 0.7782 (tp)
REVERT: C  283 MET cc_start: 0.8495 (mmp) cc_final: 0.8111 (mmm)
REVERT: C  314 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7506 (mp10)
REVERT: C  356 TRP cc_start: 0.7590 (m100) cc_final: 0.7299 (m100)
REVERT: A  159 VAL cc_start: 0.8731 (p) cc_final: 0.8467 (m)
REVERT: A  171 LEU cc_start: 0.9337 (mp) cc_final: 0.9109 (mp)
REVERT: A  216 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8520 (pp)
REVERT: A  221 LEU cc_start: 0.7905 (tp) cc_final: 0.7689 (tp)
REVERT: A  283 MET cc_start: 0.8322 (mmp) cc_final: 0.8092 (mmm)
REVERT: B  137 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7815 (mm-40)
REVERT: B  159 VAL cc_start: 0.8593 (p) cc_final: 0.8274 (m)
REVERT: B  315 LYS cc_start: 0.8402 (tppt) cc_final: 0.7694 (ttmt)
  outliers start: 49
  outliers final: 35
  residues processed: 206
  average time/residue: 0.0688
  time to fit residues: 21.6976
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  346 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.091493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.081766 restraints weight = 24268.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.083835 restraints weight = 12433.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.085222 restraints weight = 7515.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.086191 restraints weight = 5145.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.086847 restraints weight = 3848.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8865  Z= 0.184
  Angle     :  0.881  14.581  12042  Z= 0.425
  Chirality :  0.050   0.193   1341
  Planarity :  0.005   0.051   1536
  Dihedral  :  8.254  59.888   1245
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.87 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.36 (0.24), residues: 1068
  helix: -1.10 (0.28), residues: 330
  sheet: -1.22 (0.35), residues: 210
  loop : -1.99 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 254 
 TYR   0.026   0.002   TYR C 166 
 PHE   0.014   0.002   PHE C 200 
 TRP   0.022   0.002   TRP B  79 
 HIS   0.005   0.001   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 8865)
  covalent geometry    : angle       0.88095 (12042)
  hydrogen bonds       : bond        0.03694 (  264)
  hydrogen bonds       : angle       5.86709 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 182
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C  133 TYR cc_start: 0.7797 (t80) cc_final: 0.7269 (t80)
REVERT: C  159 VAL cc_start: 0.8590 (p) cc_final: 0.8333 (m)
REVERT: C  221 LEU cc_start: 0.8099 (tp) cc_final: 0.7850 (tp)
REVERT: C  314 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7530 (mp10)
REVERT: C  355 MET cc_start: 0.7846 (mtp) cc_final: 0.7541 (mpp)
REVERT: C  356 TRP cc_start: 0.7504 (m100) cc_final: 0.7201 (m100)
REVERT: A  159 VAL cc_start: 0.8717 (p) cc_final: 0.8457 (m)
REVERT: A  171 LEU cc_start: 0.9338 (mp) cc_final: 0.9118 (mp)
REVERT: A  216 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8517 (pp)
REVERT: A  283 MET cc_start: 0.8365 (mmp) cc_final: 0.8100 (mmm)
REVERT: B  101 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.5317 (t-90)
REVERT: B  159 VAL cc_start: 0.8585 (p) cc_final: 0.8262 (m)
REVERT: B  315 LYS cc_start: 0.8397 (tppt) cc_final: 0.7666 (ttmt)
  outliers start: 47
  outliers final: 34
  residues processed: 214
  average time/residue: 0.0722
  time to fit residues: 23.3492
Evaluate side-chains
  186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 HIS
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 40 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 107 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN
B 371 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.091106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.081317 restraints weight = 24645.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.083407 restraints weight = 12576.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.084824 restraints weight = 7557.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.085767 restraints weight = 5147.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.086449 restraints weight = 3875.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8865  Z= 0.199
  Angle     :  0.900  10.568  12042  Z= 0.434
  Chirality :  0.050   0.197   1341
  Planarity :  0.005   0.053   1536
  Dihedral  :  8.232  59.044   1245
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.01 %
    Favored  : 86.99 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 21.28 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.24), residues: 1068
  helix: -1.01 (0.28), residues: 330
  sheet: -1.29 (0.35), residues: 213
  loop : -2.00 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 254 
 TYR   0.023   0.002   TYR C 166 
 PHE   0.013   0.002   PHE A 127 
 TRP   0.043   0.003   TRP A  79 
 HIS   0.005   0.001   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8865)
  covalent geometry    : angle       0.90028 (12042)
  hydrogen bonds       : bond        0.03711 (  264)
  hydrogen bonds       : angle       5.88422 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 166
  time to evaluate  : 0.372 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8571 (p) cc_final: 0.8315 (m)
REVERT: C  221 LEU cc_start: 0.8077 (tp) cc_final: 0.7831 (tp)
REVERT: C  283 MET cc_start: 0.8545 (mmp) cc_final: 0.8127 (mmm)
REVERT: C  314 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7601 (mp10)
REVERT: C  356 TRP cc_start: 0.7498 (m100) cc_final: 0.7270 (m100)
REVERT: A  159 VAL cc_start: 0.8739 (p) cc_final: 0.8477 (m)
REVERT: A  171 LEU cc_start: 0.9312 (mp) cc_final: 0.9087 (mp)
REVERT: A  216 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8522 (pp)
REVERT: A  283 MET cc_start: 0.8387 (mmp) cc_final: 0.8145 (mmm)
REVERT: B  101 HIS cc_start: 0.5692 (OUTLIER) cc_final: 0.5290 (t-90)
REVERT: B  159 VAL cc_start: 0.8666 (p) cc_final: 0.8362 (m)
REVERT: B  315 LYS cc_start: 0.8444 (tppt) cc_final: 0.7731 (ttmt)
  outliers start: 47
  outliers final: 34
  residues processed: 197
  average time/residue: 0.0670
  time to fit residues: 20.4674
Evaluate side-chains
  179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 HIS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 6 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 371 HIS
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.090176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.080416 restraints weight = 24487.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082446 restraints weight = 12712.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.083756 restraints weight = 7752.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084767 restraints weight = 5405.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.085432 restraints weight = 4042.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8865  Z= 0.235
  Angle     :  0.931   9.462  12042  Z= 0.454
  Chirality :  0.052   0.209   1341
  Planarity :  0.006   0.054   1536
  Dihedral  :  8.329  56.317   1245
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.08 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 21.82 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.44 (0.24), residues: 1068
  helix: -1.02 (0.28), residues: 327
  sheet: -1.33 (0.35), residues: 213
  loop : -2.11 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 290 
 TYR   0.041   0.002   TYR A 166 
 PHE   0.016   0.002   PHE C 200 
 TRP   0.030   0.003   TRP A  79 
 HIS   0.006   0.002   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 8865)
  covalent geometry    : angle       0.93104 (12042)
  hydrogen bonds       : bond        0.03933 (  264)
  hydrogen bonds       : angle       6.00465 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 150
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  159 VAL cc_start: 0.8608 (p) cc_final: 0.8337 (m)
REVERT: C  221 LEU cc_start: 0.8142 (tp) cc_final: 0.7900 (tp)
REVERT: C  283 MET cc_start: 0.8585 (mmp) cc_final: 0.8306 (mmm)
REVERT: C  314 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7632 (mp10)
REVERT: A  159 VAL cc_start: 0.8768 (p) cc_final: 0.8504 (m)
REVERT: A  171 LEU cc_start: 0.9373 (mp) cc_final: 0.8996 (mp)
REVERT: A  216 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8523 (pp)
REVERT: A  314 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7792 (mm110)
REVERT: B  101 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.5506 (t-90)
REVERT: B  159 VAL cc_start: 0.8660 (p) cc_final: 0.8349 (m)
REVERT: B  315 LYS cc_start: 0.8479 (tppt) cc_final: 0.7772 (ttmt)
  outliers start: 52
  outliers final: 39
  residues processed: 185
  average time/residue: 0.0682
  time to fit residues: 19.5066
Evaluate side-chains
  183 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  314 GLN
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 HIS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  330 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 ASN ** 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 = 0.3272 r_free = 0.3272 target = 0.090482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.080772 restraints weight = 24509.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.082814 restraints weight = 12686.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.084210 restraints weight = 7711.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.085189 restraints weight = 5280.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.085842 restraints weight = 3950.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.5443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8865  Z= 0.214
  Angle     :  0.917   9.276  12042  Z= 0.447
  Chirality :  0.051   0.207   1341
  Planarity :  0.005   0.055   1536
  Dihedral  :  8.276  54.361   1245
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.99 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.37 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.24), residues: 1068
  helix: -1.06 (0.27), residues: 330
  sheet: -1.23 (0.35), residues: 210
  loop : -2.19 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 290 
 TYR   0.036   0.002   TYR A 166 
 PHE   0.015   0.002   PHE C 200 
 TRP   0.030   0.003   TRP B  79 
 HIS   0.012   0.002   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8865)
  covalent geometry    : angle       0.91701 (12042)
  hydrogen bonds       : bond        0.03809 (  264)
  hydrogen bonds       : angle       5.98908 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 152
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: C  133 TYR cc_start: 0.7892 (t80) cc_final: 0.7597 (t80)
REVERT: C  159 VAL cc_start: 0.8605 (p) cc_final: 0.8314 (m)
REVERT: C  221 LEU cc_start: 0.8140 (tp) cc_final: 0.7903 (tp)
REVERT: C  283 MET cc_start: 0.8589 (mmp) cc_final: 0.8314 (mmm)
REVERT: C  314 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7592 (mp10)
REVERT: C  355 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7585 (mpp)
REVERT: C  356 TRP cc_start: 0.7718 (m100) cc_final: 0.7391 (m100)
REVERT: A  159 VAL cc_start: 0.8755 (p) cc_final: 0.8487 (m)
REVERT: A  171 LEU cc_start: 0.9347 (mp) cc_final: 0.9097 (mp)
REVERT: A  216 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: A  247 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7996 (m)
REVERT: B  101 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.5457 (t-90)
REVERT: B  137 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7804 (mp10)
REVERT: B  159 VAL cc_start: 0.8626 (p) cc_final: 0.8310 (m)
REVERT: B  315 LYS cc_start: 0.8455 (tppt) cc_final: 0.7736 (ttmt)
  outliers start: 48
  outliers final: 36
  residues processed: 182
  average time/residue: 0.0645
  time to fit residues: 18.3236
Evaluate side-chains
  181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  355 MET
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 HIS
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  179 ASP
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 58 optimal weight:   30.0000
   overall best weight:    2.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.093364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.083801 restraints weight = 24352.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.085871 restraints weight = 12389.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.087278 restraints weight = 7480.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088253 restraints weight = 5089.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.088854 restraints weight = 3790.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.5749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8865  Z= 0.155
  Angle     :  0.900  12.774  12042  Z= 0.431
  Chirality :  0.050   0.213   1341
  Planarity :  0.005   0.056   1536
  Dihedral  :  7.868  59.102   1245
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.67 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.00 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.24), residues: 1068
  helix: -0.97 (0.28), residues: 330
  sheet: -1.10 (0.36), residues: 201
  loop : -2.16 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 290 
 TYR   0.036   0.002   TYR A 166 
 PHE   0.018   0.001   PHE B 223 
 TRP   0.027   0.004   TRP B  79 
 HIS   0.011   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8865)
  covalent geometry    : angle       0.89968 (12042)
  hydrogen bonds       : bond        0.03440 (  264)
  hydrogen bonds       : angle       5.81219 (  657)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: C  133 TYR cc_start: 0.7743 (t80) cc_final: 0.7469 (t80)
REVERT: C  159 VAL cc_start: 0.8512 (p) cc_final: 0.8244 (m)
REVERT: C  356 TRP cc_start: 0.7487 (m100) cc_final: 0.7049 (m100)
REVERT: A  159 VAL cc_start: 0.8750 (p) cc_final: 0.8475 (m)
REVERT: A  216 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8551 (pp)
REVERT: B  159 VAL cc_start: 0.8563 (p) cc_final: 0.8289 (m)
REVERT: B  249 THR cc_start: 0.8586 (m) cc_final: 0.8319 (t)
REVERT: B  315 LYS cc_start: 0.8215 (tppt) cc_final: 0.7411 (ttmm)
  outliers start: 36
  outliers final: 29
  residues processed: 191
  average time/residue: 0.0750
  time to fit residues: 21.4311
Evaluate side-chains
  184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  246 GLN
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 4 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   chunk 67 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0070
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.7804

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.095053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.085454 restraints weight = 23988.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.087558 restraints weight = 12218.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.089012 restraints weight = 7380.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089984 restraints weight = 4984.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.090668 restraints weight = 3699.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.6019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8865  Z= 0.148
  Angle     :  0.903  12.097  12042  Z= 0.430
  Chirality :  0.050   0.205   1341
  Planarity :  0.005   0.056   1536
  Dihedral  :  7.597  58.172   1245
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.77 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.97 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.25), residues: 1068
  helix: -0.72 (0.29), residues: 309
  sheet: -1.03 (0.36), residues: 201
  loop : -1.92 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 290 
 TYR   0.036   0.002   TYR A 166 
 PHE   0.020   0.001   PHE B 223 
 TRP   0.037   0.004   TRP B  79 
 HIS   0.010   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8865)
  covalent geometry    : angle       0.90337 (12042)
  hydrogen bonds       : bond        0.03340 (  264)
  hydrogen bonds       : angle       5.71029 (  657)

===============================================================================
Job complete
usr+sys time: 1263.69 seconds
wall clock time: 22 minutes 47.40 seconds (1367.40 seconds total)