Starting phenix.real_space_refine
on Thu Mar 13 05:44:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6avb_7008/03_2025/6avb_7008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6avb_7008/03_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_7008/03_2025/6avb_7008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6avb_7008/03_2025/6avb_7008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6avb_7008/03_2025/6avb_7008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6avb_7008/03_2025/6avb_7008.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8673
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      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: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.17, per 1000 atoms: 0.60
  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: 2.57
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.99
  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: 2.28

  Time building geometry restraints manager: 2.88 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             0.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.530
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.120
-------------------------------------------------------------------------------
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= 0.580
  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 : 27.43
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.003   TRP C  86 
 HIS   0.009   0.003   HIS A  87 
 PHE   0.031   0.003   PHE B 262 
 TYR   0.028   0.003   TYR A 218 
 ARG   0.009   0.001   ARG C 254 

*********************** 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  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: C  118 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7923 (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: 0.8404 (m)
REVERT: C  325 MET cc_start: 0.8267 (ttp) cc_final: 0.8023 (mtt)
REVERT: C  356 TRP cc_start: 0.7797 (m100) cc_final: 0.7330 (m100)
REVERT: A  118 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7903 (mtpt)
REVERT: A  159 VAL cc_start: 0.8816 (p) cc_final: 0.8510 (m)
REVERT: A  299 MET cc_start: 0.8180 (ptm) cc_final: 0.7877 (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: 0.7493 (m100)
REVERT: B   79 TRP cc_start: 0.8017 (m100) cc_final: 0.6528 (m-90)
REVERT: B  123 MET cc_start: 0.9098 (mmt) cc_final: 0.8870 (mmt)
REVERT: B  159 VAL cc_start: 0.8789 (p) cc_final: 0.8457 (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: 0.2430
  time to fit residues: 80.9815
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  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.092097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082504 restraints weight = 24210.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084557 restraints weight = 12122.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.085918 restraints weight = 7223.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8865  Z= 0.286
  Angle     :  0.943   9.162  12042  Z= 0.463
  Chirality :  0.053   0.195   1341
  Planarity :  0.006   0.054   1536
  Dihedral  :  9.305  58.524   1245
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.96 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  :  9.88 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.22), residues: 1068
  helix: -2.45 (0.24), residues: 324
  sheet: -1.49 (0.34), residues: 210
  loop : -2.50 (0.22), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A  79 
 HIS   0.009   0.002   HIS A  88 
 PHE   0.019   0.002   PHE C 352 
 TYR   0.021   0.002   TYR B 218 
 ARG   0.005   0.001   ARG A 183 

*********************** 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
  261 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 220
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8415 (tpt) cc_final: 0.8104 (tpt)
REVERT: C  159 VAL cc_start: 0.8665 (p) cc_final: 0.8366 (m)
REVERT: C  353 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7290 (tt0)
REVERT: C  356 TRP cc_start: 0.7706 (m100) cc_final: 0.7284 (m-90)
REVERT: A  148 THR cc_start: 0.8382 (t) cc_final: 0.8043 (m)
REVERT: A  159 VAL cc_start: 0.8790 (p) cc_final: 0.8498 (m)
REVERT: A  183 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8658 (mtm110)
REVERT: A  216 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  356 TRP cc_start: 0.7688 (m100) cc_final: 0.7316 (m100)
REVERT: B  107 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: B  133 TYR cc_start: 0.7871 (t80) cc_final: 0.7621 (t80)
REVERT: B  159 VAL cc_start: 0.8589 (p) cc_final: 0.8215 (m)
REVERT: B  216 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8256 (pp)
REVERT: B  315 LYS cc_start: 0.8308 (tppt) cc_final: 0.7713 (ttmt)
REVERT: B  355 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7103 (mpp)
  outliers start: 41
  outliers final: 25
  residues processed: 240
  average time/residue: 0.1651
  time to fit residues: 57.5796
Evaluate side-chains
  190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  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  179 ASP
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  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 2 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 121 GLN
A 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.090655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.081148 restraints weight = 25054.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.083148 restraints weight = 12499.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.084504 restraints weight = 7472.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8865  Z= 0.328
  Angle     :  0.925  11.806  12042  Z= 0.451
  Chirality :  0.052   0.209   1341
  Planarity :  0.005   0.055   1536
  Dihedral  :  8.738  59.262   1245
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 14.88 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.23), residues: 1068
  helix: -1.73 (0.26), residues: 339
  sheet: -1.38 (0.35), residues: 210
  loop : -2.40 (0.23), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  79 
 HIS   0.004   0.002   HIS A 173 
 PHE   0.016   0.002   PHE B 262 
 TYR   0.023   0.002   TYR B 218 
 ARG   0.005   0.001   ARG A 290 

*********************** 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
  235 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 0.895 
Fit side-chains
REVERT: C   82 MET cc_start: 0.8508 (tpt) cc_final: 0.8194 (tpt)
REVERT: C  159 VAL cc_start: 0.8694 (p) cc_final: 0.8376 (m)
REVERT: C  349 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7865 (pp)
REVERT: C  356 TRP cc_start: 0.7766 (m100) cc_final: 0.7360 (m100)
REVERT: A  148 THR cc_start: 0.8467 (t) cc_final: 0.8146 (m)
REVERT: A  159 VAL cc_start: 0.8811 (p) cc_final: 0.8501 (m)
REVERT: A  216 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8515 (pp)
REVERT: A  283 MET cc_start: 0.8347 (mmp) cc_final: 0.8022 (mmm)
REVERT: A  356 TRP cc_start: 0.7747 (m100) cc_final: 0.7299 (m100)
REVERT: B   12 ASN cc_start: 0.7758 (m-40) cc_final: 0.7527 (m-40)
REVERT: B  159 VAL cc_start: 0.8632 (p) cc_final: 0.8272 (m)
REVERT: B  315 LYS cc_start: 0.8425 (tppt) cc_final: 0.7699 (ttmm)
REVERT: B  349 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (pp)
REVERT: B  355 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7633 (mtp)
  outliers start: 49
  outliers final: 30
  residues processed: 215
  average time/residue: 0.1611
  time to fit residues: 51.6815
Evaluate side-chains
  179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
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  247 VAL
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 C residue  349 LEU
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  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  247 VAL
Chi-restraints excluded: chain A residue  300 SER
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   85 ILE
Chi-restraints excluded: chain B residue  118 LYS
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  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  355 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 72 optimal weight:   30.0000
   chunk 104 optimal weight:    7.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
C  12 ASN
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.092738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083231 restraints weight = 24553.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.085256 restraints weight = 12296.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.086646 restraints weight = 7345.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8865  Z= 0.233
  Angle     :  0.867  12.195  12042  Z= 0.414
  Chirality :  0.050   0.188   1341
  Planarity :  0.005   0.050   1536
  Dihedral  :  8.105  59.781   1245
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 16.72 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.24), residues: 1068
  helix: -1.31 (0.27), residues: 339
  sheet: -1.32 (0.35), residues: 210
  loop : -2.16 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  79 
 HIS   0.004   0.001   HIS B  88 
 PHE   0.015   0.002   PHE A 200 
 TYR   0.030   0.002   TYR A 166 
 ARG   0.004   0.001   ARG B 290 

*********************** 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
  231 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 184
  time to evaluate  : 0.986 
Fit side-chains
REVERT: C   82 MET cc_start: 0.8564 (tpt) cc_final: 0.8319 (tpt)
REVERT: C  133 TYR cc_start: 0.7752 (t80) cc_final: 0.7462 (t80)
REVERT: C  159 VAL cc_start: 0.8630 (p) cc_final: 0.8349 (m)
REVERT: C  221 LEU cc_start: 0.8109 (tp) cc_final: 0.7822 (tp)
REVERT: C  283 MET cc_start: 0.8384 (mmp) cc_final: 0.7923 (mmm)
REVERT: C  314 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7486 (mp10)
REVERT: C  356 TRP cc_start: 0.7666 (m100) cc_final: 0.7068 (m100)
REVERT: A  107 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: A  121 GLN cc_start: 0.8543 (tp40) cc_final: 0.8321 (tm-30)
REVERT: A  137 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7782 (mp10)
REVERT: A  159 VAL cc_start: 0.8749 (p) cc_final: 0.8468 (m)
REVERT: A  216 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8352 (pp)
REVERT: A  221 LEU cc_start: 0.7950 (tp) cc_final: 0.7711 (tp)
REVERT: A  283 MET cc_start: 0.8412 (mmp) cc_final: 0.8042 (mmm)
REVERT: B  159 VAL cc_start: 0.8558 (p) cc_final: 0.8245 (m)
REVERT: B  315 LYS cc_start: 0.8291 (tppt) cc_final: 0.7600 (ttmt)
REVERT: B  330 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (pt)
REVERT: B  349 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8126 (pp)
  outliers start: 47
  outliers final: 25
  residues processed: 211
  average time/residue: 0.1677
  time to fit residues: 53.3647
Evaluate side-chains
  197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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   77 THR
Chi-restraints excluded: chain C residue   85 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 A residue    8 LEU
Chi-restraints excluded: chain A residue   43 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  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   77 THR
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  247 VAL
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  330 ILE
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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  40 HIS
B  87 HIS
B 128 ASN
B 371 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.089588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.079906 restraints weight = 24521.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.081897 restraints weight = 12592.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083262 restraints weight = 7627.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8865  Z= 0.371
  Angle     :  0.927   9.336  12042  Z= 0.450
  Chirality :  0.052   0.212   1341
  Planarity :  0.006   0.053   1536
  Dihedral  :  8.510  59.944   1245
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.27 %
    Favored  : 87.73 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 18.78 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.24), residues: 1068
  helix: -1.35 (0.27), residues: 330
  sheet: -1.45 (0.35), residues: 213
  loop : -2.08 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  79 
 HIS   0.005   0.002   HIS B  88 
 PHE   0.019   0.002   PHE A 352 
 TYR   0.025   0.002   TYR B 218 
 ARG   0.004   0.001   ARG A 290 

*********************** 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
  222 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 169
  time to evaluate  : 0.975 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8695 (p) cc_final: 0.8383 (m)
REVERT: C  221 LEU cc_start: 0.8104 (tp) cc_final: 0.7812 (tp)
REVERT: C  283 MET cc_start: 0.8542 (mmp) cc_final: 0.8145 (mmm)
REVERT: C  314 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7616 (mp10)
REVERT: C  356 TRP cc_start: 0.7719 (m100) cc_final: 0.7512 (m100)
REVERT: A  159 VAL cc_start: 0.8797 (p) cc_final: 0.8491 (m)
REVERT: A  171 LEU cc_start: 0.9352 (mp) cc_final: 0.9085 (mp)
REVERT: A  216 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8480 (pp)
REVERT: A  221 LEU cc_start: 0.7925 (tp) cc_final: 0.7634 (tp)
REVERT: A  283 MET cc_start: 0.8360 (mmp) cc_final: 0.8143 (mmm)
REVERT: A  349 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8095 (pp)
REVERT: B  159 VAL cc_start: 0.8650 (p) cc_final: 0.8313 (m)
REVERT: B  315 LYS cc_start: 0.8478 (tppt) cc_final: 0.7689 (ttmm)
REVERT: B  349 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8192 (pp)
REVERT: B  355 MET cc_start: 0.7705 (mtp) cc_final: 0.7472 (mpp)
  outliers start: 53
  outliers final: 34
  residues processed: 204
  average time/residue: 0.1644
  time to fit residues: 49.8932
Evaluate side-chains
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  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  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  212 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  349 LEU
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  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  260 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   chunk 66 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 104 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 73 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    4.9788

-------------------------------------------------------------------------------
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 = 0.090615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.080907 restraints weight = 24110.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.082928 restraints weight = 12366.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.084334 restraints weight = 7510.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.4996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8865  Z= 0.297
  Angle     :  0.886   8.144  12042  Z= 0.429
  Chirality :  0.051   0.201   1341
  Planarity :  0.005   0.051   1536
  Dihedral  :  8.327  59.848   1245
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 19.76 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.24), residues: 1068
  helix: -1.12 (0.28), residues: 330
  sheet: -1.31 (0.35), residues: 210
  loop : -2.09 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  79 
 HIS   0.006   0.001   HIS B  88 
 PHE   0.016   0.002   PHE A 200 
 TYR   0.023   0.002   TYR B 218 
 ARG   0.003   0.001   ARG A 290 

*********************** 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
  219 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 167
  time to evaluate  : 1.083 
Fit side-chains
REVERT: C   82 MET cc_start: 0.8627 (tpt) cc_final: 0.8148 (tpt)
REVERT: C  159 VAL cc_start: 0.8644 (p) cc_final: 0.8369 (m)
REVERT: C  221 LEU cc_start: 0.8066 (tp) cc_final: 0.7792 (tp)
REVERT: C  314 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7618 (mp10)
REVERT: C  356 TRP cc_start: 0.7579 (m100) cc_final: 0.7334 (m100)
REVERT: A  104 LEU cc_start: 0.8983 (tt) cc_final: 0.8737 (tp)
REVERT: A  159 VAL cc_start: 0.8759 (p) cc_final: 0.8483 (m)
REVERT: A  171 LEU cc_start: 0.9343 (mp) cc_final: 0.9096 (mp)
REVERT: A  216 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8399 (pp)
REVERT: A  221 LEU cc_start: 0.7893 (tp) cc_final: 0.7627 (tp)
REVERT: A  283 MET cc_start: 0.8348 (mmp) cc_final: 0.8083 (mmm)
REVERT: A  349 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8155 (pp)
REVERT: B  159 VAL cc_start: 0.8620 (p) cc_final: 0.8297 (m)
REVERT: B  315 LYS cc_start: 0.8461 (tppt) cc_final: 0.7759 (ttmt)
REVERT: B  349 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8118 (pp)
  outliers start: 52
  outliers final: 36
  residues processed: 201
  average time/residue: 0.1765
  time to fit residues: 54.3241
Evaluate side-chains
  188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
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  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  212 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   43 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  139 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  179 ASP
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.091670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.081905 restraints weight = 24233.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.083973 restraints weight = 12347.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.085381 restraints weight = 7469.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8865  Z= 0.261
  Angle     :  0.874  10.480  12042  Z= 0.419
  Chirality :  0.049   0.199   1341
  Planarity :  0.005   0.050   1536
  Dihedral  :  8.104  58.805   1245
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 21.39 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.24), residues: 1068
  helix: -1.12 (0.27), residues: 348
  sheet: -1.21 (0.35), residues: 213
  loop : -2.12 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  79 
 HIS   0.005   0.001   HIS B  88 
 PHE   0.012   0.002   PHE A 127 
 TYR   0.024   0.002   TYR C 166 
 ARG   0.006   0.001   ARG B 254 

*********************** 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
  229 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 178
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8612 (tpt) cc_final: 0.8147 (tpt)
REVERT: C  121 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8149 (tm-30)
REVERT: C  159 VAL cc_start: 0.8607 (p) cc_final: 0.8348 (m)
REVERT: C  221 LEU cc_start: 0.8120 (tp) cc_final: 0.7881 (tp)
REVERT: C  283 MET cc_start: 0.8501 (mmp) cc_final: 0.8081 (mmm)
REVERT: C  305 MET cc_start: 0.7769 (mpp) cc_final: 0.7542 (mpt)
REVERT: C  314 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (mm110)
REVERT: C  356 TRP cc_start: 0.7432 (m100) cc_final: 0.7139 (m100)
REVERT: A  104 LEU cc_start: 0.8989 (tt) cc_final: 0.8704 (tp)
REVERT: A  121 GLN cc_start: 0.8645 (tp40) cc_final: 0.8406 (tm-30)
REVERT: A  159 VAL cc_start: 0.8744 (p) cc_final: 0.8497 (m)
REVERT: A  171 LEU cc_start: 0.9294 (mp) cc_final: 0.9072 (mp)
REVERT: A  216 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8383 (pp)
REVERT: A  283 MET cc_start: 0.8373 (mmp) cc_final: 0.8146 (mmm)
REVERT: A  349 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8086 (pp)
REVERT: B  101 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.5143 (t-90)
REVERT: B  159 VAL cc_start: 0.8708 (p) cc_final: 0.8405 (m)
REVERT: B  315 LYS cc_start: 0.8395 (tppt) cc_final: 0.7657 (ttmt)
REVERT: B  349 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8068 (pp)
REVERT: B  355 MET cc_start: 0.7938 (mtp) cc_final: 0.7572 (mpp)
  outliers start: 51
  outliers final: 33
  residues processed: 212
  average time/residue: 0.1576
  time to fit residues: 50.8329
Evaluate side-chains
  190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
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   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  121 GLN
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  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  212 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  349 LEU
Chi-restraints excluded: chain B residue   54 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  101 HIS
Chi-restraints excluded: chain B residue  105 LEU
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  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0570
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   overall best weight:    4.0106

-------------------------------------------------------------------------------
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 = 0.3302 r_free = 0.3302 target = 0.092015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082200 restraints weight = 24580.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084285 restraints weight = 12590.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.085674 restraints weight = 7589.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.5363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8865  Z= 0.271
  Angle     :  0.898  10.846  12042  Z= 0.430
  Chirality :  0.050   0.192   1341
  Planarity :  0.005   0.050   1536
  Dihedral  :  8.053  58.569   1245
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.42 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.24 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.24), residues: 1068
  helix: -1.18 (0.27), residues: 345
  sheet: -1.10 (0.35), residues: 213
  loop : -2.14 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  79 
 HIS   0.006   0.001   HIS B  88 
 PHE   0.019   0.002   PHE B 223 
 TYR   0.023   0.002   TYR C 166 
 ARG   0.004   0.001   ARG B 290 

*********************** 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
  213 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 167
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
REVERT: C  104 LEU cc_start: 0.8787 (tt) cc_final: 0.8512 (tp)
REVERT: C  121 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8189 (tm-30)
REVERT: C  159 VAL cc_start: 0.8596 (p) cc_final: 0.8325 (m)
REVERT: C  221 LEU cc_start: 0.8075 (tp) cc_final: 0.7848 (tp)
REVERT: C  283 MET cc_start: 0.8506 (mmp) cc_final: 0.8143 (mmm)
REVERT: C  356 TRP cc_start: 0.7426 (m100) cc_final: 0.7194 (m100)
REVERT: A  121 GLN cc_start: 0.8669 (tp40) cc_final: 0.8447 (tm-30)
REVERT: A  159 VAL cc_start: 0.8792 (p) cc_final: 0.8529 (m)
REVERT: A  171 LEU cc_start: 0.9310 (mp) cc_final: 0.9068 (mp)
REVERT: A  216 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8429 (pp)
REVERT: A  283 MET cc_start: 0.8367 (mmp) cc_final: 0.8151 (mmm)
REVERT: B  101 HIS cc_start: 0.5515 (OUTLIER) cc_final: 0.5255 (t-90)
REVERT: B  142 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mt)
REVERT: B  159 VAL cc_start: 0.8642 (p) cc_final: 0.8331 (m)
REVERT: B  315 LYS cc_start: 0.8391 (tppt) cc_final: 0.7633 (ttmt)
REVERT: B  349 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8087 (pp)
REVERT: B  355 MET cc_start: 0.7845 (mtp) cc_final: 0.7554 (mpp)
  outliers start: 46
  outliers final: 36
  residues processed: 196
  average time/residue: 0.1830
  time to fit residues: 54.2262
Evaluate side-chains
  192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  121 GLN
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  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  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  212 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 B residue   43 VAL
Chi-restraints excluded: chain B residue   54 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  101 HIS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  179 ASP
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.094948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.085197 restraints weight = 24246.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087311 restraints weight = 12324.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.088750 restraints weight = 7436.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8865  Z= 0.213
  Angle     :  0.866  10.653  12042  Z= 0.413
  Chirality :  0.049   0.191   1341
  Planarity :  0.005   0.051   1536
  Dihedral  :  7.632  58.461   1245
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.42 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.76 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.25), residues: 1068
  helix: -1.00 (0.28), residues: 330
  sheet: -0.83 (0.36), residues: 201
  loop : -2.01 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 356 
 HIS   0.005   0.001   HIS B  88 
 PHE   0.022   0.002   PHE B 223 
 TYR   0.024   0.001   TYR C 166 
 ARG   0.004   0.000   ARG B 210 

*********************** 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
  222 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 186
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8568 (tpt) cc_final: 0.8063 (tpt)
REVERT: C  104 LEU cc_start: 0.8746 (tt) cc_final: 0.8417 (tp)
REVERT: C  121 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7975 (tm-30)
REVERT: C  159 VAL cc_start: 0.8562 (p) cc_final: 0.8301 (m)
REVERT: C  283 MET cc_start: 0.8485 (mmp) cc_final: 0.8149 (mmm)
REVERT: C  356 TRP cc_start: 0.7263 (m100) cc_final: 0.6946 (m100)
REVERT: A  104 LEU cc_start: 0.8910 (tt) cc_final: 0.8697 (tp)
REVERT: A  159 VAL cc_start: 0.8734 (p) cc_final: 0.8480 (m)
REVERT: A  216 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8456 (pp)
REVERT: A  283 MET cc_start: 0.8387 (mmp) cc_final: 0.8180 (mmm)
REVERT: B  101 HIS cc_start: 0.5314 (OUTLIER) cc_final: 0.5060 (t-90)
REVERT: B  142 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8693 (mt)
REVERT: B  159 VAL cc_start: 0.8580 (p) cc_final: 0.8320 (m)
REVERT: B  315 LYS cc_start: 0.8176 (tppt) cc_final: 0.7327 (ttmm)
REVERT: B  349 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8072 (pp)
REVERT: B  355 MET cc_start: 0.7908 (mtp) cc_final: 0.7629 (mpp)
  outliers start: 36
  outliers final: 23
  residues processed: 206
  average time/residue: 0.1664
  time to fit residues: 51.3450
Evaluate side-chains
  190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
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   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  121 GLN
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 C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   54 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  101 HIS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0070
   chunk 42 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 23 optimal weight:    0.3980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
C 137 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.098208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.088398 restraints weight = 23946.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.090598 restraints weight = 12216.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.092097 restraints weight = 7324.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.6163

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= 0.200
  Angle     :  0.907  13.497  12042  Z= 0.426
  Chirality :  0.049   0.206   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  7.220  55.798   1245
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 25.62 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.25), residues: 1068
  helix: -0.70 (0.29), residues: 312
  sheet: -0.92 (0.36), residues: 201
  loop : -1.76 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B  79 
 HIS   0.013   0.001   HIS A 101 
 PHE   0.026   0.002   PHE B 223 
 TYR   0.028   0.001   TYR C 166 
 ARG   0.005   0.001   ARG C 183 

********************** 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: 24
    poor density    : 183
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8539 (tpt) cc_final: 0.8028 (tpt)
REVERT: C  104 LEU cc_start: 0.8579 (tt) cc_final: 0.8247 (tp)
REVERT: C  121 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8032 (tm-30)
REVERT: C  159 VAL cc_start: 0.8336 (p) cc_final: 0.8119 (m)
REVERT: A  159 VAL cc_start: 0.8580 (p) cc_final: 0.8294 (m)
REVERT: A  216 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (pp)
REVERT: A  263 GLN cc_start: 0.8321 (mt0) cc_final: 0.7991 (mt0)
REVERT: B  101 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.4831 (t-90)
REVERT: B  159 VAL cc_start: 0.8543 (p) cc_final: 0.8258 (m)
REVERT: B  344 SER cc_start: 0.8639 (t) cc_final: 0.8207 (p)
REVERT: B  349 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8084 (pp)
REVERT: B  355 MET cc_start: 0.7770 (mtp) cc_final: 0.7529 (mpp)
  outliers start: 24
  outliers final: 17
  residues processed: 192
  average time/residue: 0.1593
  time to fit residues: 45.5453
Evaluate side-chains
  187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  121 GLN
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   64 ILE
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  151 ILE
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0170
   chunk 68 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0970
   chunk 95 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 137 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.100629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090753 restraints weight = 23875.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.092958 restraints weight = 12063.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.094353 restraints weight = 7223.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.6485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8865  Z= 0.198
  Angle     :  0.895  13.227  12042  Z= 0.421
  Chirality :  0.049   0.193   1341
  Planarity :  0.005   0.053   1536
  Dihedral  :  7.013  55.703   1245
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 26.82 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.25), residues: 1068
  helix: -0.55 (0.29), residues: 309
  sheet: -0.74 (0.37), residues: 195
  loop : -1.60 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 356 
 HIS   0.013   0.001   HIS A 101 
 PHE   0.024   0.001   PHE B 223 
 TYR   0.028   0.001   TYR C 166 
 ARG   0.005   0.001   ARG C 290 

===============================================================================
Job complete
usr+sys time: 2473.79 seconds
wall clock time: 45 minutes 34.97 seconds (2734.97 seconds total)