Starting phenix.real_space_refine
on Thu Feb 13 04:03:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6avb_7008/02_2025/6avb_7008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6avb_7008/02_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_7008/02_2025/6avb_7008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6avb_7008/02_2025/6avb_7008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6avb_7008/02_2025/6avb_7008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6avb_7008/02_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-5592/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: 2.55
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.95
  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: 2.31

  Time building geometry restraints manager: 2.80 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.560
  Find NCS groups from input model:        0.150
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.350
-------------------------------------------------------------------------------
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  : 1.050 
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: 0.2495
  time to fit residues: 83.4379
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  : 1.007 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082513 restraints weight = 24210.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.084520 restraints weight = 12119.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.085906 restraints weight = 7275.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
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  : 1.009 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8556 (tpt) cc_final: 0.8210 (tpt)
REVERT: C  159 VAL cc_start: 0.8656 (p) cc_final: 0.8363 (m)
REVERT: C  353 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7313 (tt0)
REVERT: C  356 TRP cc_start: 0.7697 (m100) cc_final: 0.7284 (m-90)
REVERT: A  148 THR cc_start: 0.8402 (t) cc_final: 0.8061 (m)
REVERT: A  159 VAL cc_start: 0.8787 (p) cc_final: 0.8500 (m)
REVERT: A  183 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8642 (mtm110)
REVERT: A  216 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8545 (pp)
REVERT: A  356 TRP cc_start: 0.7682 (m100) cc_final: 0.7278 (m100)
REVERT: B  107 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: B  133 TYR cc_start: 0.7900 (t80) cc_final: 0.7625 (t80)
REVERT: B  137 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8348 (mm110)
REVERT: B  159 VAL cc_start: 0.8582 (p) cc_final: 0.8209 (m)
REVERT: B  216 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8294 (pp)
REVERT: B  315 LYS cc_start: 0.8327 (tppt) cc_final: 0.7709 (ttmt)
REVERT: B  355 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7070 (mpp)
  outliers start: 41
  outliers final: 25
  residues processed: 240
  average time/residue: 0.1677
  time to fit residues: 58.3093
Evaluate side-chains
  191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   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  40 HIS
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 121 GLN
A 280 ASN
B  40 HIS
B  87 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.090577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081043 restraints weight = 25057.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083035 restraints weight = 12589.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.084390 restraints weight = 7544.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8865  Z= 0.325
  Angle     :  0.924  11.570  12042  Z= 0.450
  Chirality :  0.052   0.203   1341
  Planarity :  0.005   0.054   1536
  Dihedral  :  8.711  58.902   1245
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 14.77 %
    Favored  : 80.02 %
  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: -2.98 (0.23), residues: 1068
  helix: -1.71 (0.26), residues: 339
  sheet: -1.40 (0.35), residues: 210
  loop : -2.39 (0.23), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   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
  233 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 185
  time to evaluate  : 0.953 
Fit side-chains
REVERT: C   82 MET cc_start: 0.8534 (tpt) cc_final: 0.8211 (tpt)
REVERT: C  159 VAL cc_start: 0.8692 (p) cc_final: 0.8378 (m)
REVERT: C  349 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7866 (pp)
REVERT: C  356 TRP cc_start: 0.7769 (m100) cc_final: 0.7450 (m100)
REVERT: A  148 THR cc_start: 0.8436 (t) cc_final: 0.8105 (m)
REVERT: A  159 VAL cc_start: 0.8804 (p) cc_final: 0.8493 (m)
REVERT: A  216 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8522 (pp)
REVERT: A  221 LEU cc_start: 0.8173 (tp) cc_final: 0.7910 (tp)
REVERT: A  283 MET cc_start: 0.8341 (mmp) cc_final: 0.7998 (mmm)
REVERT: A  356 TRP cc_start: 0.7749 (m100) cc_final: 0.7294 (m100)
REVERT: B   12 ASN cc_start: 0.7739 (m-40) cc_final: 0.7474 (m-40)
REVERT: B  137 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8249 (mm-40)
REVERT: B  159 VAL cc_start: 0.8636 (p) cc_final: 0.8256 (m)
REVERT: B  315 LYS cc_start: 0.8432 (tppt) cc_final: 0.7703 (ttmm)
REVERT: B  349 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (pp)
REVERT: B  355 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7595 (mtp)
  outliers start: 48
  outliers final: 29
  residues processed: 213
  average time/residue: 0.1571
  time to fit residues: 50.2599
Evaluate side-chains
  178 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
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  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:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0010
   chunk 15 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   chunk 104 optimal weight:    6.9990
   overall best weight:    2.3190

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.093777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084222 restraints weight = 24453.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.086270 restraints weight = 12223.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.087583 restraints weight = 7293.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8865  Z= 0.213
  Angle     :  0.856  12.462  12042  Z= 0.407
  Chirality :  0.049   0.188   1341
  Planarity :  0.005   0.049   1536
  Dihedral  :  7.944  59.956   1245
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 17.48 %
    Favored  : 77.85 %
  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: -2.55 (0.24), residues: 1068
  helix: -1.28 (0.27), residues: 354
  sheet: -1.30 (0.35), residues: 210
  loop : -2.12 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  79 
 HIS   0.005   0.001   HIS B  87 
 PHE   0.014   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
  240 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 197
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 MET cc_start: 0.8591 (tpt) cc_final: 0.8223 (tpt)
REVERT: C  118 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7922 (mtmm)
REVERT: C  159 VAL cc_start: 0.8626 (p) cc_final: 0.8356 (m)
REVERT: C  221 LEU cc_start: 0.8072 (tp) cc_final: 0.7793 (tp)
REVERT: C  283 MET cc_start: 0.8386 (mmp) cc_final: 0.7905 (mmm)
REVERT: C  314 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7439 (mp10)
REVERT: C  356 TRP cc_start: 0.7606 (m100) cc_final: 0.7250 (m-90)
REVERT: A  107 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: A  121 GLN cc_start: 0.8540 (tp40) cc_final: 0.8333 (tm-30)
REVERT: A  137 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7792 (mp10)
REVERT: A  159 VAL cc_start: 0.8725 (p) cc_final: 0.8440 (m)
REVERT: A  216 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8368 (pp)
REVERT: A  221 LEU cc_start: 0.7844 (tp) cc_final: 0.7607 (tp)
REVERT: A  283 MET cc_start: 0.8405 (mmp) cc_final: 0.8030 (mmm)
REVERT: B  137 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7944 (mm-40)
REVERT: B  159 VAL cc_start: 0.8524 (p) cc_final: 0.8181 (m)
REVERT: B  315 LYS cc_start: 0.8247 (tppt) cc_final: 0.7626 (ttmt)
REVERT: B  330 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (pt)
REVERT: B  349 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8130 (pp)
  outliers start: 43
  outliers final: 22
  residues processed: 221
  average time/residue: 0.1640
  time to fit residues: 53.3372
Evaluate side-chains
  194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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   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  151 ILE
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:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  40 HIS
A 314 GLN
B 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.090700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.080941 restraints weight = 24354.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.082952 restraints weight = 12458.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.084336 restraints weight = 7563.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8865  Z= 0.331
  Angle     :  0.903   9.180  12042  Z= 0.437
  Chirality :  0.051   0.199   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  8.387  59.640   1245
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 18.02 %
    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: -2.66 (0.24), residues: 1068
  helix: -1.42 (0.26), residues: 348
  sheet: -1.33 (0.35), residues: 210
  loop : -2.16 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  79 
 HIS   0.005   0.002   HIS B  88 
 PHE   0.018   0.002   PHE A 352 
 TYR   0.024   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
  232 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 172
  time to evaluate  : 1.027 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8697 (p) cc_final: 0.8396 (m)
REVERT: C  221 LEU cc_start: 0.8084 (tp) cc_final: 0.7817 (tp)
REVERT: C  283 MET cc_start: 0.8509 (mmp) cc_final: 0.8078 (mmm)
REVERT: C  314 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: C  356 TRP cc_start: 0.7605 (m100) cc_final: 0.7320 (m100)
REVERT: A  159 VAL cc_start: 0.8762 (p) cc_final: 0.8494 (m)
REVERT: A  171 LEU cc_start: 0.9344 (mp) cc_final: 0.9088 (mp)
REVERT: A  216 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8348 (pp)
REVERT: A  221 LEU cc_start: 0.7893 (tp) cc_final: 0.7602 (tp)
REVERT: A  283 MET cc_start: 0.8316 (mmp) cc_final: 0.8095 (mmm)
REVERT: B  137 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7903 (mm-40)
REVERT: B  159 VAL cc_start: 0.8631 (p) cc_final: 0.8289 (m)
REVERT: B  315 LYS cc_start: 0.8467 (tppt) cc_final: 0.7663 (ttmm)
REVERT: B  349 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8144 (pp)
REVERT: B  355 MET cc_start: 0.7814 (mtp) cc_final: 0.7590 (mpp)
  outliers start: 60
  outliers final: 36
  residues processed: 210
  average time/residue: 0.1645
  time to fit residues: 51.2186
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 160
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  246 GLN
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  205 GLU
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  313 MET
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:    1.9990
   chunk 22 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 104 optimal weight:    8.9990
   chunk 94 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 121 GLN
B 371 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.089392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.079749 restraints weight = 24317.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.081711 restraints weight = 12496.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.083085 restraints weight = 7595.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   8865  Z= 0.383
  Angle     :  0.917   8.471  12042  Z= 0.451
  Chirality :  0.053   0.216   1341
  Planarity :  0.006   0.052   1536
  Dihedral  :  8.456  58.667   1245
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.27 %
    Favored  : 87.73 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 20.52 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.71 (0.24), residues: 1068
  helix: -1.33 (0.27), residues: 345
  sheet: -1.44 (0.35), residues: 213
  loop : -2.26 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  79 
 HIS   0.006   0.002   HIS B  88 
 PHE   0.015   0.002   PHE A 127 
 TYR   0.026   0.002   TYR B 218 
 ARG   0.004   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
  209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 155
  time to evaluate  : 0.930 
Fit side-chains
REVERT: C  159 VAL cc_start: 0.8677 (p) cc_final: 0.8384 (m)
REVERT: C  221 LEU cc_start: 0.8127 (tp) cc_final: 0.7848 (tp)
REVERT: C  283 MET cc_start: 0.8595 (mmp) cc_final: 0.8247 (mmm)
REVERT: C  314 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7701 (mp10)
REVERT: C  356 TRP cc_start: 0.7630 (m100) cc_final: 0.7419 (m100)
REVERT: A  104 LEU cc_start: 0.8991 (tt) cc_final: 0.8760 (tp)
REVERT: A  121 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8200 (tp40)
REVERT: A  159 VAL cc_start: 0.8788 (p) cc_final: 0.8531 (m)
REVERT: A  171 LEU cc_start: 0.9382 (mp) cc_final: 0.9104 (mp)
REVERT: A  216 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8501 (pp)
REVERT: A  221 LEU cc_start: 0.7898 (tp) cc_final: 0.7626 (tp)
REVERT: A  283 MET cc_start: 0.8378 (mmp) cc_final: 0.8156 (mmm)
REVERT: A  349 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8109 (pp)
REVERT: B  101 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5587 (t-90)
REVERT: B  159 VAL cc_start: 0.8653 (p) cc_final: 0.8321 (m)
REVERT: B  315 LYS cc_start: 0.8488 (tppt) cc_final: 0.7801 (ttmt)
  outliers start: 54
  outliers final: 37
  residues processed: 191
  average time/residue: 0.1608
  time to fit residues: 45.9482
Evaluate side-chains
  183 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  179 ASP
Chi-restraints excluded: chain A residue  205 GLU
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  101 HIS
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  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  317 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  330 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    5.7990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.089707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.080034 restraints weight = 24484.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.082021 restraints weight = 12531.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.083409 restraints weight = 7580.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8865  Z= 0.338
  Angle     :  0.916  11.985  12042  Z= 0.442
  Chirality :  0.051   0.209   1341
  Planarity :  0.006   0.051   1536
  Dihedral  :  8.361  57.196   1245
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 21.50 %
    Favored  : 72.53 %
  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: -2.77 (0.24), residues: 1068
  helix: -1.38 (0.26), residues: 366
  sheet: -1.42 (0.35), residues: 213
  loop : -2.34 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  79 
 HIS   0.006   0.001   HIS B  88 
 PHE   0.030   0.002   PHE C 223 
 TYR   0.024   0.002   TYR B 218 
 ARG   0.004   0.001   ARG A 290 

*********************** 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
  209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 154
  time to evaluate  : 0.973 
Fit side-chains
REVERT: C  121 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (tp-100)
REVERT: C  159 VAL cc_start: 0.8657 (p) cc_final: 0.8378 (m)
REVERT: C  221 LEU cc_start: 0.8190 (tp) cc_final: 0.7938 (tp)
REVERT: C  314 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7704 (mp10)
REVERT: C  356 TRP cc_start: 0.7602 (m100) cc_final: 0.7383 (m100)
REVERT: A  104 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8736 (tp)
REVERT: A  159 VAL cc_start: 0.8780 (p) cc_final: 0.8517 (m)
REVERT: A  171 LEU cc_start: 0.9362 (mp) cc_final: 0.9095 (mp)
REVERT: A  216 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8416 (pp)
REVERT: A  221 LEU cc_start: 0.7867 (tp) cc_final: 0.7622 (tp)
REVERT: A  349 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8075 (pp)
REVERT: B  101 HIS cc_start: 0.5812 (OUTLIER) cc_final: 0.5404 (t-90)
REVERT: B  137 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7933 (mp10)
REVERT: B  159 VAL cc_start: 0.8656 (p) cc_final: 0.8322 (m)
REVERT: B  315 LYS cc_start: 0.8463 (tppt) cc_final: 0.7761 (ttmt)
REVERT: B  355 MET cc_start: 0.7805 (mtp) cc_final: 0.7582 (mpp)
  outliers start: 55
  outliers final: 34
  residues processed: 191
  average time/residue: 0.1574
  time to fit residues: 45.3717
Evaluate side-chains
  181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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  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  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  104 LEU
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  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   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  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3257 r_free = 0.3257 target = 0.089562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.079841 restraints weight = 24729.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.081861 restraints weight = 12724.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083256 restraints weight = 7694.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.5277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8865  Z= 0.362
  Angle     :  0.939  11.517  12042  Z= 0.455
  Chirality :  0.052   0.218   1341
  Planarity :  0.006   0.051   1536
  Dihedral  :  8.397  56.091   1245
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.27 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 21.82 %
    Favored  : 72.20 %
  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: -2.80 (0.23), residues: 1068
  helix: -1.40 (0.25), residues: 363
  sheet: -1.26 (0.35), residues: 210
  loop : -2.44 (0.24), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  79 
 HIS   0.006   0.002   HIS A 275 
 PHE   0.022   0.002   PHE C 223 
 TYR   0.026   0.002   TYR B 218 
 ARG   0.005   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
  202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 147
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: C  104 LEU cc_start: 0.8801 (tt) cc_final: 0.8520 (tp)
REVERT: C  121 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8238 (tp-100)
REVERT: C  159 VAL cc_start: 0.8683 (p) cc_final: 0.8373 (m)
REVERT: C  221 LEU cc_start: 0.8220 (tp) cc_final: 0.7917 (tp)
REVERT: C  283 MET cc_start: 0.8438 (mmp) cc_final: 0.7997 (mmm)
REVERT: C  314 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7693 (mp10)
REVERT: A  104 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: A  159 VAL cc_start: 0.8811 (p) cc_final: 0.8535 (m)
REVERT: A  171 LEU cc_start: 0.9359 (mp) cc_final: 0.9030 (mp)
REVERT: A  216 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8440 (pp)
REVERT: A  221 LEU cc_start: 0.7902 (tp) cc_final: 0.7650 (tp)
REVERT: A  349 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8034 (pp)
REVERT: B  101 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.5584 (t-90)
REVERT: B  137 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7981 (mp10)
REVERT: B  159 VAL cc_start: 0.8722 (p) cc_final: 0.8384 (m)
REVERT: B  315 LYS cc_start: 0.8486 (tppt) cc_final: 0.7788 (ttmt)
REVERT: B  355 MET cc_start: 0.7800 (mtp) cc_final: 0.7559 (mpp)
  outliers start: 55
  outliers final: 39
  residues processed: 188
  average time/residue: 0.1540
  time to fit residues: 43.6630
Evaluate side-chains
  181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 136
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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  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  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  142 LEU
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  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   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  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  139 VAL
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  300 SER
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.091910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.082088 restraints weight = 24296.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.084151 restraints weight = 12471.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.085542 restraints weight = 7551.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8865  Z= 0.256
  Angle     :  0.890  10.804  12042  Z= 0.427
  Chirality :  0.050   0.197   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  8.111  59.234   1245
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.89 %
    Favored  : 88.01 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 23.67 %
    Favored  : 71.66 %
  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: -2.55 (0.24), residues: 1068
  helix: -1.12 (0.27), residues: 348
  sheet: -1.08 (0.36), residues: 201
  loop : -2.35 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B  79 
 HIS   0.014   0.002   HIS A 101 
 PHE   0.029   0.002   PHE B 223 
 TYR   0.024   0.002   TYR A 166 
 ARG   0.005   0.000   ARG B 290 

*********************** 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
  204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 161
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: C  104 LEU cc_start: 0.8799 (tt) cc_final: 0.8485 (tp)
REVERT: C  121 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (tm-30)
REVERT: C  159 VAL cc_start: 0.8597 (p) cc_final: 0.8324 (m)
REVERT: C  221 LEU cc_start: 0.8151 (tp) cc_final: 0.7926 (tp)
REVERT: C  283 MET cc_start: 0.8554 (mmp) cc_final: 0.8108 (mmm)
REVERT: C  314 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7592 (mp10)
REVERT: C  356 TRP cc_start: 0.7558 (m100) cc_final: 0.7182 (m100)
REVERT: A  104 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8739 (tp)
REVERT: A  121 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8119 (tm-30)
REVERT: A  159 VAL cc_start: 0.8729 (p) cc_final: 0.8477 (m)
REVERT: A  171 LEU cc_start: 0.9288 (mp) cc_final: 0.9070 (mp)
REVERT: A  216 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8423 (pp)
REVERT: A  221 LEU cc_start: 0.7652 (tp) cc_final: 0.7422 (tp)
REVERT: A  349 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8053 (pp)
REVERT: B  116 ARG cc_start: 0.6791 (ptt180) cc_final: 0.6585 (ptt90)
REVERT: B  159 VAL cc_start: 0.8651 (p) cc_final: 0.8345 (m)
REVERT: B  315 LYS cc_start: 0.8158 (tppt) cc_final: 0.7420 (ttmm)
REVERT: B  355 MET cc_start: 0.7893 (mtp) cc_final: 0.7612 (mpp)
  outliers start: 43
  outliers final: 34
  residues processed: 191
  average time/residue: 0.1555
  time to fit residues: 44.4966
Evaluate side-chains
  185 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
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  300 SER
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  179 ASP
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   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  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  247 VAL
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0270
   chunk 42 optimal weight:    0.0970
   chunk 78 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    2.8242

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.093277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.083405 restraints weight = 24159.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.085492 restraints weight = 12370.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.086830 restraints weight = 7466.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8865  Z= 0.238
  Angle     :  0.895  10.276  12042  Z= 0.428
  Chirality :  0.050   0.194   1341
  Planarity :  0.005   0.052   1536
  Dihedral  :  7.889  58.910   1245
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.70 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 24.43 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.24 (0.25), residues: 1068
  helix: -0.85 (0.28), residues: 330
  sheet: -1.01 (0.36), residues: 201
  loop : -2.09 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B  79 
 HIS   0.011   0.001   HIS A 101 
 PHE   0.026   0.002   PHE B 223 
 TYR   0.024   0.002   TYR C 166 
 ARG   0.004   0.001   ARG B 210 

********************** 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
  197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: C  104 LEU cc_start: 0.8763 (tt) cc_final: 0.8407 (tp)
REVERT: C  121 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8073 (tm-30)
REVERT: C  159 VAL cc_start: 0.8568 (p) cc_final: 0.8304 (m)
REVERT: C  283 MET cc_start: 0.8565 (mmp) cc_final: 0.8147 (mmm)
REVERT: C  314 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7525 (mp10)
REVERT: C  356 TRP cc_start: 0.7496 (m100) cc_final: 0.7118 (m100)
REVERT: A  121 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8147 (tm-30)
REVERT: A  159 VAL cc_start: 0.8813 (p) cc_final: 0.8546 (m)
REVERT: A  171 LEU cc_start: 0.9273 (mp) cc_final: 0.9072 (mp)
REVERT: A  216 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (pp)
REVERT: B  101 HIS cc_start: 0.5386 (OUTLIER) cc_final: 0.5089 (t-90)
REVERT: B  116 ARG cc_start: 0.6817 (ptt180) cc_final: 0.6575 (ptt90)
REVERT: B  159 VAL cc_start: 0.8615 (p) cc_final: 0.8325 (m)
REVERT: B  315 LYS cc_start: 0.8086 (tppt) cc_final: 0.7302 (ttmm)
REVERT: B  355 MET cc_start: 0.7973 (mtp) cc_final: 0.7630 (mpp)
  outliers start: 38
  outliers final: 30
  residues processed: 185
  average time/residue: 0.1606
  time to fit residues: 43.9508
Evaluate side-chains
  184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
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  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  314 GLN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  179 ASP
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 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  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  260 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 41 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3298 r_free = 0.3298 target = 0.091802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.081897 restraints weight = 24433.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.083957 restraints weight = 12588.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.085356 restraints weight = 7630.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8865  Z= 0.307
  Angle     :  0.929  13.568  12042  Z= 0.446
  Chirality :  0.052   0.237   1341
  Planarity :  0.006   0.052   1536
  Dihedral  :  7.955  53.483   1245
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.08 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 24.21 %
    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: -2.51 (0.24), residues: 1068
  helix: -1.07 (0.27), residues: 348
  sheet: -1.03 (0.36), residues: 204
  loop : -2.36 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP B  79 
 HIS   0.009   0.002   HIS A 101 
 PHE   0.029   0.002   PHE C 223 
 TYR   0.024   0.002   TYR C 166 
 ARG   0.004   0.001   ARG B 290 

===============================================================================
Job complete
usr+sys time: 2272.78 seconds
wall clock time: 41 minutes 51.32 seconds (2511.32 seconds total)