Starting phenix.real_space_refine
on Sat Sep 12 08:34:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5oof_3839/09_2026/5oof_3839.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      5      5.21       5
     S     105      5.16       5
     C    9235      2.51       5
     N    2470      2.21       5
     O    2815      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14640
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 2.91, per 1000 atoms: 0.20
  Number of scatterers: 14640
  At special positions: 0
  Unit cell: (98.04, 91.2, 190.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     105     16.00
     P      10     15.00
     Mg      5     11.99
     O    2815      8.00
     N    2470      7.00
     C    9235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 651.8 milliseconds
  

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3430

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 30 sheets defined
      52.3% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.879A  pdb=" N   ARG A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 172 through 175
    Processing helix  chain 'A' and resid 181 through 194
    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 202 through 217
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 252 through 260
      Proline residue:  A 258  - end of helix
    Processing helix  chain 'A' and resid 261 through 262
      No H-bonds generated for 'chain 'A' and resid 261 through 262'
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 4.680A  pdb=" N   LYS A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ASP A 292 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 350 through 356
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 372
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 92
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.878A  pdb=" N   ARG B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 172 through 175
    Processing helix  chain 'B' and resid 181 through 194
    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 202 through 217
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 252 through 260
      Proline residue:  B 258  - end of helix
    Processing helix  chain 'B' and resid 261 through 262
      No H-bonds generated for 'chain 'B' and resid 261 through 262'
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 286 through 295
      removed outlier: 4.681A  pdb=" N   LYS B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASP B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 308 through 321
    Processing helix  chain 'B' and resid 334 through 336
      No H-bonds generated for 'chain 'B' and resid 334 through 336'
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 350 through 356
    Processing helix  chain 'B' and resid 359 through 366
    Processing helix  chain 'B' and resid 367 through 372
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 3.878A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 194
    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 202 through 217
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 252 through 260
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 261 through 262
      No H-bonds generated for 'chain 'C' and resid 261 through 262'
    Processing helix  chain 'C' and resid 263 through 268
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 286 through 295
      removed outlier: 4.680A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 350 through 356
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 367 through 372
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 78 through 92
    Processing helix  chain 'D' and resid 97 through 101
    Processing helix  chain 'D' and resid 112 through 126
      removed outlier: 3.878A  pdb=" N   ARG D 116 " --> pdb=" O   PRO D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 146
    Processing helix  chain 'D' and resid 172 through 175
    Processing helix  chain 'D' and resid 181 through 194
    Processing helix  chain 'D' and resid 195 through 197
      No H-bonds generated for 'chain 'D' and resid 195 through 197'
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 222 through 230
    Processing helix  chain 'D' and resid 252 through 260
      Proline residue:  D 258  - end of helix
    Processing helix  chain 'D' and resid 261 through 262
      No H-bonds generated for 'chain 'D' and resid 261 through 262'
    Processing helix  chain 'D' and resid 263 through 268
    Processing helix  chain 'D' and resid 273 through 284
    Processing helix  chain 'D' and resid 286 through 295
      removed outlier: 4.680A  pdb=" N   LYS D 291 " --> pdb=" O   ILE D 287 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ASP D 292 " --> pdb=" O   ASP D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 306
    Processing helix  chain 'D' and resid 308 through 321
    Processing helix  chain 'D' and resid 334 through 336
      No H-bonds generated for 'chain 'D' and resid 334 through 336'
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 356
    Processing helix  chain 'D' and resid 359 through 366
    Processing helix  chain 'D' and resid 367 through 372
    Processing helix  chain 'E' and resid 55 through 61
    Processing helix  chain 'E' and resid 78 through 92
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 112 through 126
      removed outlier: 3.879A  pdb=" N   ARG E 116 " --> pdb=" O   PRO E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 137 through 146
    Processing helix  chain 'E' and resid 172 through 175
    Processing helix  chain 'E' and resid 181 through 194
    Processing helix  chain 'E' and resid 195 through 197
      No H-bonds generated for 'chain 'E' and resid 195 through 197'
    Processing helix  chain 'E' and resid 202 through 217
    Processing helix  chain 'E' and resid 222 through 230
    Processing helix  chain 'E' and resid 252 through 260
      Proline residue:  E 258  - end of helix
    Processing helix  chain 'E' and resid 261 through 262
      No H-bonds generated for 'chain 'E' and resid 261 through 262'
    Processing helix  chain 'E' and resid 263 through 268
    Processing helix  chain 'E' and resid 273 through 284
    Processing helix  chain 'E' and resid 286 through 295
      removed outlier: 4.680A  pdb=" N   LYS E 291 " --> pdb=" O   ILE E 287 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASP E 292 " --> pdb=" O   ASP E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 301 through 306
    Processing helix  chain 'E' and resid 308 through 321
    Processing helix  chain 'E' and resid 334 through 336
      No H-bonds generated for 'chain 'E' and resid 334 through 336'
    Processing helix  chain 'E' and resid 337 through 349
    Processing helix  chain 'E' and resid 350 through 356
    Processing helix  chain 'E' and resid 359 through 366
    Processing helix  chain 'E' and resid 367 through 372
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.514A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   CYS A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170
      removed outlier: 5.923A  pdb=" N   ILE A 151 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ASN A 297 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.514A  pdb=" N   LEU B   8 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR B 106 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   CYS B  10 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170
    Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170
      removed outlier: 5.924A  pdb=" N   ILE B 151 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ASN B 297 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.514A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   CYS C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170
      removed outlier: 5.923A  pdb=" N   ILE C 151 " --> pdb=" O   VAL C 298 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.514A  pdb=" N   LEU D   8 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   THR D 106 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   CYS D  10 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54
    Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170
    Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170
      removed outlier: 5.923A  pdb=" N   ILE D 151 " --> pdb=" O   VAL D 298 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ASN D 297 " --> pdb=" O   ILE D 330 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241
    Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32
      removed outlier: 6.513A  pdb=" N   LEU E   8 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR E 106 " --> pdb=" O   LEU E   8 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   CYS E  10 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54
    Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72
    Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170
    Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170
      removed outlier: 5.922A  pdb=" N   ILE E 151 " --> pdb=" O   VAL E 298 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ASN E 297 " --> pdb=" O   ILE E 330 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241

    765 hydrogen bonds defined for protein.
    1875 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: 2.81

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 3328
        1.32 -     1.44: 3451
        1.44 -     1.56: 7996
        1.56 -     1.69: 0
        1.69 -     1.81: 185
  Bond restraints: 14960
  Sorted by residual:
  bond pdb=" CA  SER C 155 "
       pdb=" C   SER C 155 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 9.60e-03 1.09e+04 1.86e+01
  bond pdb=" CA  SER B 155 "
       pdb=" C   SER B 155 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 9.60e-03 1.09e+04 1.84e+01
  bond pdb=" CA  SER E 155 "
       pdb=" C   SER E 155 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 9.60e-03 1.09e+04 1.81e+01
  bond pdb=" CA  SER D 155 "
       pdb=" C   SER D 155 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 9.60e-03 1.09e+04 1.79e+01
  bond pdb=" CA  SER A 155 "
       pdb=" C   SER A 155 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 9.60e-03 1.09e+04 1.79e+01
  ... (remaining 14955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 19238
        2.91 -     5.82: 879
        5.82 -     8.73: 148
        8.73 -    11.64: 35
       11.64 -    14.55: 5
  Bond angle restraints: 20305
  Sorted by residual:
  angle pdb=" C   GLY B 366 "
        pdb=" N   PRO B 367 "
        pdb=" CA  PRO B 367 "
      ideal   model   delta    sigma   weight residual
     119.84  129.55   -9.71 1.25e+00 6.40e-01 6.04e+01
  angle pdb=" C   GLY D 366 "
        pdb=" N   PRO D 367 "
        pdb=" CA  PRO D 367 "
      ideal   model   delta    sigma   weight residual
     119.84  129.54   -9.70 1.25e+00 6.40e-01 6.02e+01
  angle pdb=" C   GLY E 366 "
        pdb=" N   PRO E 367 "
        pdb=" CA  PRO E 367 "
      ideal   model   delta    sigma   weight residual
     119.84  129.53   -9.69 1.25e+00 6.40e-01 6.02e+01
  angle pdb=" C   GLY A 366 "
        pdb=" N   PRO A 367 "
        pdb=" CA  PRO A 367 "
      ideal   model   delta    sigma   weight residual
     119.84  129.53   -9.69 1.25e+00 6.40e-01 6.00e+01
  angle pdb=" C   GLY C 366 "
        pdb=" N   PRO C 367 "
        pdb=" CA  PRO C 367 "
      ideal   model   delta    sigma   weight residual
     119.84  129.48   -9.64 1.25e+00 6.40e-01 5.95e+01
  ... (remaining 20300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.52: 8835
       29.52 -    59.04: 135
       59.04 -    88.56: 20
       88.56 -   118.08: 0
      118.08 -   147.61: 5
  Dihedral angle restraints: 8995
    sinusoidal: 3635
      harmonic: 5360
  Sorted by residual:
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   87.61 -147.61     1      2.00e+01 2.50e-03 4.43e+01
  dihedral pdb=" C5' ADP E 401 "
           pdb=" O5' ADP E 401 "
           pdb=" PA  ADP E 401 "
           pdb=" O2A ADP E 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   87.57 -147.57     1      2.00e+01 2.50e-03 4.43e+01
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   87.56 -147.56     1      2.00e+01 2.50e-03 4.43e+01
  ... (remaining 8992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 907
       0.047 -    0.094: 909
       0.094 -    0.140: 308
       0.140 -    0.187: 93
       0.187 -    0.234: 38
  Chirality restraints: 2255
  Sorted by residual:
  chirality pdb=" CA  ASP A 157 "
            pdb=" N   ASP A 157 "
            pdb=" C   ASP A 157 "
            pdb=" CB  ASP A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  ASP B 157 "
            pdb=" N   ASP B 157 "
            pdb=" C   ASP B 157 "
            pdb=" CB  ASP B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ASP E 157 "
            pdb=" N   ASP E 157 "
            pdb=" C   ASP E 157 "
            pdb=" CB  ASP E 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2252 not shown)

  Planarity restraints: 2595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 375 "   -0.033 2.00e-02 2.50e+03   6.58e-02 4.33e+01
        pdb=" C   PHE D 375 "    0.114 2.00e-02 2.50e+03
        pdb=" O   PHE D 375 "   -0.041 2.00e-02 2.50e+03
        pdb=" OXT PHE D 375 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E 375 "    0.032 2.00e-02 2.50e+03   6.57e-02 4.31e+01
        pdb=" C   PHE E 375 "   -0.114 2.00e-02 2.50e+03
        pdb=" O   PHE E 375 "    0.041 2.00e-02 2.50e+03
        pdb=" OXT PHE E 375 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 375 "   -0.032 2.00e-02 2.50e+03   6.57e-02 4.31e+01
        pdb=" C   PHE B 375 "    0.114 2.00e-02 2.50e+03
        pdb=" O   PHE B 375 "   -0.041 2.00e-02 2.50e+03
        pdb=" OXT PHE B 375 "   -0.040 2.00e-02 2.50e+03
  ... (remaining 2592 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 71
        2.59 -     3.17: 13898
        3.17 -     3.74: 22255
        3.74 -     4.32: 34236
        4.32 -     4.90: 53454
  Nonbonded interactions: 123914
  Sorted by model distance:
  nonbonded pdb=" O1B ADP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" O1B ADP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" O1B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" O1B ADP E 401 "
            pdb="MG    MG E 402 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" O1B ADP B 401 "
            pdb="MG    MG B 402 "
     model   vdw
     2.011 2.170
  ... (remaining 123909 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.250
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
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      :  0.015   0.052  14960  Z= 0.964
  Angle     :  1.532  14.555  20305  Z= 0.993
  Chirality :  0.075   0.234   2255
  Planarity :  0.016   0.143   2595
  Dihedral  : 11.806 147.605   5565
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  2.73 %
    Allowed  :  6.28 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.19), residues: 1830
  helix: -1.44 (0.16), residues: 780
  sheet: -1.22 (0.28), residues: 235
  loop : -0.01 (0.25), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 183 
 TYR   0.030   0.005   TYR B  69 
 PHE   0.013   0.003   PHE C 375 
 TRP   0.031   0.006   TRP C 340 
 HIS   0.010   0.002   HIS D 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01535 /  0.96 (14960)
  covalent geometry    : angle       1.53219 /  0.99 (20305)
  hydrogen bonds       : bond        0.17424 / 11.60 (  755)
  hydrogen bonds       : angle       7.38131 /  5.17 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 408
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 ILE cc_start: 0.9238 (mt) cc_final: 0.8981 (mp)
REVERT: A  176 MET cc_start: 0.8871 (mmm) cc_final: 0.8640 (mmt)
REVERT: A  283 MET cc_start: 0.9192 (mmp) cc_final: 0.8962 (mmt)
REVERT: A  328 LYS cc_start: 0.8714 (tttt) cc_final: 0.8452 (tttm)
REVERT: A  355 MET cc_start: 0.8432 (mmm) cc_final: 0.8217 (mmm)
REVERT: B   47 MET cc_start: 0.5700 (mtm) cc_final: 0.5438 (tpt)
REVERT: C  123 MET cc_start: 0.8724 (mmp) cc_final: 0.8482 (mmt)
REVERT: D   51 ASP cc_start: 0.7474 (p0) cc_final: 0.6842 (p0)
REVERT: D  113 LYS cc_start: 0.8803 (mttt) cc_final: 0.8112 (mtpp)
REVERT: E   12 ASN cc_start: 0.8292 (t0) cc_final: 0.8005 (p0)
REVERT: E   78 ASN cc_start: 0.8630 (t0) cc_final: 0.8177 (t0)
REVERT: E  269 MET cc_start: 0.8429 (tpp) cc_final: 0.8210 (mmt)
REVERT: E  354 GLN cc_start: 0.8334 (pt0) cc_final: 0.7932 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 408
  average time/residue: 0.1502
  time to fit residues: 85.4178
Evaluate side-chains
  184 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  12 ASN
B 121 GLN
B 314 GLN
C  92 ASN
C 162 ASN
C 246 GLN
D 162 ASN
D 371 HIS
E 162 ASN
E 371 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.104071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.090091 restraints weight = 25271.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.21
r_work: 0.2980 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14960  Z= 0.150
  Angle     :  0.666   7.168  20305  Z= 0.344
  Chirality :  0.045   0.157   2255
  Planarity :  0.007   0.070   2595
  Dihedral  :  7.276  89.635   2085
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.66 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  7.86 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.20), residues: 1830
  helix:  0.37 (0.19), residues: 770
  sheet: -1.03 (0.30), residues: 235
  loop :  0.44 (0.23), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 210 
 TYR   0.016   0.001   TYR D 306 
 PHE   0.022   0.001   PHE A 352 
 TRP   0.009   0.001   TRP E  79 
 HIS   0.005   0.001   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (14960)
  covalent geometry    : angle       0.66575 /  0.34 (20305)
  hydrogen bonds       : bond        0.04464 /  2.94 (  755)
  hydrogen bonds       : angle       5.19940 /  3.67 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 261
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A  151 ILE cc_start: 0.9154 (mm) cc_final: 0.8793 (tp)
REVERT: A  246 GLN cc_start: 0.8347 (mt0) cc_final: 0.8117 (mt0)
REVERT: A  285 CYS cc_start: 0.7260 (m) cc_final: 0.6882 (m)
REVERT: A  297 ASN cc_start: 0.8460 (m110) cc_final: 0.8233 (t0)
REVERT: A  355 MET cc_start: 0.8780 (mmm) cc_final: 0.8342 (mmm)
REVERT: A  362 TYR cc_start: 0.8506 (t80) cc_final: 0.8249 (t80)
REVERT: B    9 VAL cc_start: 0.9153 (t) cc_final: 0.8825 (m)
REVERT: B  107 GLU cc_start: 0.8019 (pt0) cc_final: 0.7786 (pt0)
REVERT: B  192 ILE cc_start: 0.9184 (mm) cc_final: 0.8726 (pt)
REVERT: B  355 MET cc_start: 0.7748 (tpp) cc_final: 0.7510 (mmt)
REVERT: C  118 LYS cc_start: 0.8988 (mttt) cc_final: 0.8527 (mmmt)
REVERT: D   47 MET cc_start: 0.3927 (mmt) cc_final: 0.0631 (mmp)
REVERT: D   51 ASP cc_start: 0.8165 (p0) cc_final: 0.7600 (p0)
REVERT: D  113 LYS cc_start: 0.8683 (mttt) cc_final: 0.8426 (mttp)
REVERT: D  227 MET cc_start: 0.8622 (tpp) cc_final: 0.8382 (mtp)
REVERT: E   11 ASP cc_start: 0.8802 (t0) cc_final: 0.8520 (t70)
REVERT: E  113 LYS cc_start: 0.8577 (mttt) cc_final: 0.8263 (mtpm)
  outliers start: 21
  outliers final: 8
  residues processed: 275
  average time/residue: 0.1189
  time to fit residues: 49.1277
Evaluate side-chains
  193 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 185
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   96 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0470
   chunk 80 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 175 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0980
   overall best weight:    1.5482

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 121 GLN
B 162 ASN
C 246 GLN
D  12 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.100164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.086350 restraints weight = 26146.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.22
r_work: 0.2923 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14960  Z= 0.166
  Angle     :  0.628   6.110  20305  Z= 0.318
  Chirality :  0.044   0.151   2255
  Planarity :  0.005   0.049   2595
  Dihedral  :  6.281  64.337   2085
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.61 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.97 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.20), residues: 1830
  helix:  0.81 (0.19), residues: 770
  sheet: -0.88 (0.30), residues: 235
  loop :  0.65 (0.23), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 147 
 TYR   0.011   0.001   TYR D 198 
 PHE   0.011   0.001   PHE A 352 
 TRP   0.014   0.001   TRP D  79 
 HIS   0.006   0.001   HIS D  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.17 (14960)
  covalent geometry    : angle       0.62759 /  0.32 (20305)
  hydrogen bonds       : bond        0.04195 /  2.76 (  755)
  hydrogen bonds       : angle       4.76280 /  3.35 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  285 CYS cc_start: 0.7611 (m) cc_final: 0.7228 (m)
REVERT: A  298 VAL cc_start: 0.9055 (t) cc_final: 0.8794 (p)
REVERT: A  299 MET cc_start: 0.9127 (mmm) cc_final: 0.8860 (mmm)
REVERT: A  355 MET cc_start: 0.8765 (mmm) cc_final: 0.8317 (mmm)
REVERT: B    9 VAL cc_start: 0.9335 (t) cc_final: 0.8972 (m)
REVERT: B   71 ILE cc_start: 0.9364 (mt) cc_final: 0.9129 (mt)
REVERT: B   82 MET cc_start: 0.9221 (tpt) cc_final: 0.9001 (tpt)
REVERT: B  192 ILE cc_start: 0.9207 (mm) cc_final: 0.8795 (pt)
REVERT: C  118 LYS cc_start: 0.9059 (mttt) cc_final: 0.8579 (mmmt)
REVERT: D    9 VAL cc_start: 0.9437 (t) cc_final: 0.9080 (m)
REVERT: D   47 MET cc_start: 0.3245 (mmt) cc_final: -0.0056 (mmp)
REVERT: D   51 ASP cc_start: 0.8090 (p0) cc_final: 0.7574 (p0)
REVERT: D  136 ILE cc_start: 0.8788 (mm) cc_final: 0.8518 (tp)
REVERT: D  299 MET cc_start: 0.8890 (mmp) cc_final: 0.8597 (mmm)
REVERT: E   16 LEU cc_start: 0.9416 (mt) cc_final: 0.9199 (mp)
REVERT: E  120 THR cc_start: 0.9396 (m) cc_final: 0.9173 (p)
REVERT: E  248 ILE cc_start: 0.9201 (mt) cc_final: 0.8987 (tt)
  outliers start: 25
  outliers final: 13
  residues processed: 224
  average time/residue: 0.1127
  time to fit residues: 38.9866
Evaluate side-chains
  184 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  239 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 115 optimal weight:    9.9990
   chunk 178 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 246 GLN
C 371 HIS
D  12 ASN
D  40 HIS
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.096991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.083319 restraints weight = 26315.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.21
r_work: 0.2871 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14960  Z= 0.219
  Angle     :  0.657   8.851  20305  Z= 0.330
  Chirality :  0.046   0.152   2255
  Planarity :  0.005   0.041   2595
  Dihedral  :  6.257  60.281   2085
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.50 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.73 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.20), residues: 1830
  helix:  0.87 (0.19), residues: 765
  sheet: -0.72 (0.27), residues: 305
  loop :  0.65 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 147 
 TYR   0.011   0.001   TYR D 166 
 PHE   0.012   0.001   PHE A 255 
 TRP   0.013   0.002   TRP D  79 
 HIS   0.006   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.22 (14960)
  covalent geometry    : angle       0.65663 /  0.33 (20305)
  hydrogen bonds       : bond        0.04431 /  2.92 (  755)
  hydrogen bonds       : angle       4.71839 /  3.31 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A  299 MET cc_start: 0.9193 (mmm) cc_final: 0.8960 (mmm)
REVERT: B   71 ILE cc_start: 0.9465 (mt) cc_final: 0.9227 (mt)
REVERT: B   82 MET cc_start: 0.9217 (tpt) cc_final: 0.9011 (tpt)
REVERT: B  192 ILE cc_start: 0.9203 (mm) cc_final: 0.8788 (pt)
REVERT: D    9 VAL cc_start: 0.9446 (t) cc_final: 0.9096 (m)
REVERT: D   47 MET cc_start: 0.3525 (mmt) cc_final: 0.0386 (mmp)
REVERT: D   51 ASP cc_start: 0.8169 (p0) cc_final: 0.7732 (p0)
REVERT: D   82 MET cc_start: 0.9302 (tpt) cc_final: 0.8830 (tpt)
REVERT: D  136 ILE cc_start: 0.8745 (mm) cc_final: 0.8531 (tp)
REVERT: D  250 ILE cc_start: 0.9001 (mm) cc_final: 0.8747 (mt)
REVERT: E  120 THR cc_start: 0.9420 (m) cc_final: 0.9035 (p)
  outliers start: 40
  outliers final: 26
  residues processed: 216
  average time/residue: 0.1044
  time to fit residues: 35.6959
Evaluate side-chains
  201 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  345 ILE
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  129 VAL
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  226 GLU
Chi-restraints excluded: chain E residue  249 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 118 optimal weight:    0.7980
   chunk 10 optimal weight:    9.9990
   chunk 90 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 160 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 246 GLN
D  40 HIS
D 353 GLN
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.100104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.086504 restraints weight = 25932.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.22
r_work: 0.2929 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14960  Z= 0.118
  Angle     :  0.585   6.437  20305  Z= 0.289
  Chirality :  0.043   0.146   2255
  Planarity :  0.004   0.042   2595
  Dihedral  :  5.873  51.011   2085
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.22 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.40 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.20), residues: 1830
  helix:  1.06 (0.20), residues: 765
  sheet: -0.53 (0.28), residues: 305
  loop :  0.72 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 116 
 TYR   0.013   0.001   TYR C 306 
 PHE   0.007   0.001   PHE C  31 
 TRP   0.009   0.001   TRP D  79 
 HIS   0.007   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (14960)
  covalent geometry    : angle       0.58461 /  0.29 (20305)
  hydrogen bonds       : bond        0.03547 /  2.33 (  755)
  hydrogen bonds       : angle       4.49094 /  3.15 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (t160)
REVERT: A   40 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6878 (p-80)
REVERT: A  285 CYS cc_start: 0.7760 (m) cc_final: 0.7458 (m)
REVERT: A  355 MET cc_start: 0.8678 (mmm) cc_final: 0.8461 (mmm)
REVERT: B   82 MET cc_start: 0.9194 (tpt) cc_final: 0.8878 (tpp)
REVERT: B  192 ILE cc_start: 0.9169 (mm) cc_final: 0.8854 (pt)
REVERT: C  132 MET cc_start: 0.8704 (ttp) cc_final: 0.8417 (ttp)
REVERT: C  224 GLU cc_start: 0.8220 (tp30) cc_final: 0.8019 (tp30)
REVERT: D    9 VAL cc_start: 0.9396 (t) cc_final: 0.9034 (m)
REVERT: D   47 MET cc_start: 0.2775 (mmt) cc_final: 0.0042 (mmt)
REVERT: D   51 ASP cc_start: 0.8115 (p0) cc_final: 0.7679 (p0)
REVERT: D  136 ILE cc_start: 0.8742 (mm) cc_final: 0.8489 (tp)
REVERT: E   16 LEU cc_start: 0.9450 (mt) cc_final: 0.9225 (mp)
REVERT: E   47 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.3340 (tpt)
REVERT: E  120 THR cc_start: 0.9434 (m) cc_final: 0.9135 (p)
REVERT: E  151 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8666 (tp)
REVERT: E  246 GLN cc_start: 0.8778 (tt0) cc_final: 0.8245 (mt0)
REVERT: E  325 MET cc_start: 0.8848 (mmm) cc_final: 0.8282 (mmm)
  outliers start: 32
  outliers final: 18
  residues processed: 219
  average time/residue: 0.1079
  time to fit residues: 36.9838
Evaluate side-chains
  198 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  353 GLN
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  226 GLU
Chi-restraints excluded: chain E residue  288 ASP
Chi-restraints excluded: chain E residue  338 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 168 optimal weight:    0.9980
   chunk 35 optimal weight:    7.9990
   chunk 169 optimal weight:    0.8980
   chunk 184 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 154 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 GLN
D  12 ASN
D  40 HIS
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.097947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.084333 restraints weight = 26179.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.22
r_work: 0.2888 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14960  Z= 0.172
  Angle     :  0.607   6.418  20305  Z= 0.301
  Chirality :  0.044   0.151   2255
  Planarity :  0.004   0.038   2595
  Dihedral  :  5.838  50.837   2085
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.44 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.65 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.20), residues: 1830
  helix:  1.01 (0.20), residues: 765
  sheet: -0.07 (0.32), residues: 265
  loop :  0.43 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.008   0.001   TYR D 294 
 PHE   0.015   0.001   PHE E 223 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.007   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.17 (14960)
  covalent geometry    : angle       0.60717 /  0.30 (20305)
  hydrogen bonds       : bond        0.03878 /  2.56 (  755)
  hydrogen bonds       : angle       4.50976 /  3.16 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 181
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (t160)
REVERT: A   40 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.6983 (p-80)
REVERT: A  299 MET cc_start: 0.9011 (mmm) cc_final: 0.8795 (mmt)
REVERT: B    9 VAL cc_start: 0.9411 (t) cc_final: 0.9176 (m)
REVERT: B   82 MET cc_start: 0.9204 (tpt) cc_final: 0.8973 (tpt)
REVERT: B  192 ILE cc_start: 0.9168 (mm) cc_final: 0.8828 (pt)
REVERT: C  224 GLU cc_start: 0.8249 (tp30) cc_final: 0.8037 (tp30)
REVERT: D    9 VAL cc_start: 0.9412 (t) cc_final: 0.9053 (m)
REVERT: D   47 MET cc_start: 0.3035 (mmt) cc_final: 0.0297 (mmt)
REVERT: D   51 ASP cc_start: 0.8259 (p0) cc_final: 0.7600 (p0)
REVERT: D  136 ILE cc_start: 0.8719 (mm) cc_final: 0.8439 (tp)
REVERT: D  353 GLN cc_start: 0.7616 (mp10) cc_final: 0.7367 (mp10)
REVERT: E   16 LEU cc_start: 0.9457 (mt) cc_final: 0.9239 (mp)
REVERT: E   47 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.3351 (tpt)
REVERT: E  120 THR cc_start: 0.9443 (m) cc_final: 0.9048 (p)
REVERT: E  227 MET cc_start: 0.8528 (tpp) cc_final: 0.8297 (mpp)
REVERT: E  246 GLN cc_start: 0.8841 (tt0) cc_final: 0.8293 (mt0)
REVERT: E  355 MET cc_start: 0.8039 (tpp) cc_final: 0.7466 (mmt)
  outliers start: 45
  outliers final: 34
  residues processed: 212
  average time/residue: 0.1029
  time to fit residues: 34.3781
Evaluate side-chains
  205 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  229 THR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  289 ILE
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  226 GLU
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  288 ASP
Chi-restraints excluded: chain E residue  338 SER
Chi-restraints excluded: chain E residue  360 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 173 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   chunk 156 optimal weight:    0.4980
   chunk 139 optimal weight:    4.9990
   chunk 116 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 133 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 141 optimal weight:    3.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 246 GLN
D  12 ASN
D  40 HIS
E  12 ASN
E  40 HIS
E 353 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.100924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.087353 restraints weight = 25799.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.22
r_work: 0.2938 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14960  Z= 0.106
  Angle     :  0.573   6.032  20305  Z= 0.282
  Chirality :  0.042   0.150   2255
  Planarity :  0.004   0.041   2595
  Dihedral  :  5.646  49.412   2085
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.22 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.80 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.20), residues: 1830
  helix:  1.12 (0.20), residues: 765
  sheet:  0.04 (0.33), residues: 255
  loop :  0.49 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.011   0.001   TYR C 306 
 PHE   0.024   0.001   PHE C 223 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.006   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 (14960)
  covalent geometry    : angle       0.57298 /  0.28 (20305)
  hydrogen bonds       : bond        0.03358 /  2.21 (  755)
  hydrogen bonds       : angle       4.40644 /  3.08 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 193
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8537 (t160)
REVERT: A   40 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.6872 (p-80)
REVERT: B    9 VAL cc_start: 0.9351 (t) cc_final: 0.9082 (m)
REVERT: B   25 ASP cc_start: 0.8120 (p0) cc_final: 0.7829 (t0)
REVERT: B   82 MET cc_start: 0.9213 (tpt) cc_final: 0.8892 (tpp)
REVERT: B  192 ILE cc_start: 0.9194 (mm) cc_final: 0.8923 (pt)
REVERT: C  132 MET cc_start: 0.8734 (ttp) cc_final: 0.8452 (ttp)
REVERT: C  224 GLU cc_start: 0.7975 (tp30) cc_final: 0.7760 (tp30)
REVERT: D    9 VAL cc_start: 0.9343 (t) cc_final: 0.9016 (m)
REVERT: D   47 MET cc_start: 0.2776 (mmt) cc_final: 0.0438 (mmt)
REVERT: D   51 ASP cc_start: 0.8189 (p0) cc_final: 0.7547 (p0)
REVERT: E   16 LEU cc_start: 0.9438 (mt) cc_final: 0.9209 (mp)
REVERT: E   47 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.3415 (tpt)
REVERT: E  120 THR cc_start: 0.9435 (m) cc_final: 0.9063 (p)
REVERT: E  151 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8637 (tp)
REVERT: E  246 GLN cc_start: 0.8835 (tt0) cc_final: 0.8283 (mt0)
REVERT: E  354 GLN cc_start: 0.8848 (pt0) cc_final: 0.8502 (pt0)
REVERT: E  360 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8251 (mt0)
  outliers start: 42
  outliers final: 23
  residues processed: 222
  average time/residue: 0.1044
  time to fit residues: 36.9022
Evaluate side-chains
  201 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  239 SER
Chi-restraints excluded: chain E residue  288 ASP
Chi-restraints excluded: chain E residue  338 SER
Chi-restraints excluded: chain E residue  360 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 120 optimal weight:    0.0870
   chunk 165 optimal weight:    9.9990
   chunk 122 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 150 optimal weight:    0.9980
   chunk 175 optimal weight:    3.9990
   chunk 172 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   overall best weight:    2.0164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 GLN
D  12 ASN
D  40 HIS
D 353 GLN
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.097499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.083916 restraints weight = 26329.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.23
r_work: 0.2882 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.4648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14960  Z= 0.188
  Angle     :  0.621   7.083  20305  Z= 0.307
  Chirality :  0.044   0.152   2255
  Planarity :  0.004   0.037   2595
  Dihedral  :  5.788  49.144   2085
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.55 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.19 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.20), residues: 1830
  helix:  1.05 (0.20), residues: 760
  sheet: -0.05 (0.33), residues: 255
  loop :  0.36 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 147 
 TYR   0.009   0.001   TYR D 294 
 PHE   0.015   0.001   PHE E 223 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.006   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.19 (14960)
  covalent geometry    : angle       0.62126 /  0.31 (20305)
  hydrogen bonds       : bond        0.03944 /  2.60 (  755)
  hydrogen bonds       : angle       4.51120 /  3.16 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 182
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8538 (t160)
REVERT: A   40 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6962 (p-80)
REVERT: B    9 VAL cc_start: 0.9430 (t) cc_final: 0.9180 (m)
REVERT: B   82 MET cc_start: 0.9204 (tpt) cc_final: 0.8962 (tpt)
REVERT: B  192 ILE cc_start: 0.9181 (mm) cc_final: 0.8831 (pt)
REVERT: C  224 GLU cc_start: 0.8253 (tp30) cc_final: 0.8020 (tp30)
REVERT: D    9 VAL cc_start: 0.9401 (t) cc_final: 0.9023 (m)
REVERT: D   47 MET cc_start: 0.3070 (mmt) cc_final: 0.0601 (mmt)
REVERT: D   51 ASP cc_start: 0.8354 (p0) cc_final: 0.7708 (p0)
REVERT: D  136 ILE cc_start: 0.8713 (mm) cc_final: 0.8404 (tp)
REVERT: D  234 SER cc_start: 0.7383 (t) cc_final: 0.7162 (m)
REVERT: E   16 LEU cc_start: 0.9463 (mt) cc_final: 0.9250 (mp)
REVERT: E   47 MET cc_start: 0.5148 (OUTLIER) cc_final: 0.3448 (tpt)
REVERT: E  120 THR cc_start: 0.9452 (m) cc_final: 0.9164 (p)
REVERT: E  246 GLN cc_start: 0.8867 (tt0) cc_final: 0.8195 (mt0)
REVERT: E  354 GLN cc_start: 0.8903 (pt0) cc_final: 0.8555 (pt0)
  outliers start: 44
  outliers final: 34
  residues processed: 212
  average time/residue: 0.1093
  time to fit residues: 36.0925
Evaluate side-chains
  209 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 172
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain D residue  353 GLN
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  239 SER
Chi-restraints excluded: chain E residue  249 THR
Chi-restraints excluded: chain E residue  288 ASP
Chi-restraints excluded: chain E residue  338 SER
Chi-restraints excluded: chain E residue  360 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 179 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9980
   chunk 168 optimal weight:    0.8980
   overall best weight:    0.7194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  12 ASN
D  40 HIS
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.100702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.087203 restraints weight = 25886.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.21
r_work: 0.2940 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14960  Z= 0.110
  Angle     :  0.586   7.647  20305  Z= 0.287
  Chirality :  0.042   0.150   2255
  Planarity :  0.004   0.041   2595
  Dihedral  :  5.614  48.851   2085
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.44 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.95 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.20), residues: 1830
  helix:  1.14 (0.20), residues: 765
  sheet:  0.05 (0.33), residues: 255
  loop :  0.43 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  28 
 TYR   0.012   0.001   TYR C 306 
 PHE   0.008   0.001   PHE E 223 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.005   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 (14960)
  covalent geometry    : angle       0.58639 /  0.29 (20305)
  hydrogen bonds       : bond        0.03328 /  2.19 (  755)
  hydrogen bonds       : angle       4.40154 /  3.08 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 0.591 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8584 (t160)
REVERT: A   40 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6801 (p-80)
REVERT: B    9 VAL cc_start: 0.9374 (t) cc_final: 0.9109 (m)
REVERT: B   25 ASP cc_start: 0.8123 (p0) cc_final: 0.7812 (t0)
REVERT: B   82 MET cc_start: 0.9211 (tpt) cc_final: 0.8901 (tpp)
REVERT: B  192 ILE cc_start: 0.9208 (mm) cc_final: 0.8954 (pt)
REVERT: C  132 MET cc_start: 0.8610 (ttp) cc_final: 0.8319 (ttp)
REVERT: C  224 GLU cc_start: 0.8029 (tp30) cc_final: 0.7810 (tp30)
REVERT: D    9 VAL cc_start: 0.9306 (t) cc_final: 0.8946 (m)
REVERT: D   47 MET cc_start: 0.2834 (mmt) cc_final: 0.0299 (mmt)
REVERT: D   51 ASP cc_start: 0.8348 (p0) cc_final: 0.7715 (p0)
REVERT: D  132 MET cc_start: 0.8762 (ptm) cc_final: 0.8484 (ptm)
REVERT: D  299 MET cc_start: 0.8788 (mmp) cc_final: 0.8542 (mmm)
REVERT: D  353 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7254 (mp10)
REVERT: E   16 LEU cc_start: 0.9447 (mt) cc_final: 0.9223 (mp)
REVERT: E   34 ILE cc_start: 0.9468 (tp) cc_final: 0.9102 (pt)
REVERT: E   41 GLN cc_start: 0.8184 (tp40) cc_final: 0.7709 (mt0)
REVERT: E   47 MET cc_start: 0.4875 (OUTLIER) cc_final: 0.3418 (tpt)
REVERT: E  120 THR cc_start: 0.9449 (m) cc_final: 0.9068 (p)
REVERT: E  246 GLN cc_start: 0.8839 (tt0) cc_final: 0.8246 (mt0)
REVERT: E  353 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7818 (mm110)
REVERT: E  354 GLN cc_start: 0.8839 (pt0) cc_final: 0.8481 (pt0)
REVERT: E  360 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8263 (mt0)
  outliers start: 35
  outliers final: 26
  residues processed: 210
  average time/residue: 0.1026
  time to fit residues: 33.8247
Evaluate side-chains
  212 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain D residue  353 GLN
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  288 ASP
Chi-restraints excluded: chain E residue  360 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 183 optimal weight:    0.1980
   chunk 137 optimal weight:    0.0050
   chunk 135 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0670
   chunk 42 optimal weight:    2.9990
   chunk 129 optimal weight:    0.6980
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.2332

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  12 ASN
D 353 GLN
E  12 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.103558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.090105 restraints weight = 25628.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.22
r_work: 0.2988 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.4966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14960  Z= 0.095
  Angle     :  0.570   7.282  20305  Z= 0.278
  Chirality :  0.042   0.147   2255
  Planarity :  0.004   0.041   2595
  Dihedral  :  5.323  44.761   2085
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.11 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.40 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.20), residues: 1830
  helix:  1.27 (0.20), residues: 765
  sheet: -0.18 (0.29), residues: 325
  loop :  0.72 (0.24), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  28 
 TYR   0.012   0.001   TYR C 306 
 PHE   0.009   0.001   PHE D  31 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.005   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.09 (14960)
  covalent geometry    : angle       0.56952 /  0.28 (20305)
  hydrogen bonds       : bond        0.03058 /  2.02 (  755)
  hydrogen bonds       : angle       4.32702 /  3.03 ( 1875)

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

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 207
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6020 (p-80)
REVERT: A  334 GLU cc_start: 0.8345 (tt0) cc_final: 0.8075 (tt0)
REVERT: B    9 VAL cc_start: 0.9305 (t) cc_final: 0.9015 (m)
REVERT: B   25 ASP cc_start: 0.8020 (p0) cc_final: 0.7793 (t0)
REVERT: B  192 ILE cc_start: 0.9204 (mm) cc_final: 0.8926 (pt)
REVERT: C  132 MET cc_start: 0.8633 (ttp) cc_final: 0.8366 (ttp)
REVERT: C  227 MET cc_start: 0.8498 (mmm) cc_final: 0.8069 (tpp)
REVERT: D    9 VAL cc_start: 0.9289 (t) cc_final: 0.8936 (m)
REVERT: D   47 MET cc_start: 0.2489 (mmt) cc_final: 0.0262 (mmt)
REVERT: D   51 ASP cc_start: 0.8243 (p0) cc_final: 0.7625 (p0)
REVERT: D  132 MET cc_start: 0.8700 (ptm) cc_final: 0.8431 (ptm)
REVERT: D  176 MET cc_start: 0.8825 (mmm) cc_final: 0.8409 (mtt)
REVERT: D  299 MET cc_start: 0.8761 (mmp) cc_final: 0.8512 (mmm)
REVERT: E   16 LEU cc_start: 0.9428 (mt) cc_final: 0.9212 (mp)
REVERT: E   34 ILE cc_start: 0.9433 (tp) cc_final: 0.9144 (pt)
REVERT: E   41 GLN cc_start: 0.8186 (tp40) cc_final: 0.7717 (mt0)
REVERT: E   47 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.3726 (tpt)
REVERT: E  120 THR cc_start: 0.9447 (m) cc_final: 0.9075 (p)
REVERT: E  223 PHE cc_start: 0.7865 (t80) cc_final: 0.7631 (t80)
REVERT: E  246 GLN cc_start: 0.8844 (tt0) cc_final: 0.8241 (mt0)
REVERT: E  269 MET cc_start: 0.8982 (tpp) cc_final: 0.8644 (mtp)
REVERT: E  325 MET cc_start: 0.8306 (tpp) cc_final: 0.8087 (tpp)
REVERT: E  353 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7808 (mm110)
REVERT: E  354 GLN cc_start: 0.8791 (pt0) cc_final: 0.8359 (pt0)
REVERT: E  355 MET cc_start: 0.7532 (mmt) cc_final: 0.6855 (mmt)
REVERT: E  360 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8338 (mt0)
  outliers start: 28
  outliers final: 17
  residues processed: 226
  average time/residue: 0.1034
  time to fit residues: 36.7957
Evaluate side-chains
  211 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   47 MET
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain D residue  353 GLN
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  239 SER
Chi-restraints excluded: chain E residue  360 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 148 optimal weight:   10.0000
   chunk 168 optimal weight:    0.8980
   chunk 175 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   chunk 126 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  12 ASN
B 353 GLN
D  12 ASN
D  40 HIS
D 353 GLN
E  12 ASN
E  40 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.102157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.088707 restraints weight = 25854.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.22
r_work: 0.2964 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14960  Z= 0.110
  Angle     :  0.580   7.936  20305  Z= 0.282
  Chirality :  0.042   0.148   2255
  Planarity :  0.004   0.040   2595
  Dihedral  :  5.295  42.430   2085
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  3.22 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.36 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.20), residues: 1830
  helix:  1.28 (0.20), residues: 765
  sheet: -0.15 (0.29), residues: 325
  loop :  0.75 (0.24), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  28 
 TYR   0.009   0.001   TYR C 306 
 PHE   0.012   0.001   PHE E 352 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.005   0.001   HIS E 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 (14960)
  covalent geometry    : angle       0.58026 /  0.28 (20305)
  hydrogen bonds       : bond        0.03208 /  2.12 (  755)
  hydrogen bonds       : angle       4.30407 /  3.03 ( 1875)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3200.13 seconds
wall clock time: 55 minutes 50.60 seconds (3350.60 seconds total)