Starting phenix.real_space_refine
on Thu Mar  5 01:37:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rys_24747/03_2026/7rys_24747.cif"
  }
  resolution = 3.7
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6124 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      28      5.16       5
     C    8528      2.51       5
     N    2080      2.21       5
     O    2256      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12900
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3094
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 23, 'TRANS': 365}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 131
          Unusual residues: {'PGW': 7}
          Classifications: {'RNA': 1, 'undetermined': 7}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 248
          Unresolved non-hydrogen angles: 288
          Unresolved non-hydrogen dihedrals: 251
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PGW:plan-3': 6, 'PGW:plan-1': 5, 'PGW:plan-2': 5}
          Unresolved non-hydrogen planarities: 56
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.18, per 1000 atoms: 0.17
  Number of scatterers: 12900
  At special positions: 0
  Unit cell: (108.009, 108.009, 113.464, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P       8     15.00
     O    2256      8.00
     N    2080      7.00
     C    8528      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: 1.06
  Conformation dependent library (CDL) restraints added in 588.9 milliseconds
  

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2952

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 8 sheets defined
      62.7% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 36
      Proline residue:  A  31  - end of helix
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 4.109A  pdb=" N   LEU A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
      removed outlier: 4.193A  pdb=" N   LEU A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 3.998A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 113
      removed outlier: 3.791A  pdb=" N   VAL A 110 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.735A  pdb=" N   ALA A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 158
      removed outlier: 3.949A  pdb=" N   LEU A 137 " --> pdb=" O   ALA A 133 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A 157 " --> pdb=" O   CYS A 153 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU A 158 " --> pdb=" O   GLY A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 182
    Processing helix  chain 'A' and resid 193 through 223
      removed outlier: 4.220A  pdb=" N   ALA A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 246
      removed outlier: 3.639A  pdb=" N   LEU A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 236 " --> pdb=" O   HIS A 232 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 242 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 268
      removed outlier: 3.722A  pdb=" N   ILE A 257 " --> pdb=" O   GLN A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 277
    Processing helix  chain 'A' and resid 280 through 292
      removed outlier: 3.587A  pdb=" N   GLU A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 315
      removed outlier: 3.508A  pdb=" N   ILE A 314 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   LEU A 315 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 3.942A  pdb=" N   ILE A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 404
      removed outlier: 3.591A  pdb=" N   PHE A 397 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 418
      removed outlier: 3.543A  pdb=" N   ALA A 408 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 36
      Proline residue:  B  31  - end of helix
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 4.110A  pdb=" N   LEU B  49 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
      removed outlier: 4.193A  pdb=" N   LEU B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
      removed outlier: 3.999A  pdb=" N   LEU B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 113
      removed outlier: 3.791A  pdb=" N   VAL B 110 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG B 111 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 4.735A  pdb=" N   ALA B 120 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 158
      removed outlier: 3.949A  pdb=" N   LEU B 137 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS B 149 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER B 157 " --> pdb=" O   CYS B 153 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU B 158 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 182
    Processing helix  chain 'B' and resid 193 through 223
      removed outlier: 4.220A  pdb=" N   ALA B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLY B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER B 223 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 246
      removed outlier: 3.638A  pdb=" N   LEU B 231 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 236 " --> pdb=" O   HIS B 232 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE B 242 " --> pdb=" O   ARG B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 268
      removed outlier: 3.721A  pdb=" N   ILE B 257 " --> pdb=" O   GLN B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 277
    Processing helix  chain 'B' and resid 280 through 292
      removed outlier: 3.586A  pdb=" N   GLU B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
      removed outlier: 3.508A  pdb=" N   ILE B 314 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 373
      removed outlier: 3.942A  pdb=" N   ILE B 372 " --> pdb=" O   GLU B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 404
      removed outlier: 3.591A  pdb=" N   PHE B 397 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 418
      removed outlier: 3.543A  pdb=" N   ALA B 408 " --> pdb=" O   TYR B 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 36
      Proline residue:  C  31  - end of helix
    Processing helix  chain 'C' and resid 44 through 53
      removed outlier: 4.109A  pdb=" N   LEU C  49 " --> pdb=" O   PRO C  45 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA C  50 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 89
      removed outlier: 4.193A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 106
      removed outlier: 3.997A  pdb=" N   LEU C 106 " --> pdb=" O   SER C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 113
      removed outlier: 3.790A  pdb=" N   VAL C 110 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG C 111 " --> pdb=" O   SER C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 122
      removed outlier: 4.735A  pdb=" N   ALA C 120 " --> pdb=" O   ILE C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 158
      removed outlier: 3.949A  pdb=" N   LEU C 137 " --> pdb=" O   ALA C 133 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER C 157 " --> pdb=" O   CYS C 153 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU C 158 " --> pdb=" O   GLY C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 182
    Processing helix  chain 'C' and resid 193 through 223
      removed outlier: 4.219A  pdb=" N   ALA C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY C 212 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER C 223 " --> pdb=" O   ALA C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 246
      removed outlier: 3.639A  pdb=" N   LEU C 231 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL C 236 " --> pdb=" O   HIS C 232 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE C 242 " --> pdb=" O   ARG C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 268
      removed outlier: 3.721A  pdb=" N   ILE C 257 " --> pdb=" O   GLN C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 277
    Processing helix  chain 'C' and resid 280 through 292
      removed outlier: 3.587A  pdb=" N   GLU C 290 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 315
      removed outlier: 3.508A  pdb=" N   ILE C 314 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   LEU C 315 " --> pdb=" O   ARG C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 373
      removed outlier: 3.942A  pdb=" N   ILE C 372 " --> pdb=" O   GLU C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 393 through 404
      removed outlier: 3.591A  pdb=" N   PHE C 397 " --> pdb=" O   ASP C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 418
      removed outlier: 3.543A  pdb=" N   ALA C 408 " --> pdb=" O   TYR C 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 36
      Proline residue:  D  31  - end of helix
    Processing helix  chain 'D' and resid 44 through 53
      removed outlier: 4.109A  pdb=" N   LEU D  49 " --> pdb=" O   PRO D  45 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA D  50 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 89
      removed outlier: 4.194A  pdb=" N   LEU D  89 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 106
      removed outlier: 3.997A  pdb=" N   LEU D 106 " --> pdb=" O   SER D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 113
      removed outlier: 3.792A  pdb=" N   VAL D 110 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG D 111 " --> pdb=" O   SER D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 114 through 122
      removed outlier: 4.736A  pdb=" N   ALA D 120 " --> pdb=" O   ILE D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 158
      removed outlier: 3.949A  pdb=" N   LEU D 137 " --> pdb=" O   ALA D 133 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL D 141 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER D 157 " --> pdb=" O   CYS D 153 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU D 158 " --> pdb=" O   GLY D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 182
    Processing helix  chain 'D' and resid 193 through 223
      removed outlier: 4.220A  pdb=" N   ALA D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY D 212 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER D 223 " --> pdb=" O   ALA D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 246
      removed outlier: 3.638A  pdb=" N   LEU D 231 " --> pdb=" O   ALA D 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL D 236 " --> pdb=" O   HIS D 232 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 268
      removed outlier: 3.721A  pdb=" N   ILE D 257 " --> pdb=" O   GLN D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 277
    Processing helix  chain 'D' and resid 280 through 292
      removed outlier: 3.587A  pdb=" N   GLU D 290 " --> pdb=" O   ALA D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 315
      removed outlier: 3.507A  pdb=" N   ILE D 314 " --> pdb=" O   ILE D 310 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   LEU D 315 " --> pdb=" O   ARG D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 368 through 373
      removed outlier: 3.941A  pdb=" N   ILE D 372 " --> pdb=" O   GLU D 368 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 393 through 404
      removed outlier: 3.591A  pdb=" N   PHE D 397 " --> pdb=" O   ASP D 393 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 418
      removed outlier: 3.543A  pdb=" N   ALA D 408 " --> pdb=" O   TYR D 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322
      removed outlier: 7.105A  pdb=" N   ASP A 388 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL A 338 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A 339 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.701A  pdb=" N   VAL A 381 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322
      removed outlier: 7.105A  pdb=" N   ASP B 388 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL B 338 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 339 " --> pdb=" O   PHE B 366 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 330
      removed outlier: 6.700A  pdb=" N   VAL B 381 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322
      removed outlier: 7.105A  pdb=" N   ASP C 388 " --> pdb=" O   ASN C 342 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL C 338 " --> pdb=" O   LEU C 392 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR C 339 " --> pdb=" O   PHE C 366 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 330
      removed outlier: 6.700A  pdb=" N   VAL C 381 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322
      removed outlier: 7.105A  pdb=" N   ASP D 388 " --> pdb=" O   ASN D 342 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL D 338 " --> pdb=" O   LEU D 392 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR D 339 " --> pdb=" O   PHE D 366 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 330
      removed outlier: 6.701A  pdb=" N   VAL D 381 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)

    668 hydrogen bonds defined for protein.
    1932 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.69

  Time building geometry restraints manager: 1.44 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: 2043
        1.32 -     1.44: 3259
        1.44 -     1.57: 7790
        1.57 -     1.69: 16
        1.69 -     1.81: 48
  Bond restraints: 13156
  Sorted by residual:
  bond pdb=" C10 PGW D 503 "
       pdb=" C9  PGW D 503 "
    ideal  model  delta    sigma   weight residual
    1.333  1.509 -0.176 2.00e-02 2.50e+03 7.76e+01
  bond pdb=" C10 PGW B 503 "
       pdb=" C9  PGW B 503 "
    ideal  model  delta    sigma   weight residual
    1.333  1.509 -0.176 2.00e-02 2.50e+03 7.73e+01
  bond pdb=" C10 PGW A 503 "
       pdb=" C9  PGW A 503 "
    ideal  model  delta    sigma   weight residual
    1.333  1.508 -0.175 2.00e-02 2.50e+03 7.69e+01
  bond pdb=" C10 PGW C 503 "
       pdb=" C9  PGW C 503 "
    ideal  model  delta    sigma   weight residual
    1.333  1.508 -0.175 2.00e-02 2.50e+03 7.65e+01
  bond pdb=" C   GLY B 332 "
       pdb=" N   GLU B 333 "
    ideal  model  delta    sigma   weight residual
    1.330  1.424 -0.094 1.38e-02 5.25e+03 4.61e+01
  ... (remaining 13151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 17071
        2.58 -     5.16: 578
        5.16 -     7.73: 119
        7.73 -    10.31: 20
       10.31 -    12.89: 8
  Bond angle restraints: 17796
  Sorted by residual:
  angle pdb=" N   TYR C 259 "
        pdb=" CA  TYR C 259 "
        pdb=" C   TYR C 259 "
      ideal   model   delta    sigma   weight residual
     111.14  104.24    6.90 1.08e+00 8.57e-01 4.08e+01
  angle pdb=" N   TYR D 259 "
        pdb=" CA  TYR D 259 "
        pdb=" C   TYR D 259 "
      ideal   model   delta    sigma   weight residual
     111.14  104.25    6.89 1.08e+00 8.57e-01 4.07e+01
  angle pdb=" N   TYR A 259 "
        pdb=" CA  TYR A 259 "
        pdb=" C   TYR A 259 "
      ideal   model   delta    sigma   weight residual
     111.14  104.26    6.88 1.08e+00 8.57e-01 4.06e+01
  angle pdb=" N   TYR B 259 "
        pdb=" CA  TYR B 259 "
        pdb=" C   TYR B 259 "
      ideal   model   delta    sigma   weight residual
     111.14  104.30    6.84 1.08e+00 8.57e-01 4.01e+01
  angle pdb=" N   LEU A  98 "
        pdb=" CA  LEU A  98 "
        pdb=" C   LEU A  98 "
      ideal   model   delta    sigma   weight residual
     113.19  106.71    6.48 1.19e+00 7.06e-01 2.97e+01
  ... (remaining 17791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.90: 7800
       34.90 -    69.79: 172
       69.79 -   104.69: 8
      104.69 -   139.58: 24
      139.58 -   174.48: 8
  Dihedral angle restraints: 8012
    sinusoidal: 3444
      harmonic: 4568
  Sorted by residual:
  dihedral pdb=" C07 PGW B 503 "
           pdb=" C06 PGW B 503 "
           pdb=" C10 PGW B 503 "
           pdb=" C9  PGW B 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     110.06  -64.42  174.48     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C07 PGW C 503 "
           pdb=" C06 PGW C 503 "
           pdb=" C10 PGW C 503 "
           pdb=" C9  PGW C 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     110.06  -64.39  174.45     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C07 PGW A 503 "
           pdb=" C06 PGW A 503 "
           pdb=" C10 PGW A 503 "
           pdb=" C9  PGW A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     110.06  -64.39  174.45     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 8009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1443
       0.048 -    0.096: 462
       0.096 -    0.144: 107
       0.144 -    0.192: 44
       0.192 -    0.240: 28
  Chirality restraints: 2084
  Sorted by residual:
  chirality pdb=" CA  LEU C  98 "
            pdb=" N   LEU C  98 "
            pdb=" C   LEU C  98 "
            pdb=" CB  LEU C  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  LEU A  98 "
            pdb=" N   LEU A  98 "
            pdb=" C   LEU A  98 "
            pdb=" CB  LEU A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  LEU B  98 "
            pdb=" N   LEU B  98 "
            pdb=" C   LEU B  98 "
            pdb=" CB  LEU B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 2081 not shown)

  Planarity restraints: 2156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW C 503 "   -0.067 2.00e-02 2.50e+03   6.68e-02 4.47e+01
        pdb=" C10 PGW C 503 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  PGW C 503 "   -0.067 2.00e-02 2.50e+03
        pdb=" C9  PGW C 503 "    0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW A 503 "    0.067 2.00e-02 2.50e+03   6.68e-02 4.46e+01
        pdb=" C10 PGW A 503 "   -0.067 2.00e-02 2.50e+03
        pdb=" C8  PGW A 503 "    0.067 2.00e-02 2.50e+03
        pdb=" C9  PGW A 503 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW B 503 "   -0.067 2.00e-02 2.50e+03   6.67e-02 4.45e+01
        pdb=" C10 PGW B 503 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  PGW B 503 "   -0.067 2.00e-02 2.50e+03
        pdb=" C9  PGW B 503 "    0.066 2.00e-02 2.50e+03
  ... (remaining 2153 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2428
        2.78 -     3.31: 12335
        3.31 -     3.84: 19546
        3.84 -     4.37: 22523
        4.37 -     4.90: 38964
  Nonbonded interactions: 95796
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 308 "
            pdb=" OH  TYR B 404 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLU A 308 "
            pdb=" OH  TYR A 404 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLU C 308 "
            pdb=" OH  TYR C 404 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OE1 GLU D 308 "
            pdb=" OH  TYR D 404 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR B 186 "
            pdb=" OG1 THR C 180 "
     model   vdw
     2.254 3.040
  ... (remaining 95791 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.070
  Set scattering table:                    0.030
  Process input model:                     11.410
  Find NCS groups from input model:        0.090
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
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      :  0.007   0.176  13156  Z= 0.444
  Angle     :  1.122  12.890  17796  Z= 0.655
  Chirality :  0.056   0.240   2084
  Planarity :  0.008   0.067   2156
  Dihedral  : 18.240 174.480   5060
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.80 %
    Favored  : 97.90 %
  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: -1.42 (0.21), residues: 1532
  helix: -0.45 (0.17), residues: 936
  sheet: -1.24 (0.42), residues: 112
  loop : -1.61 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 399 
 TYR   0.014   0.002   TYR A 259 
 PHE   0.030   0.003   PHE D 340 
 TRP   0.011   0.001   TRP D 264 
 HIS   0.007   0.002   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 (13156)
  covalent geometry    : angle       1.12188 (17796)
  hydrogen bonds       : bond        0.18075 (  668)
  hydrogen bonds       : angle       6.62188 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 223
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  229 LYS cc_start: 0.8680 (tptt) cc_final: 0.8464 (tptt)
REVERT: A  261 ASP cc_start: 0.7486 (t70) cc_final: 0.7195 (t0)
REVERT: B  261 ASP cc_start: 0.7680 (t70) cc_final: 0.7390 (t0)
REVERT: C  261 ASP cc_start: 0.7734 (t70) cc_final: 0.7444 (t0)
REVERT: D  341 ILE cc_start: 0.8245 (mm) cc_final: 0.8039 (mm)
  outliers start: 4
  outliers final: 0
  residues processed: 227
  average time/residue: 0.1184
  time to fit residues: 37.7065
Evaluate side-chains
  167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0670
   chunk 122 optimal weight:    0.0000
   chunk 91 optimal weight:    0.0040
   chunk 149 optimal weight:    7.9990
   overall best weight:    0.3134

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 253 GLN
B 131 ASN
B 364 GLN
C 131 ASN
D 131 ASN
D 253 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.213914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.195738 restraints weight = 14889.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.195319 restraints weight = 17643.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.194057 restraints weight = 18461.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.192892 restraints weight = 18335.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.191599 restraints weight = 17263.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13156  Z= 0.131
  Angle     :  0.706   8.753  17796  Z= 0.332
  Chirality :  0.042   0.166   2084
  Planarity :  0.005   0.048   2156
  Dihedral  : 16.773 150.951   2112
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.59 %
    Favored  : 88.96 %
  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: -0.72 (0.22), residues: 1532
  helix:  0.25 (0.18), residues: 944
  sheet: -1.80 (0.35), residues: 132
  loop : -1.39 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 417 
 TYR   0.013   0.001   TYR D 357 
 PHE   0.020   0.002   PHE D 365 
 TRP   0.009   0.001   TRP C 264 
 HIS   0.006   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13156)
  covalent geometry    : angle       0.70596 (17796)
  hydrogen bonds       : bond        0.04475 (  668)
  hydrogen bonds       : angle       4.46951 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 199
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  103 PRO cc_start: 0.6842 (Cg_endo) cc_final: 0.6621 (Cg_exo)
REVERT: A  261 ASP cc_start: 0.7460 (t70) cc_final: 0.7115 (t0)
REVERT: B  261 ASP cc_start: 0.7568 (t70) cc_final: 0.7214 (t0)
REVERT: C  261 ASP cc_start: 0.7597 (t70) cc_final: 0.7322 (t0)
REVERT: D  210 MET cc_start: 0.6733 (mpp) cc_final: 0.6234 (mpp)
  outliers start: 6
  outliers final: 3
  residues processed: 202
  average time/residue: 0.1175
  time to fit residues: 33.6383
Evaluate side-chains
  162 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 159
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain D residue  140 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0040
   chunk 95 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 118 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 126 optimal weight:    0.5980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
B  99 HIS
C  99 HIS
** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  99 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.212678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.194723 restraints weight = 14827.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.190047 restraints weight = 20772.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.189336 restraints weight = 23024.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.188521 restraints weight = 20094.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.187464 restraints weight = 18740.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13156  Z= 0.125
  Angle     :  0.660   8.100  17796  Z= 0.308
  Chirality :  0.041   0.150   2084
  Planarity :  0.005   0.047   2156
  Dihedral  : 14.609 133.974   2112
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 12.91 %
    Favored  : 86.26 %
  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: -0.39 (0.22), residues: 1532
  helix:  0.50 (0.18), residues: 956
  sheet: -1.79 (0.36), residues: 124
  loop : -1.26 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 330 
 TYR   0.011   0.001   TYR D 357 
 PHE   0.020   0.001   PHE D 365 
 TRP   0.007   0.001   TRP B 264 
 HIS   0.002   0.001   HIS A 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13156)
  covalent geometry    : angle       0.65963 (17796)
  hydrogen bonds       : bond        0.03798 (  668)
  hydrogen bonds       : angle       4.10562 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 186
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 PRO cc_start: 0.6824 (Cg_endo) cc_final: 0.6623 (Cg_exo)
REVERT: A  261 ASP cc_start: 0.7541 (t70) cc_final: 0.7210 (t0)
REVERT: B  261 ASP cc_start: 0.7576 (t70) cc_final: 0.7226 (t0)
REVERT: B  277 LYS cc_start: 0.8195 (pttt) cc_final: 0.7377 (mttp)
REVERT: C  261 ASP cc_start: 0.7637 (t70) cc_final: 0.7332 (t0)
REVERT: D  210 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6561 (mpp)
  outliers start: 11
  outliers final: 5
  residues processed: 194
  average time/residue: 0.1309
  time to fit residues: 35.6371
Evaluate side-chains
  166 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  210 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 109 optimal weight:    0.0000
   chunk 37 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 128 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 104 optimal weight:    0.4980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
D  99 HIS
D 364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.212076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.193484 restraints weight = 14906.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.192693 restraints weight = 18102.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.191983 restraints weight = 17263.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.191349 restraints weight = 16567.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.190810 restraints weight = 16649.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13156  Z= 0.125
  Angle     :  0.650   7.863  17796  Z= 0.303
  Chirality :  0.041   0.161   2084
  Planarity :  0.005   0.053   2156
  Dihedral  : 13.295 133.511   2112
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.89 %
    Favored  : 84.83 %
  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: -0.23 (0.22), residues: 1532
  helix:  0.61 (0.18), residues: 960
  sheet: -1.78 (0.35), residues: 124
  loop : -1.14 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 399 
 TYR   0.010   0.001   TYR D 175 
 PHE   0.017   0.001   PHE D 365 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.002   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13156)
  covalent geometry    : angle       0.64958 (17796)
  hydrogen bonds       : bond        0.03595 (  668)
  hydrogen bonds       : angle       3.97914 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 PRO cc_start: 0.6784 (Cg_endo) cc_final: 0.6575 (Cg_exo)
REVERT: A  210 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6736 (mpp)
REVERT: A  261 ASP cc_start: 0.7514 (t70) cc_final: 0.7150 (t0)
REVERT: A  265 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6731 (tt0)
REVERT: B  261 ASP cc_start: 0.7555 (t70) cc_final: 0.7226 (t0)
REVERT: B  277 LYS cc_start: 0.8232 (pttt) cc_final: 0.7396 (mttp)
REVERT: C  210 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6760 (mpp)
REVERT: C  261 ASP cc_start: 0.7538 (t70) cc_final: 0.7207 (t0)
REVERT: D  210 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6545 (mpp)
  outliers start: 17
  outliers final: 7
  residues processed: 187
  average time/residue: 0.1244
  time to fit residues: 32.5996
Evaluate side-chains
  165 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  210 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 113 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
D 364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.209188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.191537 restraints weight = 14758.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.189692 restraints weight = 17097.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.188145 restraints weight = 16885.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.187201 restraints weight = 16142.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.186185 restraints weight = 16112.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13156  Z= 0.159
  Angle     :  0.670   7.755  17796  Z= 0.316
  Chirality :  0.043   0.149   2084
  Planarity :  0.005   0.057   2156
  Dihedral  : 12.439 133.567   2112
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.39 %
    Favored  : 82.73 %
  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: -0.21 (0.22), residues: 1532
  helix:  0.63 (0.18), residues: 956
  sheet: -1.66 (0.36), residues: 124
  loop : -1.18 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 399 
 TYR   0.013   0.001   TYR C 175 
 PHE   0.014   0.002   PHE D 365 
 TRP   0.006   0.001   TRP D  15 
 HIS   0.003   0.001   HIS C 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (13156)
  covalent geometry    : angle       0.67036 (17796)
  hydrogen bonds       : bond        0.03893 (  668)
  hydrogen bonds       : angle       4.05855 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6673 (mpp)
REVERT: A  261 ASP cc_start: 0.7555 (t70) cc_final: 0.7203 (t0)
REVERT: B  114 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8169 (ttmm)
REVERT: B  210 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6436 (mpp)
REVERT: B  261 ASP cc_start: 0.7574 (t70) cc_final: 0.7214 (t0)
REVERT: B  364 GLN cc_start: 0.7156 (mt0) cc_final: 0.6887 (mt0)
REVERT: C  210 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6753 (mpp)
  outliers start: 25
  outliers final: 17
  residues processed: 185
  average time/residue: 0.1240
  time to fit residues: 32.3467
Evaluate side-chains
  178 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  289 MET
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  210 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0470
   chunk 136 optimal weight:    0.9990
   chunk 140 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   overall best weight:    0.6682

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
D 253 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.210699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.190659 restraints weight = 14693.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.190380 restraints weight = 17627.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.190123 restraints weight = 15330.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.189841 restraints weight = 15956.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.189668 restraints weight = 15844.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13156  Z= 0.128
  Angle     :  0.657   7.877  17796  Z= 0.307
  Chirality :  0.042   0.150   2084
  Planarity :  0.005   0.058   2156
  Dihedral  : 11.756 133.345   2112
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.52 %
    Favored  : 81.46 %
  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:  0.05 (0.22), residues: 1532
  helix:  0.81 (0.18), residues: 960
  sheet: -1.31 (0.38), residues: 124
  loop : -1.13 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 399 
 TYR   0.009   0.001   TYR A 175 
 PHE   0.016   0.001   PHE A 397 
 TRP   0.005   0.001   TRP B 176 
 HIS   0.002   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13156)
  covalent geometry    : angle       0.65681 (17796)
  hydrogen bonds       : bond        0.03459 (  668)
  hydrogen bonds       : angle       3.88584 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  261 ASP cc_start: 0.7581 (t70) cc_final: 0.7269 (t0)
REVERT: B  210 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6697 (mpp)
REVERT: B  261 ASP cc_start: 0.7605 (t70) cc_final: 0.7280 (t0)
REVERT: C  210 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6574 (mpp)
REVERT: D   99 HIS cc_start: 0.5244 (m-70) cc_final: 0.5037 (m170)
REVERT: D  210 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6283 (mpp)
  outliers start: 27
  outliers final: 16
  residues processed: 185
  average time/residue: 0.1284
  time to fit residues: 33.2285
Evaluate side-chains
  170 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  381 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 146 optimal weight:    0.0050
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 110 optimal weight:    0.4980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.210695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.191191 restraints weight = 14660.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.186568 restraints weight = 20459.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.185130 restraints weight = 23494.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.184264 restraints weight = 21919.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.183682 restraints weight = 19358.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13156  Z= 0.129
  Angle     :  0.665   7.996  17796  Z= 0.310
  Chirality :  0.042   0.150   2084
  Planarity :  0.005   0.052   2156
  Dihedral  : 11.372 133.330   2112
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.34 %
    Favored  : 80.56 %
  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:  0.16 (0.22), residues: 1532
  helix:  0.88 (0.18), residues: 960
  sheet: -1.18 (0.39), residues: 124
  loop : -1.06 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 399 
 TYR   0.010   0.001   TYR B 175 
 PHE   0.020   0.001   PHE D 397 
 TRP   0.005   0.001   TRP D  15 
 HIS   0.002   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13156)
  covalent geometry    : angle       0.66478 (17796)
  hydrogen bonds       : bond        0.03427 (  668)
  hydrogen bonds       : angle       3.86393 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7228 (tpp) cc_final: 0.6907 (mpp)
REVERT: A  261 ASP cc_start: 0.7633 (t70) cc_final: 0.7322 (t0)
REVERT: B  210 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6768 (mpp)
REVERT: B  261 ASP cc_start: 0.7622 (t70) cc_final: 0.7289 (t0)
REVERT: B  310 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7280 (mt)
REVERT: C  210 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6770 (mpp)
REVERT: C  310 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7273 (mt)
REVERT: D   99 HIS cc_start: 0.5353 (m-70) cc_final: 0.5135 (m170)
REVERT: D  210 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6233 (mpp)
  outliers start: 28
  outliers final: 19
  residues processed: 166
  average time/residue: 0.1195
  time to fit residues: 28.4172
Evaluate side-chains
  167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  381 VAL
Chi-restraints excluded: chain D residue  392 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 130 optimal weight:    0.0970
   chunk 81 optimal weight:    0.0040
   chunk 48 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 150 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 138 optimal weight:    4.9990
   chunk 140 optimal weight:    0.9980
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.212184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.195608 restraints weight = 14444.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.192461 restraints weight = 19320.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.190276 restraints weight = 25185.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.189573 restraints weight = 23289.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.189157 restraints weight = 19598.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13156  Z= 0.120
  Angle     :  0.657   8.500  17796  Z= 0.305
  Chirality :  0.041   0.150   2084
  Planarity :  0.005   0.049   2156
  Dihedral  : 10.986 133.615   2112
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.87 %
    Favored  : 80.03 %
  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:  0.32 (0.22), residues: 1532
  helix:  0.98 (0.18), residues: 960
  sheet: -0.96 (0.41), residues: 124
  loop : -0.99 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 399 
 TYR   0.009   0.001   TYR B 357 
 PHE   0.021   0.001   PHE D 397 
 TRP   0.005   0.001   TRP B 176 
 HIS   0.002   0.000   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (13156)
  covalent geometry    : angle       0.65662 (17796)
  hydrogen bonds       : bond        0.03175 (  668)
  hydrogen bonds       : angle       3.74529 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6979 (mpp)
REVERT: A  261 ASP cc_start: 0.7541 (t70) cc_final: 0.7259 (t0)
REVERT: A  310 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: B  210 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6566 (mpp)
REVERT: B  261 ASP cc_start: 0.7537 (t70) cc_final: 0.7233 (t0)
REVERT: B  310 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7225 (mt)
REVERT: B  388 ASP cc_start: 0.7782 (p0) cc_final: 0.7579 (p0)
REVERT: C  210 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6672 (mpp)
REVERT: C  310 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7218 (mt)
REVERT: D  210 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6373 (mpp)
  outliers start: 28
  outliers final: 18
  residues processed: 167
  average time/residue: 0.1252
  time to fit residues: 29.3892
Evaluate side-chains
  171 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  338 VAL
Chi-restraints excluded: chain D residue  392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 146 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0770
   chunk 83 optimal weight:    4.9990
   chunk 134 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 141 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0980
   chunk 13 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.212113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.193398 restraints weight = 14625.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.191729 restraints weight = 17495.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.191114 restraints weight = 16823.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.190629 restraints weight = 16055.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.190301 restraints weight = 16749.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13156  Z= 0.121
  Angle     :  0.657   7.881  17796  Z= 0.305
  Chirality :  0.041   0.157   2084
  Planarity :  0.005   0.052   2156
  Dihedral  : 10.852 133.487   2112
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.09 %
    Favored  : 80.03 %
  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:  0.36 (0.22), residues: 1532
  helix:  1.00 (0.18), residues: 960
  sheet: -0.89 (0.41), residues: 124
  loop : -0.96 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 399 
 TYR   0.009   0.001   TYR B 175 
 PHE   0.013   0.001   PHE A 366 
 TRP   0.004   0.001   TRP B 264 
 HIS   0.002   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (13156)
  covalent geometry    : angle       0.65723 (17796)
  hydrogen bonds       : bond        0.03189 (  668)
  hydrogen bonds       : angle       3.72727 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7141 (tpp) cc_final: 0.6876 (mpp)
REVERT: A  261 ASP cc_start: 0.7544 (t70) cc_final: 0.7271 (t0)
REVERT: A  310 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7216 (mt)
REVERT: B  210 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6446 (mpp)
REVERT: B  261 ASP cc_start: 0.7540 (t70) cc_final: 0.7251 (t0)
REVERT: B  310 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7237 (mt)
REVERT: C  210 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6571 (mpp)
REVERT: C  310 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7202 (mt)
REVERT: D  210 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6222 (mpp)
  outliers start: 25
  outliers final: 18
  residues processed: 158
  average time/residue: 0.1166
  time to fit residues: 26.0630
Evaluate side-chains
  163 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  338 VAL
Chi-restraints excluded: chain D residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 140 optimal weight:    3.9990
   chunk 110 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0030
   chunk 50 optimal weight:    0.0270
   chunk 79 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.7452

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.211362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.191608 restraints weight = 14705.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.189070 restraints weight = 18833.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.186209 restraints weight = 23954.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.184832 restraints weight = 23095.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.183422 restraints weight = 23678.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13156  Z= 0.133
  Angle     :  0.675   7.983  17796  Z= 0.316
  Chirality :  0.042   0.185   2084
  Planarity :  0.005   0.043   2156
  Dihedral  : 10.837 133.415   2112
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.17 %
    Favored  : 79.88 %
  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:  0.31 (0.22), residues: 1532
  helix:  0.96 (0.18), residues: 960
  sheet: -0.94 (0.42), residues: 124
  loop : -0.97 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 399 
 TYR   0.010   0.001   TYR A 175 
 PHE   0.013   0.001   PHE B 397 
 TRP   0.004   0.001   TRP D  15 
 HIS   0.002   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13156)
  covalent geometry    : angle       0.67454 (17796)
  hydrogen bonds       : bond        0.03351 (  668)
  hydrogen bonds       : angle       3.74117 ( 1932)

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

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

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3064 Ramachandran restraints generated.
    1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 MET cc_start: 0.7193 (tpp) cc_final: 0.6970 (mpp)
REVERT: A  261 ASP cc_start: 0.7617 (t70) cc_final: 0.7325 (t0)
REVERT: A  310 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7337 (mt)
REVERT: B  210 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6594 (mpp)
REVERT: B  261 ASP cc_start: 0.7587 (t70) cc_final: 0.7271 (t0)
REVERT: B  310 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7305 (mt)
REVERT: B  354 LYS cc_start: 0.6304 (mmtm) cc_final: 0.6084 (mmtm)
REVERT: C  210 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6696 (mpp)
REVERT: C  310 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7294 (mt)
REVERT: D  210 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6290 (mpp)
  outliers start: 26
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1242
  time to fit residues: 26.5731
Evaluate side-chains
  161 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  210 MET
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  156 MET
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  210 MET
Chi-restraints excluded: chain D residue  338 VAL
Chi-restraints excluded: chain D residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 110 optimal weight:    9.9990
   chunk 103 optimal weight:    0.2980
   chunk 139 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.210108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.189946 restraints weight = 14635.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.189440 restraints weight = 17409.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.189158 restraints weight = 16608.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.188751 restraints weight = 15470.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.188242 restraints weight = 17155.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13156  Z= 0.150
  Angle     :  0.694  13.809  17796  Z= 0.322
  Chirality :  0.043   0.169   2084
  Planarity :  0.005   0.043   2156
  Dihedral  : 10.951 133.320   2112
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.17 %
    Favored  : 79.80 %
  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:  0.22 (0.22), residues: 1532
  helix:  0.89 (0.18), residues: 960
  sheet: -0.96 (0.41), residues: 124
  loop : -0.98 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 399 
 TYR   0.012   0.001   TYR C 175 
 PHE   0.013   0.001   PHE B 397 
 TRP   0.005   0.001   TRP C  15 
 HIS   0.002   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (13156)
  covalent geometry    : angle       0.69355 (17796)
  hydrogen bonds       : bond        0.03573 (  668)
  hydrogen bonds       : angle       3.81572 ( 1932)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1786.65 seconds
wall clock time: 31 minutes 37.83 seconds (1897.83 seconds total)