Starting phenix.real_space_refine
on Wed Mar  4 20:40:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6z7q_11112/03_2026/6z7q_11112.cif"
  }
  resolution = 3.8
  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=   0.003 sd=   0.975
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   10575      2.51       5
     N    2880      2.21       5
     O    3150      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16665
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3333
          Classifications: {'peptide': 416}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 389}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 2.94, per 1000 atoms: 0.18
  Number of scatterers: 16665
  At special positions: 0
  Unit cell: (121.797, 122.838, 111.387, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    3150      8.00
     N    2880      7.00
     C   10575      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: 1.70
  Conformation dependent library (CDL) restraints added in 720.9 milliseconds
  

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3950

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 35 sheets defined
      7.7% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 172 through 190
      removed outlier: 3.503A  pdb=" N   ILE A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP A 178 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN A 182 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   VAL A 185 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR A 188 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
      removed outlier: 3.502A  pdb=" N   GLU A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 292 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   GLN A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 190
      removed outlier: 3.503A  pdb=" N   ILE B 177 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP B 178 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ASN B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL B 185 " --> pdb=" O   ASN B 181 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR B 188 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
      removed outlier: 3.502A  pdb=" N   GLU B 289 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE B 292 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   GLN B 293 " --> pdb=" O   GLU B 289 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS B 294 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 190
      removed outlier: 3.504A  pdb=" N   ILE C 177 " --> pdb=" O   GLU C 173 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP C 178 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN C 182 " --> pdb=" O   ASP C 178 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL C 185 " --> pdb=" O   ASN C 181 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR C 188 " --> pdb=" O   ILE C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 296
      removed outlier: 3.502A  pdb=" N   GLU C 289 " --> pdb=" O   VAL C 285 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA C 290 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE C 292 " --> pdb=" O   TYR C 288 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   GLN C 293 " --> pdb=" O   GLU C 289 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS C 294 " --> pdb=" O   ALA C 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 190
      removed outlier: 3.504A  pdb=" N   ILE D 177 " --> pdb=" O   GLU D 173 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN D 182 " --> pdb=" O   ASP D 178 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL D 185 " --> pdb=" O   ASN D 181 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR D 188 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 296
      removed outlier: 3.502A  pdb=" N   GLU D 289 " --> pdb=" O   VAL D 285 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ALA D 290 " --> pdb=" O   ALA D 286 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE D 292 " --> pdb=" O   TYR D 288 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   GLN D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS D 294 " --> pdb=" O   ALA D 290 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 172 through 190
      removed outlier: 3.503A  pdb=" N   ILE E 177 " --> pdb=" O   GLU E 173 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP E 178 " --> pdb=" O   THR E 174 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN E 182 " --> pdb=" O   ASP E 178 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL E 185 " --> pdb=" O   ASN E 181 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR E 188 " --> pdb=" O   ILE E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 296
      removed outlier: 3.501A  pdb=" N   GLU E 289 " --> pdb=" O   VAL E 285 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ALA E 290 " --> pdb=" O   ALA E 286 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE E 292 " --> pdb=" O   TYR E 288 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   GLN E 293 " --> pdb=" O   GLU E 289 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LYS E 294 " --> pdb=" O   ALA E 290 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126
    Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 143
      removed outlier: 3.654A  pdb=" N   PHE A 141 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 148
    Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322
      removed outlier: 4.355A  pdb=" N   ASP A 322 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG A 326 " --> pdb=" O   ASP A 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 404
      removed outlier: 4.396A  pdb=" N   TRP A 376 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL A 402 " --> pdb=" O   VAL A 374 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   VAL A 374 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 413
      removed outlier: 3.567A  pdb=" N   VAL A 453 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 68
    Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 126
    Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 143
      removed outlier: 3.655A  pdb=" N   PHE B 141 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE B 164 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 148
    Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322
      removed outlier: 4.354A  pdb=" N   ASP B 322 " --> pdb=" O   ARG B 326 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG B 326 " --> pdb=" O   ASP B 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 404
      removed outlier: 4.396A  pdb=" N   TRP B 376 " --> pdb=" O   VAL B 400 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   VAL B 402 " --> pdb=" O   VAL B 374 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   VAL B 374 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 413
      removed outlier: 3.567A  pdb=" N   VAL B 453 " --> pdb=" O   LYS B 410 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 68
    Processing sheet with id=AB7, first strand: chain 'C' and resid 125 through 126
    Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 143
      removed outlier: 3.655A  pdb=" N   PHE C 141 " --> pdb=" O   PHE C 164 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE C 164 " --> pdb=" O   PHE C 141 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 148
    Processing sheet with id=AC1, first strand: chain 'C' and resid 321 through 322
      removed outlier: 4.355A  pdb=" N   ASP C 322 " --> pdb=" O   ARG C 326 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG C 326 " --> pdb=" O   ASP C 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 404
      removed outlier: 4.396A  pdb=" N   TRP C 376 " --> pdb=" O   VAL C 400 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL C 402 " --> pdb=" O   VAL C 374 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   VAL C 374 " --> pdb=" O   VAL C 402 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 413
      removed outlier: 3.568A  pdb=" N   VAL C 453 " --> pdb=" O   LYS C 410 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 68
    Processing sheet with id=AC5, first strand: chain 'D' and resid 125 through 126
    Processing sheet with id=AC6, first strand: chain 'D' and resid 140 through 143
      removed outlier: 3.655A  pdb=" N   PHE D 141 " --> pdb=" O   PHE D 164 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE D 164 " --> pdb=" O   PHE D 141 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 146 through 148
    Processing sheet with id=AC8, first strand: chain 'D' and resid 321 through 322
      removed outlier: 4.356A  pdb=" N   ASP D 322 " --> pdb=" O   ARG D 326 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'D' and resid 399 through 404
      removed outlier: 4.396A  pdb=" N   TRP D 376 " --> pdb=" O   VAL D 400 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL D 402 " --> pdb=" O   VAL D 374 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   VAL D 374 " --> pdb=" O   VAL D 402 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 410 through 413
      removed outlier: 3.568A  pdb=" N   VAL D 453 " --> pdb=" O   LYS D 410 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 67 through 68
    Processing sheet with id=AD3, first strand: chain 'E' and resid 125 through 126
    Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 143
      removed outlier: 3.654A  pdb=" N   PHE E 141 " --> pdb=" O   PHE E 164 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE E 164 " --> pdb=" O   PHE E 141 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 146 through 148
    Processing sheet with id=AD6, first strand: chain 'E' and resid 321 through 322
      removed outlier: 4.355A  pdb=" N   ASP E 322 " --> pdb=" O   ARG E 326 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG E 326 " --> pdb=" O   ASP E 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'E' and resid 399 through 404
      removed outlier: 4.396A  pdb=" N   TRP E 376 " --> pdb=" O   VAL E 400 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL E 402 " --> pdb=" O   VAL E 374 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   VAL E 374 " --> pdb=" O   VAL E 402 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 410 through 413
      removed outlier: 3.567A  pdb=" N   VAL E 453 " --> pdb=" O   LYS E 410 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5490
        1.34 -     1.46: 3821
        1.46 -     1.58: 7624
        1.58 -     1.70: 0
        1.70 -     1.81: 105
  Bond restraints: 17040
  Sorted by residual:
  bond pdb=" C   PHE E 232 "
       pdb=" N   HIS E 233 "
    ideal  model  delta    sigma   weight residual
    1.333  1.294  0.039 2.74e-02 1.33e+03 2.00e+00
  bond pdb=" C   PHE D 232 "
       pdb=" N   HIS D 233 "
    ideal  model  delta    sigma   weight residual
    1.333  1.294  0.039 2.74e-02 1.33e+03 1.98e+00
  bond pdb=" C   PHE B 232 "
       pdb=" N   HIS B 233 "
    ideal  model  delta    sigma   weight residual
    1.333  1.294  0.038 2.74e-02 1.33e+03 1.97e+00
  bond pdb=" C   PHE A 232 "
       pdb=" N   HIS A 233 "
    ideal  model  delta    sigma   weight residual
    1.333  1.294  0.038 2.74e-02 1.33e+03 1.96e+00
  bond pdb=" C   PHE C 232 "
       pdb=" N   HIS C 233 "
    ideal  model  delta    sigma   weight residual
    1.333  1.295  0.038 2.74e-02 1.33e+03 1.91e+00
  ... (remaining 17035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 20635
        1.12 -     2.25: 2030
        2.25 -     3.37: 383
        3.37 -     4.49: 87
        4.49 -     5.62: 40
  Bond angle restraints: 23175
  Sorted by residual:
  angle pdb=" N   LEU C  80 "
        pdb=" CA  LEU C  80 "
        pdb=" C   LEU C  80 "
      ideal   model   delta    sigma   weight residual
     112.97  110.14    2.83 1.06e+00 8.90e-01 7.14e+00
  angle pdb=" N   LEU B  80 "
        pdb=" CA  LEU B  80 "
        pdb=" C   LEU B  80 "
      ideal   model   delta    sigma   weight residual
     112.97  110.14    2.83 1.06e+00 8.90e-01 7.13e+00
  angle pdb=" N   LEU E  80 "
        pdb=" CA  LEU E  80 "
        pdb=" C   LEU E  80 "
      ideal   model   delta    sigma   weight residual
     112.97  110.16    2.81 1.06e+00 8.90e-01 7.01e+00
  angle pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
        pdb=" C   LEU A  80 "
      ideal   model   delta    sigma   weight residual
     112.97  110.17    2.80 1.06e+00 8.90e-01 6.98e+00
  angle pdb=" N   LEU D  80 "
        pdb=" CA  LEU D  80 "
        pdb=" C   LEU D  80 "
      ideal   model   delta    sigma   weight residual
     112.97  110.18    2.79 1.06e+00 8.90e-01 6.93e+00
  ... (remaining 23170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 9116
       17.00 -    34.00: 976
       34.00 -    51.01: 128
       51.01 -    68.01: 20
       68.01 -    85.01: 35
  Dihedral angle restraints: 10275
    sinusoidal: 4180
      harmonic: 6095
  Sorted by residual:
  dihedral pdb=" CA  PHE B  89 "
           pdb=" C   PHE B  89 "
           pdb=" N   GLN B  90 "
           pdb=" CA  GLN B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.05   24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  PHE A  89 "
           pdb=" C   PHE A  89 "
           pdb=" N   GLN A  90 "
           pdb=" CA  GLN A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.05   24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  PHE C  89 "
           pdb=" C   PHE C  89 "
           pdb=" N   GLN C  90 "
           pdb=" CA  GLN C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.06   24.94     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 10272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1350
       0.028 -    0.057: 740
       0.057 -    0.085: 270
       0.085 -    0.114: 195
       0.114 -    0.142: 40
  Chirality restraints: 2595
  Sorted by residual:
  chirality pdb=" CA  ILE A 257 "
            pdb=" N   ILE A 257 "
            pdb=" C   ILE A 257 "
            pdb=" CB  ILE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE E 257 "
            pdb=" N   ILE E 257 "
            pdb=" C   ILE E 257 "
            pdb=" CB  ILE E 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE C 257 "
            pdb=" N   ILE C 257 "
            pdb=" C   ILE C 257 "
            pdb=" CB  ILE C 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 2592 not shown)

  Planarity restraints: 3015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 279 "    0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO D 280 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 280 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 280 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 279 "   -0.032 5.00e-02 4.00e+02   4.78e-02 3.65e+00
        pdb=" N   PRO B 280 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 280 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 280 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 279 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.63e+00
        pdb=" N   PRO C 280 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 280 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 280 "    0.026 5.00e-02 4.00e+02
  ... (remaining 3012 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 1473
        2.72 -     3.27: 18501
        3.27 -     3.81: 25600
        3.81 -     4.36: 32484
        4.36 -     4.90: 52739
  Nonbonded interactions: 130797
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 205 "
            pdb=" O   ILE C 441 "
     model   vdw
     2.176 3.120
  nonbonded pdb=" NZ  LYS B 205 "
            pdb=" O   ILE B 441 "
     model   vdw
     2.176 3.120
  nonbonded pdb=" NZ  LYS D 205 "
            pdb=" O   ILE D 441 "
     model   vdw
     2.176 3.120
  nonbonded pdb=" NZ  LYS A 205 "
            pdb=" O   ILE A 441 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" NZ  LYS E 205 "
            pdb=" O   ILE E 441 "
     model   vdw
     2.177 3.120
  ... (remaining 130792 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.580
  Find NCS groups from input model:        0.130
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.006   0.039  17040  Z= 0.262
  Angle     :  0.771   5.618  23175  Z= 0.425
  Chirality :  0.046   0.142   2595
  Planarity :  0.005   0.048   3015
  Dihedral  : 14.472  85.010   6325
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  : 28.57 %
    Favored  : 70.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  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: -6.49 (0.14), residues: 2030
  helix: -5.04 (0.14), residues: 145
  sheet: -5.28 (0.13), residues: 485
  loop : -4.12 (0.14), residues: 1400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 116 
 TYR   0.012   0.002   TYR D  55 
 PHE   0.010   0.001   PHE B 412 
 TRP   0.009   0.002   TRP C 161 
 HIS   0.003   0.001   HIS B  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 (17040)
  covalent geometry    : angle       0.77069 (23175)
  hydrogen bonds       : bond        0.25115 (  180)
  hydrogen bonds       : angle      10.56038 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 361
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8811 (t0) cc_final: 0.8556 (t0)
REVERT: A  146 MET cc_start: 0.8487 (ttt) cc_final: 0.7449 (ttm)
REVERT: B  117 TRP cc_start: 0.9447 (m100) cc_final: 0.9216 (m100)
REVERT: B  146 MET cc_start: 0.8517 (ttt) cc_final: 0.8028 (ttm)
REVERT: B  171 TYR cc_start: 0.9149 (m-10) cc_final: 0.8890 (m-80)
REVERT: B  239 LEU cc_start: 0.8801 (tp) cc_final: 0.8418 (tp)
REVERT: C   63 ASP cc_start: 0.8617 (t0) cc_final: 0.8266 (t0)
REVERT: C  146 MET cc_start: 0.8372 (ttt) cc_final: 0.7577 (ttm)
REVERT: C  239 LEU cc_start: 0.9006 (tp) cc_final: 0.8547 (tp)
REVERT: D   63 ASP cc_start: 0.8710 (t0) cc_final: 0.8368 (t0)
REVERT: D   64 THR cc_start: 0.9310 (p) cc_final: 0.9098 (t)
REVERT: D   81 ASN cc_start: 0.8887 (t0) cc_final: 0.8667 (t0)
REVERT: D  125 LEU cc_start: 0.9137 (tp) cc_final: 0.8930 (tp)
REVERT: D  133 ASN cc_start: 0.9393 (p0) cc_final: 0.9097 (p0)
REVERT: D  146 MET cc_start: 0.8493 (ttt) cc_final: 0.7757 (ttm)
REVERT: D  239 LEU cc_start: 0.8752 (tp) cc_final: 0.8281 (tp)
REVERT: D  484 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7618 (mtm180)
REVERT: E  116 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8618 (tpt90)
REVERT: E  133 ASN cc_start: 0.9425 (p0) cc_final: 0.9175 (p0)
REVERT: E  146 MET cc_start: 0.8646 (ttt) cc_final: 0.8150 (ttm)
REVERT: E  317 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7968 (mm-30)
REVERT: E  455 GLU cc_start: 0.8634 (tp30) cc_final: 0.8331 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 361
  average time/residue: 0.1310
  time to fit residues: 71.9231
Evaluate side-chains
  233 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0470
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0270
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0970
   chunk 122 optimal weight:    9.9990
   overall best weight:    0.6136

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 GLN
A 333 ASN
A 416 GLN
B 333 ASN
C  81 ASN
C 333 ASN
D  81 ASN
** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 181 ASN
D 333 ASN
E  81 ASN
E 333 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.131781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116934 restraints weight = 26546.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.120381 restraints weight = 13687.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122659 restraints weight = 8458.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124181 restraints weight = 5914.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.125166 restraints weight = 4513.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17040  Z= 0.134
  Angle     :  0.771   8.672  23175  Z= 0.384
  Chirality :  0.047   0.162   2595
  Planarity :  0.005   0.043   3015
  Dihedral  :  6.648  27.059   2265
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 16.35 %
    Favored  : 83.40 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.24 %
    Favored  : 78.88 %
  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: -5.43 (0.16), residues: 2030
  helix: -3.52 (0.36), residues: 155
  sheet: -4.62 (0.17), residues: 420
  loop : -3.55 (0.14), residues: 1455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  66 
 TYR   0.020   0.001   TYR E  62 
 PHE   0.009   0.001   PHE D 344 
 TRP   0.010   0.001   TRP B 359 
 HIS   0.006   0.001   HIS D  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (17040)
  covalent geometry    : angle       0.77066 (23175)
  hydrogen bonds       : bond        0.04261 (  180)
  hydrogen bonds       : angle       6.15890 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 355
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 MET cc_start: 0.7978 (ttt) cc_final: 0.7659 (ttm)
REVERT: A  173 GLU cc_start: 0.8537 (tp30) cc_final: 0.8197 (tp30)
REVERT: A  201 ASP cc_start: 0.7984 (t0) cc_final: 0.7443 (t0)
REVERT: A  223 MET cc_start: 0.8367 (mmp) cc_final: 0.8084 (mmm)
REVERT: A  460 LEU cc_start: 0.8601 (tt) cc_final: 0.8378 (tt)
REVERT: B  122 LYS cc_start: 0.8659 (mttp) cc_final: 0.8228 (mtpp)
REVERT: B  146 MET cc_start: 0.7990 (ttt) cc_final: 0.7230 (ttm)
REVERT: B  181 ASN cc_start: 0.8164 (p0) cc_final: 0.7896 (t0)
REVERT: B  201 ASP cc_start: 0.8150 (t0) cc_final: 0.7290 (t0)
REVERT: B  223 MET cc_start: 0.8685 (mmm) cc_final: 0.8405 (mmm)
REVERT: B  460 LEU cc_start: 0.8687 (tt) cc_final: 0.8454 (tt)
REVERT: C  171 TYR cc_start: 0.8640 (m-10) cc_final: 0.8421 (m-10)
REVERT: C  327 SER cc_start: 0.9102 (m) cc_final: 0.8754 (t)
REVERT: C  380 ASP cc_start: 0.7867 (t0) cc_final: 0.7636 (t0)
REVERT: C  403 GLU cc_start: 0.8105 (mp0) cc_final: 0.7782 (mp0)
REVERT: D  116 ARG cc_start: 0.8530 (tpt170) cc_final: 0.8312 (tpt90)
REVERT: D  133 ASN cc_start: 0.9276 (p0) cc_final: 0.9030 (p0)
REVERT: D  171 TYR cc_start: 0.8673 (m-10) cc_final: 0.8352 (m-10)
REVERT: D  201 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7666 (m-30)
REVERT: D  223 MET cc_start: 0.8520 (mmp) cc_final: 0.8154 (mmm)
REVERT: D  284 ASP cc_start: 0.8402 (t0) cc_final: 0.8087 (t0)
REVERT: E  146 MET cc_start: 0.8204 (ttt) cc_final: 0.7790 (ttm)
REVERT: E  156 LEU cc_start: 0.8867 (tp) cc_final: 0.8569 (pp)
REVERT: E  201 ASP cc_start: 0.7957 (t0) cc_final: 0.7140 (t0)
REVERT: E  455 GLU cc_start: 0.8434 (tp30) cc_final: 0.8212 (mm-30)
  outliers start: 54
  outliers final: 24
  residues processed: 382
  average time/residue: 0.1213
  time to fit residues: 72.3589
Evaluate side-chains
  292 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 267
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  134 GLU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  201 ASP
Chi-restraints excluded: chain D residue  270 MET
Chi-restraints excluded: chain D residue  273 ASP
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  270 MET
Chi-restraints excluded: chain E residue  273 ASP
Chi-restraints excluded: chain E residue  283 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 194 optimal weight:    4.9990
   chunk 158 optimal weight:   10.0000
   chunk 171 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:   10.0000
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 GLN
** B  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 329 ASN
** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.127856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112290 restraints weight = 27190.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115679 restraints weight = 14476.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117842 restraints weight = 9184.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.119396 restraints weight = 6618.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.120417 restraints weight = 5135.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  17040  Z= 0.192
  Angle     :  0.748   8.886  23175  Z= 0.375
  Chirality :  0.047   0.191   2595
  Planarity :  0.005   0.043   3015
  Dihedral  :  6.301  27.007   2265
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.57 %
    Favored  : 81.43 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 19.36 %
    Favored  : 74.97 %
  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: -5.23 (0.16), residues: 2030
  helix: -3.29 (0.30), residues: 185
  sheet: -4.31 (0.18), residues: 465
  loop : -3.39 (0.15), residues: 1380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 484 
 TYR   0.022   0.002   TYR C  82 
 PHE   0.012   0.001   PHE D 232 
 TRP   0.010   0.002   TRP B 343 
 HIS   0.010   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (17040)
  covalent geometry    : angle       0.74841 (23175)
  hydrogen bonds       : bond        0.04104 (  180)
  hydrogen bonds       : angle       5.75965 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 106
    poor density    : 291
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 MET cc_start: 0.7973 (ttt) cc_final: 0.7271 (ttm)
REVERT: A  148 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: A  201 ASP cc_start: 0.8119 (t0) cc_final: 0.7264 (t0)
REVERT: A  223 MET cc_start: 0.8576 (mmp) cc_final: 0.8271 (mmm)
REVERT: A  362 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7193 (tp)
REVERT: A  460 LEU cc_start: 0.8682 (tt) cc_final: 0.8432 (tt)
REVERT: B  146 MET cc_start: 0.8104 (ttt) cc_final: 0.7427 (ttm)
REVERT: B  168 GLU cc_start: 0.7537 (mp0) cc_final: 0.7234 (mp0)
REVERT: B  171 TYR cc_start: 0.8684 (m-80) cc_final: 0.8395 (m-10)
REVERT: B  201 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7782 (t0)
REVERT: B  223 MET cc_start: 0.8734 (mmm) cc_final: 0.8427 (mmm)
REVERT: B  362 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7388 (tp)
REVERT: C   63 ASP cc_start: 0.8218 (t0) cc_final: 0.7825 (m-30)
REVERT: C   68 TYR cc_start: 0.8828 (m-80) cc_final: 0.8481 (m-80)
REVERT: C  146 MET cc_start: 0.8397 (ttp) cc_final: 0.7619 (ttt)
REVERT: C  201 ASP cc_start: 0.8158 (t70) cc_final: 0.7607 (t70)
REVERT: C  251 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8732 (tt)
REVERT: C  327 SER cc_start: 0.9062 (m) cc_final: 0.8749 (t)
REVERT: C  380 ASP cc_start: 0.7886 (t0) cc_final: 0.7640 (t0)
REVERT: D  145 LEU cc_start: 0.9373 (tp) cc_final: 0.9037 (mt)
REVERT: D  171 TYR cc_start: 0.8757 (m-10) cc_final: 0.8519 (m-10)
REVERT: D  201 ASP cc_start: 0.8083 (t0) cc_final: 0.7509 (t0)
REVERT: D  223 MET cc_start: 0.8740 (mmp) cc_final: 0.8447 (mmm)
REVERT: D  362 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7066 (tp)
REVERT: E  146 MET cc_start: 0.8180 (ttt) cc_final: 0.7332 (ttm)
REVERT: E  171 TYR cc_start: 0.8609 (m-80) cc_final: 0.8200 (m-10)
REVERT: E  201 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7553 (t0)
  outliers start: 106
  outliers final: 66
  residues processed: 358
  average time/residue: 0.1071
  time to fit residues: 62.7982
Evaluate side-chains
  324 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 252
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  251 LEU
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  270 MET
Chi-restraints excluded: chain D residue  273 ASP
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  137 SER
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  270 MET
Chi-restraints excluded: chain E residue  273 ASP
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 178 optimal weight:    0.8980
   chunk 200 optimal weight:    0.7980
   chunk 154 optimal weight:    0.0870
   chunk 163 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0970
   chunk 90 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 189 optimal weight:    4.9990
   chunk 155 optimal weight:    0.0030
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.3766

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 128 ASN
B 128 ASN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 HIS
C 128 ASN
C 181 ASN
** D  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 128 ASN
** E  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.139600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.124775 restraints weight = 26834.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128228 restraints weight = 13800.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130460 restraints weight = 8495.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.131963 restraints weight = 5940.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.132989 restraints weight = 4535.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17040  Z= 0.116
  Angle     :  0.693   9.498  23175  Z= 0.343
  Chirality :  0.045   0.188   2595
  Planarity :  0.005   0.041   3015
  Dihedral  :  5.778  25.109   2265
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 19.95 %
    Favored  : 74.39 %
  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: -4.85 (0.16), residues: 2030
  helix: -2.86 (0.33), residues: 180
  sheet: -4.03 (0.19), residues: 440
  loop : -3.19 (0.15), residues: 1410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  66 
 TYR   0.024   0.002   TYR A  62 
 PHE   0.009   0.001   PHE C  89 
 TRP   0.011   0.001   TRP D 343 
 HIS   0.010   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (17040)
  covalent geometry    : angle       0.69273 (23175)
  hydrogen bonds       : bond        0.03287 (  180)
  hydrogen bonds       : angle       5.14018 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 106
    poor density    : 334
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.8672 (m-80) cc_final: 0.8452 (m-80)
REVERT: A  148 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7498 (mt-10)
REVERT: A  327 SER cc_start: 0.8772 (m) cc_final: 0.8438 (t)
REVERT: A  362 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6699 (tp)
REVERT: A  476 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7201 (mm-40)
REVERT: B  146 MET cc_start: 0.7857 (ttt) cc_final: 0.7245 (ttm)
REVERT: B  168 GLU cc_start: 0.7321 (mp0) cc_final: 0.6795 (mp0)
REVERT: B  171 TYR cc_start: 0.8525 (m-80) cc_final: 0.8092 (m-10)
REVERT: B  201 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7698 (t0)
REVERT: B  476 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7253 (mm110)
REVERT: C   63 ASP cc_start: 0.8206 (t0) cc_final: 0.7916 (m-30)
REVERT: C  128 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7377 (m-40)
REVERT: C  145 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8993 (mt)
REVERT: C  146 MET cc_start: 0.8305 (ttp) cc_final: 0.8022 (ttm)
REVERT: C  171 TYR cc_start: 0.8482 (m-10) cc_final: 0.8046 (m-10)
REVERT: C  201 ASP cc_start: 0.8011 (t70) cc_final: 0.7319 (t0)
REVERT: C  227 TYR cc_start: 0.8815 (m-80) cc_final: 0.8611 (m-80)
REVERT: C  239 LEU cc_start: 0.8922 (tp) cc_final: 0.8691 (tp)
REVERT: D  145 LEU cc_start: 0.9285 (tp) cc_final: 0.8993 (mt)
REVERT: D  171 TYR cc_start: 0.8575 (m-10) cc_final: 0.8317 (m-80)
REVERT: D  199 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6998 (pt0)
REVERT: D  201 ASP cc_start: 0.7942 (t0) cc_final: 0.7559 (t0)
REVERT: D  270 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7869 (mtt)
REVERT: D  284 ASP cc_start: 0.8399 (t0) cc_final: 0.8137 (t0)
REVERT: D  380 ASP cc_start: 0.8185 (t0) cc_final: 0.7955 (t0)
REVERT: D  476 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7352 (mm-40)
REVERT: E   68 TYR cc_start: 0.8363 (m-80) cc_final: 0.8156 (m-80)
REVERT: E  201 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7311 (m-30)
REVERT: E  223 MET cc_start: 0.8458 (mmm) cc_final: 0.8242 (mmm)
REVERT: E  239 LEU cc_start: 0.8458 (tp) cc_final: 0.8086 (tp)
REVERT: E  270 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7796 (mtt)
REVERT: E  362 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7224 (tp)
  outliers start: 106
  outliers final: 58
  residues processed: 405
  average time/residue: 0.1074
  time to fit residues: 70.5642
Evaluate side-chains
  331 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 264
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  128 ASN
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  199 GLU
Chi-restraints excluded: chain D residue  270 MET
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  134 GLU
Chi-restraints excluded: chain E residue  137 SER
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  270 MET
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  362 LEU
Chi-restraints excluded: chain E residue  466 LEU
Chi-restraints excluded: chain E residue  471 SER
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 139 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
B 128 ASN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN
C 128 ASN
** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  83 GLN
E  95 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.120709 restraints weight = 26700.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.124108 restraints weight = 13992.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126333 restraints weight = 8742.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127845 restraints weight = 6173.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128910 restraints weight = 4755.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  17040  Z= 0.148
  Angle     :  0.717   9.168  23175  Z= 0.356
  Chirality :  0.046   0.176   2595
  Planarity :  0.005   0.044   3015
  Dihedral  :  5.724  25.159   2265
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.98 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 19.57 %
    Favored  : 74.55 %
  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: -4.63 (0.17), residues: 2030
  helix: -2.73 (0.32), residues: 185
  sheet: -3.71 (0.19), residues: 485
  loop : -3.04 (0.16), residues: 1360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  66 
 TYR   0.026   0.002   TYR A 227 
 PHE   0.016   0.001   PHE B 232 
 TRP   0.015   0.001   TRP A 376 
 HIS   0.003   0.001   HIS D  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (17040)
  covalent geometry    : angle       0.71729 (23175)
  hydrogen bonds       : bond        0.03474 (  180)
  hydrogen bonds       : angle       5.05190 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 285
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7841 (t0)
REVERT: A  148 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7349 (mt-10)
REVERT: A  171 TYR cc_start: 0.8778 (m-80) cc_final: 0.8419 (m-80)
REVERT: A  327 SER cc_start: 0.8800 (m) cc_final: 0.8482 (t)
REVERT: A  476 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7242 (mm-40)
REVERT: B  122 LYS cc_start: 0.8665 (mttp) cc_final: 0.8200 (mtpp)
REVERT: B  146 MET cc_start: 0.7940 (ttt) cc_final: 0.7117 (ttm)
REVERT: B  168 GLU cc_start: 0.7426 (mp0) cc_final: 0.7134 (mp0)
REVERT: B  171 TYR cc_start: 0.8709 (m-80) cc_final: 0.8398 (m-10)
REVERT: B  181 ASN cc_start: 0.8103 (t0) cc_final: 0.7856 (t0)
REVERT: B  201 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7731 (t70)
REVERT: B  362 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7266 (tp)
REVERT: B  466 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7674 (pp)
REVERT: C   53 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7893 (pt)
REVERT: C   61 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7737 (pt)
REVERT: C   63 ASP cc_start: 0.8343 (t0) cc_final: 0.7947 (m-30)
REVERT: C   71 ASP cc_start: 0.7014 (t70) cc_final: 0.6498 (t70)
REVERT: C  146 MET cc_start: 0.8372 (ttp) cc_final: 0.7733 (ttt)
REVERT: C  171 TYR cc_start: 0.8602 (m-10) cc_final: 0.8295 (m-10)
REVERT: C  201 ASP cc_start: 0.8196 (t70) cc_final: 0.7558 (t0)
REVERT: C  270 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7864 (mtt)
REVERT: D  145 LEU cc_start: 0.9301 (tp) cc_final: 0.9020 (mt)
REVERT: D  171 TYR cc_start: 0.8725 (m-10) cc_final: 0.8451 (m-80)
REVERT: D  201 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7520 (t0)
REVERT: D  284 ASP cc_start: 0.8384 (t0) cc_final: 0.8110 (t0)
REVERT: D  327 SER cc_start: 0.8744 (m) cc_final: 0.8536 (t)
REVERT: D  380 ASP cc_start: 0.8310 (t0) cc_final: 0.8092 (t0)
REVERT: E   68 TYR cc_start: 0.8503 (m-80) cc_final: 0.8177 (m-80)
REVERT: E  146 MET cc_start: 0.8126 (ttm) cc_final: 0.6824 (ttt)
REVERT: E  201 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7302 (t0)
REVERT: E  239 LEU cc_start: 0.8566 (tp) cc_final: 0.8299 (tp)
REVERT: E  289 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7574 (mt-10)
  outliers start: 110
  outliers final: 72
  residues processed: 360
  average time/residue: 0.1086
  time to fit residues: 63.8784
Evaluate side-chains
  338 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 257
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  128 ASN
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  279 ILE
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  491 VAL
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  201 ASP
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  134 GLU
Chi-restraints excluded: chain E residue  137 SER
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  166 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  279 ILE
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 148 optimal weight:    0.2980
   chunk 44 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 186 optimal weight:    0.0670
   chunk 17 optimal weight:   10.0000
   chunk 172 optimal weight:    0.5980
   chunk 137 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.5922

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
A 181 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
C 128 ASN
** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  83 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.137073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.121966 restraints weight = 26463.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.125348 restraints weight = 13872.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.127597 restraints weight = 8704.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.129115 restraints weight = 6129.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.130156 restraints weight = 4706.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  17040  Z= 0.134
  Angle     :  0.726  12.913  23175  Z= 0.353
  Chirality :  0.044   0.148   2595
  Planarity :  0.005   0.041   3015
  Dihedral  :  5.657  24.905   2265
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 20.96 %
    Favored  : 73.21 %
  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: -4.46 (0.17), residues: 2030
  helix: -2.13 (0.33), residues: 185
  sheet: -3.68 (0.20), residues: 465
  loop : -2.98 (0.16), residues: 1380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  66 
 TYR   0.025   0.002   TYR B  62 
 PHE   0.009   0.001   PHE E 412 
 TRP   0.013   0.001   TRP D 343 
 HIS   0.003   0.001   HIS B  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (17040)
  covalent geometry    : angle       0.72591 (23175)
  hydrogen bonds       : bond        0.03441 (  180)
  hydrogen bonds       : angle       4.86198 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 109
    poor density    : 284
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7691 (t0)
REVERT: A  148 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7474 (mt-10)
REVERT: A  171 TYR cc_start: 0.8819 (m-80) cc_final: 0.8540 (m-10)
REVERT: A  327 SER cc_start: 0.8779 (m) cc_final: 0.8467 (t)
REVERT: A  476 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7277 (mm-40)
REVERT: B  146 MET cc_start: 0.7921 (ttt) cc_final: 0.6907 (ttt)
REVERT: B  171 TYR cc_start: 0.8715 (m-80) cc_final: 0.8344 (m-10)
REVERT: B  181 ASN cc_start: 0.8306 (t0) cc_final: 0.8042 (t0)
REVERT: B  201 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7753 (t0)
REVERT: B  362 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7453 (tp)
REVERT: C   53 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (pt)
REVERT: C   61 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7714 (pt)
REVERT: C   68 TYR cc_start: 0.8281 (m-10) cc_final: 0.7833 (m-10)
REVERT: C   71 ASP cc_start: 0.7172 (t70) cc_final: 0.6677 (t70)
REVERT: C  128 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7444 (m-40)
REVERT: C  146 MET cc_start: 0.8313 (ttp) cc_final: 0.7268 (ttt)
REVERT: C  171 TYR cc_start: 0.8672 (m-10) cc_final: 0.8359 (m-10)
REVERT: C  201 ASP cc_start: 0.8174 (t70) cc_final: 0.7435 (t0)
REVERT: C  239 LEU cc_start: 0.8887 (tp) cc_final: 0.8538 (tp)
REVERT: C  270 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7909 (mtt)
REVERT: D  145 LEU cc_start: 0.9330 (tp) cc_final: 0.9061 (mt)
REVERT: D  171 TYR cc_start: 0.8763 (m-10) cc_final: 0.8504 (m-80)
REVERT: D  201 ASP cc_start: 0.7910 (t0) cc_final: 0.7500 (t0)
REVERT: D  284 ASP cc_start: 0.8381 (t0) cc_final: 0.8136 (t0)
REVERT: D  327 SER cc_start: 0.8874 (m) cc_final: 0.8602 (t)
REVERT: E   68 TYR cc_start: 0.8388 (m-80) cc_final: 0.8147 (m-80)
REVERT: E  201 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7293 (t0)
REVERT: E  223 MET cc_start: 0.8445 (mmm) cc_final: 0.8177 (mmm)
  outliers start: 109
  outliers final: 84
  residues processed: 363
  average time/residue: 0.0994
  time to fit residues: 60.0028
Evaluate side-chains
  358 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 266
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  201 ASP
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  128 ASN
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  244 VAL
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  495 LEU
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  244 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  134 GLU
Chi-restraints excluded: chain E residue  137 SER
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  274 LEU
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 149 optimal weight:    8.9990
   chunk 116 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 137 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   chunk 151 optimal weight:    0.9980
   chunk 187 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 GLN
B  95 GLN
B 128 ASN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 HIS
C  83 GLN
C  95 GLN
D 396 ASN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 329 ASN
E 396 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.126793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.110357 restraints weight = 27019.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113830 restraints weight = 14315.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116111 restraints weight = 9098.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.117670 restraints weight = 6533.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118710 restraints weight = 5115.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  17040  Z= 0.263
  Angle     :  0.807  13.673  23175  Z= 0.399
  Chirality :  0.048   0.219   2595
  Planarity :  0.005   0.054   3015
  Dihedral  :  6.147  26.049   2265
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 20.80 %
    Favored  : 72.83 %
  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: -4.53 (0.17), residues: 2030
  helix: -1.87 (0.34), residues: 185
  sheet: -3.76 (0.20), residues: 465
  loop : -3.08 (0.16), residues: 1380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 444 
 TYR   0.024   0.002   TYR E  62 
 PHE   0.015   0.002   PHE A 141 
 TRP   0.024   0.003   TRP A 343 
 HIS   0.011   0.002   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (17040)
  covalent geometry    : angle       0.80653 (23175)
  hydrogen bonds       : bond        0.04254 (  180)
  hydrogen bonds       : angle       5.17559 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 119
    poor density    : 253
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: A  171 TYR cc_start: 0.9044 (m-80) cc_final: 0.8686 (m-10)
REVERT: A  327 SER cc_start: 0.8837 (m) cc_final: 0.8436 (t)
REVERT: B  134 GLU cc_start: 0.7580 (pm20) cc_final: 0.7242 (mt-10)
REVERT: B  146 MET cc_start: 0.8124 (ttt) cc_final: 0.7583 (ttt)
REVERT: C   53 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7829 (pt)
REVERT: C   63 ASP cc_start: 0.8445 (t0) cc_final: 0.7988 (m-30)
REVERT: C   68 TYR cc_start: 0.8469 (m-10) cc_final: 0.8056 (m-10)
REVERT: C   71 ASP cc_start: 0.7200 (t70) cc_final: 0.6583 (t70)
REVERT: C  146 MET cc_start: 0.8370 (ttp) cc_final: 0.7784 (ttm)
REVERT: C  171 TYR cc_start: 0.8882 (m-10) cc_final: 0.8573 (m-10)
REVERT: C  201 ASP cc_start: 0.8269 (t70) cc_final: 0.7154 (t0)
REVERT: C  223 MET cc_start: 0.8184 (mmm) cc_final: 0.7979 (mmm)
REVERT: C  270 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8062 (mtt)
REVERT: D  145 LEU cc_start: 0.9388 (tp) cc_final: 0.9115 (mt)
REVERT: D  201 ASP cc_start: 0.8101 (t0) cc_final: 0.7624 (t0)
REVERT: D  327 SER cc_start: 0.8778 (m) cc_final: 0.8569 (t)
REVERT: E   68 TYR cc_start: 0.8645 (m-80) cc_final: 0.8303 (m-80)
REVERT: E  201 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7699 (t0)
  outliers start: 119
  outliers final: 83
  residues processed: 337
  average time/residue: 0.1057
  time to fit residues: 58.9101
Evaluate side-chains
  323 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 237
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  244 VAL
Chi-restraints excluded: chain C residue  270 MET
Chi-restraints excluded: chain C residue  274 LEU
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  244 VAL
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  495 LEU
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  134 GLU
Chi-restraints excluded: chain E residue  137 SER
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  161 TRP
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  274 LEU
Chi-restraints excluded: chain E residue  279 ILE
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain E residue  471 SER
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 182 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   chunk 149 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 192 optimal weight:    1.9990
   chunk 159 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 173 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 128 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 ASN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 128 ASN
D  83 GLN
D 396 ASN
E  83 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 396 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.118428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.102645 restraints weight = 28461.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106130 restraints weight = 14137.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.108388 restraints weight = 8540.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109910 restraints weight = 5929.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110956 restraints weight = 4523.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17040  Z= 0.137
  Angle     :  0.739  12.100  23175  Z= 0.360
  Chirality :  0.045   0.211   2595
  Planarity :  0.005   0.051   3015
  Dihedral  :  5.851  25.302   2265
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.43 %
    Favored  : 85.57 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 22.62 %
    Favored  : 72.14 %
  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: -4.31 (0.17), residues: 2030
  helix: -1.33 (0.37), residues: 185
  sheet: -3.59 (0.20), residues: 485
  loop : -2.96 (0.16), residues: 1360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 116 
 TYR   0.023   0.002   TYR C  62 
 PHE   0.021   0.001   PHE A 141 
 TRP   0.014   0.002   TRP A 343 
 HIS   0.004   0.001   HIS B  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (17040)
  covalent geometry    : angle       0.73935 (23175)
  hydrogen bonds       : bond        0.03565 (  180)
  hydrogen bonds       : angle       4.91683 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 278
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7238 (mt-10)
REVERT: A  171 TYR cc_start: 0.8955 (m-80) cc_final: 0.8661 (m-10)
REVERT: A  327 SER cc_start: 0.8796 (m) cc_final: 0.8457 (t)
REVERT: A  476 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6934 (mm110)
REVERT: B   83 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7400 (tp-100)
REVERT: B  145 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8986 (mt)
REVERT: B  201 ASP cc_start: 0.8241 (t70) cc_final: 0.7760 (t0)
REVERT: B  380 ASP cc_start: 0.8013 (t70) cc_final: 0.7507 (m-30)
REVERT: C   53 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7503 (pt)
REVERT: C   68 TYR cc_start: 0.8373 (m-10) cc_final: 0.7899 (m-10)
REVERT: C  128 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7553 (m-40)
REVERT: C  146 MET cc_start: 0.8281 (ttp) cc_final: 0.7595 (ttt)
REVERT: C  171 TYR cc_start: 0.8794 (m-10) cc_final: 0.8373 (m-10)
REVERT: C  201 ASP cc_start: 0.8228 (t70) cc_final: 0.7747 (t70)
REVERT: C  476 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7669 (mm110)
REVERT: D  145 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8952 (mt)
REVERT: D  201 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7602 (t0)
REVERT: D  284 ASP cc_start: 0.8366 (t0) cc_final: 0.8031 (t0)
REVERT: D  327 SER cc_start: 0.8888 (m) cc_final: 0.8577 (t)
REVERT: D  476 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7362 (mm110)
REVERT: E  201 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7612 (m-30)
REVERT: E  223 MET cc_start: 0.8288 (mmm) cc_final: 0.7844 (mmm)
  outliers start: 98
  outliers final: 79
  residues processed: 346
  average time/residue: 0.1047
  time to fit residues: 59.2813
Evaluate side-chains
  345 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 260
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue   99 PHE
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  128 ASN
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  244 VAL
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  481 THR
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  145 LEU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  201 ASP
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  244 VAL
Chi-restraints excluded: chain D residue  274 LEU
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  466 LEU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  495 LEU
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  134 GLU
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  274 LEU
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 172 optimal weight:    9.9990
   chunk 171 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0870
   chunk 1 optimal weight:    0.0170
   chunk 147 optimal weight:    0.9990
   chunk 202 optimal weight:    7.9990
   chunk 94 optimal weight:    0.5980
   chunk 20 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
A 396 ASN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 128 ASN
** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 396 ASN
E  83 GLN
** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 396 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.108552 restraints weight = 27743.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112149 restraints weight = 13835.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.114481 restraints weight = 8338.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116060 restraints weight = 5741.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.117126 restraints weight = 4346.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17040  Z= 0.116
  Angle     :  0.726  13.649  23175  Z= 0.350
  Chirality :  0.044   0.188   2595
  Planarity :  0.005   0.050   3015
  Dihedral  :  5.562  23.658   2265
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.01 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.19 (0.17), residues: 2030
  helix: -1.02 (0.38), residues: 185
  sheet: -3.45 (0.20), residues: 495
  loop : -2.93 (0.16), residues: 1350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  54 
 TYR   0.024   0.002   TYR C  62 
 PHE   0.014   0.001   PHE B 141 
 TRP   0.014   0.002   TRP E 343 
 HIS   0.004   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (17040)
  covalent geometry    : angle       0.72627 (23175)
  hydrogen bonds       : bond        0.03349 (  180)
  hydrogen bonds       : angle       4.76372 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 305
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7780 (m-40)
REVERT: A  148 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7101 (mt-10)
REVERT: A  171 TYR cc_start: 0.9049 (m-80) cc_final: 0.8770 (m-10)
REVERT: A  239 LEU cc_start: 0.8233 (tp) cc_final: 0.7983 (tt)
REVERT: A  327 SER cc_start: 0.8679 (m) cc_final: 0.8380 (t)
REVERT: A  476 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6951 (mm-40)
REVERT: B   83 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: B  146 MET cc_start: 0.8181 (ttt) cc_final: 0.7692 (ttm)
REVERT: B  201 ASP cc_start: 0.8237 (t70) cc_final: 0.7735 (t0)
REVERT: B  289 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6885 (mt-10)
REVERT: B  380 ASP cc_start: 0.7884 (t70) cc_final: 0.7583 (m-30)
REVERT: C   71 ASP cc_start: 0.7237 (t70) cc_final: 0.6563 (t70)
REVERT: C  128 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7825 (m-40)
REVERT: C  146 MET cc_start: 0.8234 (ttp) cc_final: 0.7664 (ttt)
REVERT: C  171 TYR cc_start: 0.8744 (m-10) cc_final: 0.8425 (m-10)
REVERT: C  201 ASP cc_start: 0.8167 (t70) cc_final: 0.7724 (t70)
REVERT: C  362 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7170 (tp)
REVERT: C  476 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7642 (mm110)
REVERT: D  145 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8937 (mt)
REVERT: D  171 TYR cc_start: 0.8562 (m-80) cc_final: 0.8231 (m-10)
REVERT: D  201 ASP cc_start: 0.8028 (t0) cc_final: 0.7542 (t0)
REVERT: D  284 ASP cc_start: 0.8307 (t0) cc_final: 0.7978 (t0)
REVERT: D  327 SER cc_start: 0.8846 (m) cc_final: 0.8537 (t)
REVERT: D  380 ASP cc_start: 0.8061 (t0) cc_final: 0.7788 (t0)
REVERT: D  476 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7025 (mm110)
REVERT: E  201 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7418 (m-30)
REVERT: E  223 MET cc_start: 0.8274 (mmm) cc_final: 0.7921 (mmm)
  outliers start: 81
  outliers final: 65
  residues processed: 363
  average time/residue: 0.1038
  time to fit residues: 61.2008
Evaluate side-chains
  333 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 263
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  128 ASN
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  481 THR
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  145 LEU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  244 VAL
Chi-restraints excluded: chain D residue  274 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  466 LEU
Chi-restraints excluded: chain D residue  481 THR
Chi-restraints excluded: chain D residue  495 LEU
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 63 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   chunk 146 optimal weight:    8.9990
   chunk 145 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0370
   chunk 169 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 136 optimal weight:    9.9990
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
A 396 ASN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
C 128 ASN
D 396 ASN
E  83 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 396 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.126333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110217 restraints weight = 27813.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113828 restraints weight = 13901.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.116168 restraints weight = 8385.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117753 restraints weight = 5787.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.118834 restraints weight = 4393.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17040  Z= 0.115
  Angle     :  0.732  13.976  23175  Z= 0.351
  Chirality :  0.044   0.219   2595
  Planarity :  0.005   0.054   3015
  Dihedral  :  5.445  23.273   2265
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.20 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 25.35 %
    Favored  : 70.32 %
  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: -4.05 (0.17), residues: 2030
  helix: -1.00 (0.38), residues: 190
  sheet: -3.18 (0.21), residues: 470
  loop : -2.92 (0.16), residues: 1370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  54 
 TYR   0.024   0.001   TYR C  62 
 PHE   0.029   0.001   PHE D 232 
 TRP   0.017   0.002   TRP D 117 
 HIS   0.003   0.001   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (17040)
  covalent geometry    : angle       0.73193 (23175)
  hydrogen bonds       : bond        0.03102 (  180)
  hydrogen bonds       : angle       4.66734 (  420)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 300
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7008 (mt-10)
REVERT: A  171 TYR cc_start: 0.9080 (m-80) cc_final: 0.8761 (m-10)
REVERT: A  239 LEU cc_start: 0.8183 (tp) cc_final: 0.7925 (tt)
REVERT: A  327 SER cc_start: 0.8674 (m) cc_final: 0.8371 (t)
REVERT: B   83 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7232 (tp40)
REVERT: B  128 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7785 (m-40)
REVERT: B  146 MET cc_start: 0.8223 (ttt) cc_final: 0.7760 (ttm)
REVERT: B  171 TYR cc_start: 0.8583 (m-80) cc_final: 0.8104 (m-10)
REVERT: B  201 ASP cc_start: 0.8237 (t70) cc_final: 0.7650 (t0)
REVERT: B  284 ASP cc_start: 0.8394 (t0) cc_final: 0.7906 (t0)
REVERT: B  289 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6820 (mt-10)
REVERT: C   61 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7544 (pt)
REVERT: C   71 ASP cc_start: 0.7317 (t70) cc_final: 0.6784 (t70)
REVERT: C  146 MET cc_start: 0.8210 (ttp) cc_final: 0.7828 (ttm)
REVERT: C  171 TYR cc_start: 0.8922 (m-10) cc_final: 0.8547 (m-10)
REVERT: C  201 ASP cc_start: 0.8187 (t70) cc_final: 0.7555 (t70)
REVERT: C  476 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7612 (mm110)
REVERT: D  145 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8853 (mp)
REVERT: D  171 TYR cc_start: 0.8566 (m-80) cc_final: 0.8289 (m-10)
REVERT: D  201 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7524 (t0)
REVERT: D  284 ASP cc_start: 0.8297 (t0) cc_final: 0.7974 (t0)
REVERT: D  327 SER cc_start: 0.8873 (m) cc_final: 0.8521 (t)
REVERT: E  171 TYR cc_start: 0.8889 (m-80) cc_final: 0.8458 (m-10)
REVERT: E  201 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7425 (m-30)
REVERT: E  223 MET cc_start: 0.8247 (mmm) cc_final: 0.8001 (mmm)
  outliers start: 81
  outliers final: 65
  residues processed: 349
  average time/residue: 0.1052
  time to fit residues: 60.2233
Evaluate side-chains
  339 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 269
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  348 ASN
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  128 ASN
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain C residue  382 MET
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  481 THR
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  108 THR
Chi-restraints excluded: chain D residue  145 LEU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  201 ASP
Chi-restraints excluded: chain D residue  204 VAL
Chi-restraints excluded: chain D residue  274 LEU
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  362 LEU
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  466 LEU
Chi-restraints excluded: chain D residue  495 LEU
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue   99 PHE
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain E residue  251 LEU
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  315 VAL
Chi-restraints excluded: chain E residue  330 LEU
Chi-restraints excluded: chain E residue  402 VAL
Chi-restraints excluded: chain E residue  443 VAL
Chi-restraints excluded: chain E residue  481 THR
Chi-restraints excluded: chain E residue  495 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 177 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   chunk 202 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 154 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 190 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 199 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 ASN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 GLN
B 128 ASN
** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 ASN
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 396 ASN
** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 396 ASN
E  83 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 396 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.133016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117296 restraints weight = 26343.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120646 restraints weight = 14353.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122835 restraints weight = 9226.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.124327 restraints weight = 6678.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.125126 restraints weight = 5244.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17040  Z= 0.203
  Angle     :  0.773  13.594  23175  Z= 0.379
  Chirality :  0.047   0.246   2595
  Planarity :  0.005   0.059   3015
  Dihedral  :  5.723  28.060   2265
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.88 %
    Favored  : 85.12 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 25.35 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.05 %
  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: -4.06 (0.17), residues: 2030
  helix: -0.97 (0.38), residues: 185
  sheet: -3.34 (0.20), residues: 485
  loop : -2.85 (0.16), residues: 1360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  54 
 TYR   0.024   0.002   TYR E  62 
 PHE   0.017   0.001   PHE D 232 
 TRP   0.027   0.003   TRP D 117 
 HIS   0.005   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (17040)
  covalent geometry    : angle       0.77263 (23175)
  hydrogen bonds       : bond        0.03706 (  180)
  hydrogen bonds       : angle       4.79129 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2356.58 seconds
wall clock time: 41 minutes 50.47 seconds (2510.47 seconds total)