Starting phenix.real_space_refine
on Thu Jul 31 05:29:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ew0_28639/07_2025/8ew0_28639.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
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      72      5.16       5
     C    8588      2.51       5
     N    2419      2.21       5
     O    2557      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 98 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13636
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2276
          Classifications: {'peptide': 292}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2268
          Classifications: {'peptide': 290}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2272
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2272
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2276
          Classifications: {'peptide': 292}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 2272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2272
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 2
  Time building chain proxies: 8.33, per 1000 atoms: 0.61
  Number of scatterers: 13636
  At special positions: 0
  Unit cell: (91.84, 95.94, 155.8, 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      72     16.00
     O    2557      8.00
     N    2419      7.00
     C    8588      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: 3.49
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3168

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 3 sheets defined
      59.8% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 118
    Processing helix  chain 'A' and resid 132 through 136
      removed outlier: 3.548A  pdb=" N   TYR A 136 " --> pdb=" O   PRO A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 155
    Processing helix  chain 'A' and resid 172 through 186
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.527A  pdb=" N   CYS A 197 " --> pdb=" O   ALA A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 206
    Processing helix  chain 'A' and resid 214 through 226
    Processing helix  chain 'A' and resid 372 through 374
      No H-bonds generated for 'chain 'A' and resid 372 through 374'
    Processing helix  chain 'A' and resid 375 through 391
    Processing helix  chain 'A' and resid 398 through 421
      removed outlier: 3.603A  pdb=" N   LYS A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
    Processing helix  chain 'A' and resid 444 through 471
      removed outlier: 3.804A  pdb=" N   ILE A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 489
      removed outlier: 3.550A  pdb=" N   ALA A 480 " --> pdb=" O   ASP A 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 118
    Processing helix  chain 'B' and resid 132 through 136
      removed outlier: 3.584A  pdb=" N   TYR B 136 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 155
    Processing helix  chain 'B' and resid 172 through 186
    Processing helix  chain 'B' and resid 193 through 198
      removed outlier: 3.557A  pdb=" N   CYS B 197 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL B 198 " --> pdb=" O   HIS B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 226
    Processing helix  chain 'B' and resid 372 through 374
      No H-bonds generated for 'chain 'B' and resid 372 through 374'
    Processing helix  chain 'B' and resid 375 through 391
    Processing helix  chain 'B' and resid 398 through 421
    Processing helix  chain 'B' and resid 433 through 442
    Processing helix  chain 'B' and resid 444 through 471
      removed outlier: 3.806A  pdb=" N   ILE B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 489
    Processing helix  chain 'C' and resid 100 through 118
    Processing helix  chain 'C' and resid 132 through 136
    Processing helix  chain 'C' and resid 137 through 155
    Processing helix  chain 'C' and resid 172 through 186
    Processing helix  chain 'C' and resid 193 through 198
      removed outlier: 4.218A  pdb=" N   VAL C 198 " --> pdb=" O   HIS C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 226
      removed outlier: 3.546A  pdb=" N   PHE C 226 " --> pdb=" O   GLY C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 391
    Processing helix  chain 'C' and resid 398 through 421
    Processing helix  chain 'C' and resid 433 through 442
    Processing helix  chain 'C' and resid 444 through 471
      removed outlier: 3.867A  pdb=" N   ILE C 448 " --> pdb=" O   SER C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 489
      removed outlier: 3.515A  pdb=" N   ALA C 480 " --> pdb=" O   ASP C 476 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 118
    Processing helix  chain 'D' and resid 132 through 136
    Processing helix  chain 'D' and resid 137 through 155
      removed outlier: 3.674A  pdb=" N   LYS D 155 " --> pdb=" O   GLU D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 187
      removed outlier: 3.522A  pdb=" N   MET D 176 " --> pdb=" O   GLY D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 197
      removed outlier: 3.511A  pdb=" N   CYS D 197 " --> pdb=" O   ALA D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 206
    Processing helix  chain 'D' and resid 213 through 226
    Processing helix  chain 'D' and resid 375 through 391
    Processing helix  chain 'D' and resid 398 through 421
    Processing helix  chain 'D' and resid 433 through 442
    Processing helix  chain 'D' and resid 444 through 471
      removed outlier: 3.830A  pdb=" N   ILE D 448 " --> pdb=" O   SER D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 476 through 489
      removed outlier: 3.590A  pdb=" N   ALA D 480 " --> pdb=" O   ASP D 476 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 118
    Processing helix  chain 'E' and resid 132 through 136
    Processing helix  chain 'E' and resid 137 through 155
    Processing helix  chain 'E' and resid 172 through 186
    Processing helix  chain 'E' and resid 193 through 198
      removed outlier: 4.023A  pdb=" N   VAL E 198 " --> pdb=" O   HIS E 195 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 206
    Processing helix  chain 'E' and resid 213 through 226
    Processing helix  chain 'E' and resid 375 through 391
    Processing helix  chain 'E' and resid 398 through 421
    Processing helix  chain 'E' and resid 433 through 442
    Processing helix  chain 'E' and resid 444 through 471
      removed outlier: 3.836A  pdb=" N   ILE E 448 " --> pdb=" O   SER E 444 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 476 through 489
      removed outlier: 3.771A  pdb=" N   ALA E 480 " --> pdb=" O   ASP E 476 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 118
    Processing helix  chain 'F' and resid 132 through 136
    Processing helix  chain 'F' and resid 137 through 155
    Processing helix  chain 'F' and resid 172 through 187
    Processing helix  chain 'F' and resid 193 through 198
      removed outlier: 4.280A  pdb=" N   VAL F 198 " --> pdb=" O   HIS F 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 213 through 226
    Processing helix  chain 'F' and resid 375 through 391
    Processing helix  chain 'F' and resid 398 through 421
      removed outlier: 3.574A  pdb=" N   PHE F 421 " --> pdb=" O   LEU F 417 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 433 through 442
    Processing helix  chain 'F' and resid 444 through 471
      removed outlier: 3.873A  pdb=" N   ILE F 448 " --> pdb=" O   SER F 444 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 476 through 489
      removed outlier: 3.550A  pdb=" N   ALA F 480 " --> pdb=" O   ASP F 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166
      removed outlier: 6.510A  pdb=" N   CYS A  89 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ALA A 166 " --> pdb=" O   CYS A  89 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLY A  91 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   LYS A  90 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   ALA A 127 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   GLY A  92 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL A 129 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ARG A  94 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   LYS E  90 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ALA E 127 " --> pdb=" O   LYS E  90 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLY E  92 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   VAL E 129 " --> pdb=" O   GLY E  92 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ARG E  94 " --> pdb=" O   VAL E 129 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   CYS E  89 " --> pdb=" O   VAL E 164 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ALA E 166 " --> pdb=" O   CYS E  89 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY E  91 " --> pdb=" O   ALA E 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 166
      removed outlier: 6.535A  pdb=" N   CYS B  89 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   ALA B 166 " --> pdb=" O   CYS B  89 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLY B  91 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LYS B  90 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   ALA B 127 " --> pdb=" O   LYS B  90 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   GLY B  92 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   VAL B 129 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ARG B  94 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LYS D  90 " --> pdb=" O   ALA D 125 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ALA D 127 " --> pdb=" O   LYS D  90 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   GLY D  92 " --> pdb=" O   ALA D 127 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   VAL D 129 " --> pdb=" O   GLY D  92 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ARG D  94 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   CYS D  89 " --> pdb=" O   VAL D 164 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   ALA D 166 " --> pdb=" O   CYS D  89 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLY D  91 " --> pdb=" O   ALA D 166 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166
      removed outlier: 6.569A  pdb=" N   CYS C  89 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   ALA C 166 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY C  91 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LYS C  90 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ALA C 127 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   GLY C  92 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   VAL C 129 " --> pdb=" O   GLY C  92 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ARG C  94 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLY F  92 " --> pdb=" O   ALA F 125 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   CYS F  89 " --> pdb=" O   VAL F 164 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   ALA F 166 " --> pdb=" O   CYS F  89 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY F  91 " --> pdb=" O   ALA F 166 " (cutoff:3.500A)

    854 hydrogen bonds defined for protein.
    2469 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: 4.20

  Time building geometry restraints manager: 4.12 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: 4512
        1.34 -     1.46: 2958
        1.46 -     1.58: 6334
        1.58 -     1.70: 0
        1.70 -     1.81: 120
  Bond restraints: 13924
  Sorted by residual:
  bond pdb=" C   ARG C  86 "
       pdb=" N   THR C  87 "
    ideal  model  delta    sigma   weight residual
    1.331  1.276  0.055 1.36e-02 5.41e+03 1.64e+01
  bond pdb=" C   LYS C  53 "
       pdb=" N   PRO C  54 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.20e-02 6.94e+03 4.03e+00
  bond pdb=" C   LYS A  53 "
       pdb=" N   PRO A  54 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.20e-02 6.94e+03 4.00e+00
  bond pdb=" C   LYS B  53 "
       pdb=" N   PRO B  54 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.023 1.20e-02 6.94e+03 3.80e+00
  bond pdb=" C   LYS F  53 "
       pdb=" N   PRO F  54 "
    ideal  model  delta    sigma   weight residual
    1.329  1.351 -0.023 1.20e-02 6.94e+03 3.59e+00
  ... (remaining 13919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 18552
        2.05 -     4.10: 227
        4.10 -     6.15: 16
        6.15 -     8.20: 0
        8.20 -    10.25: 2
  Bond angle restraints: 18797
  Sorted by residual:
  angle pdb=" N   ILE F 430 "
        pdb=" CA  ILE F 430 "
        pdb=" C   ILE F 430 "
      ideal   model   delta    sigma   weight residual
     113.47  108.65    4.82 1.01e+00 9.80e-01 2.27e+01
  angle pdb=" C   ARG C  86 "
        pdb=" N   THR C  87 "
        pdb=" CA  THR C  87 "
      ideal   model   delta    sigma   weight residual
     122.70  130.94   -8.24 1.98e+00 2.55e-01 1.73e+01
  angle pdb=" CB  MET C 411 "
        pdb=" CG  MET C 411 "
        pdb=" SD  MET C 411 "
      ideal   model   delta    sigma   weight residual
     112.70  122.95  -10.25 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" C   SER C 213 "
        pdb=" N   ALA C 214 "
        pdb=" CA  ALA C 214 "
      ideal   model   delta    sigma   weight residual
     121.54  126.48   -4.94 1.91e+00 2.74e-01 6.68e+00
  angle pdb=" C   LYS C  90 "
        pdb=" N   GLY C  91 "
        pdb=" CA  GLY C  91 "
      ideal   model   delta    sigma   weight residual
     120.92  117.65    3.27 1.30e+00 5.92e-01 6.34e+00
  ... (remaining 18792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.07: 6973
       18.07 -    36.15: 951
       36.15 -    54.22: 281
       54.22 -    72.29: 56
       72.29 -    90.37: 20
  Dihedral angle restraints: 8281
    sinusoidal: 3300
      harmonic: 4981
  Sorted by residual:
  dihedral pdb=" CG  ARG A  66 "
           pdb=" CD  ARG A  66 "
           pdb=" NE  ARG A  66 "
           pdb=" CZ  ARG A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.03   48.97     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CA  ASP D 138 "
           pdb=" CB  ASP D 138 "
           pdb=" CG  ASP D 138 "
           pdb=" OD1 ASP D 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.73   59.73     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CB  GLU F 103 "
           pdb=" CG  GLU F 103 "
           pdb=" CD  GLU F 103 "
           pdb=" OE1 GLU F 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   90.37  -90.37     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 8278 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1066
       0.026 -    0.053: 561
       0.053 -    0.079: 283
       0.079 -    0.105: 102
       0.105 -    0.132: 28
  Chirality restraints: 2040
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE D  75 "
            pdb=" N   ILE D  75 "
            pdb=" C   ILE D  75 "
            pdb=" CB  ILE D  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  chirality pdb=" CA  ILE F  75 "
            pdb=" N   ILE F  75 "
            pdb=" C   ILE F  75 "
            pdb=" CB  ILE F  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 2037 not shown)

  Planarity restraints: 2425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 428 "   -0.046 5.00e-02 4.00e+02   6.92e-02 7.67e+00
        pdb=" N   PRO C 429 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO C 429 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 429 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 164 "    0.035 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO A 165 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 431 "   -0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO C 432 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO C 432 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 432 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 2422 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2178
        2.76 -     3.29: 12520
        3.29 -     3.83: 24373
        3.83 -     4.36: 28413
        4.36 -     4.90: 48543
  Nonbonded interactions: 116027
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU E 458 "
            pdb=" NH1 ARG E 462 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" NH2 ARG C  79 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OD2 ASP E  69 "
            pdb=" OG  SER E  71 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS E  90 "
            pdb=" OG1 THR E 199 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ASP B 181 "
            pdb=" OG  SER B 185 "
     model   vdw
     2.254 3.040
  ... (remaining 116022 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 53 through 422 or resid 427 through 489))
  selection = chain 'B'
  selection = (chain 'C' and (resid 53 through 422 or resid 427 through 489))
  selection = (chain 'D' and (resid 53 through 422 or resid 427 through 489))
  selection = (chain 'E' and (resid 53 through 422 or resid 427 through 489))
  selection = (chain 'F' and (resid 53 through 422 or resid 427 through 489))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  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:          0.580
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     33.400
  Find NCS groups from input model:        0.700
  Set up NCS constraints:                  0.060
  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:13.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
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      :  0.003   0.055  13924  Z= 0.150
  Angle     :  0.572  10.248  18797  Z= 0.353
  Chirality :  0.041   0.132   2040
  Planarity :  0.005   0.069   2425
  Dihedral  : 18.435  90.369   5113
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.87 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 27.20 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.21), residues: 1711
  helix:  2.65 (0.16), residues: 936
  sheet: -0.31 (0.31), residues: 279
  loop : -0.29 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 385 
 HIS   0.004   0.001   HIS D  82 
 PHE   0.010   0.001   PHE B  63 
 TYR   0.010   0.001   TYR C 190 
 ARG   0.010   0.000   ARG A  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12726 (  854)
  hydrogen bonds       : angle       4.31540 ( 2469)
  covalent geometry    : bond        0.00291 (13924)
  covalent geometry    : angle       0.57161 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 207
  time to evaluate  : 1.639 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7939 (mtp180)
REVERT: B  435 GLU cc_start: 0.7245 (pm20) cc_final: 0.6940 (pt0)
REVERT: C  472 ASN cc_start: 0.7752 (t0) cc_final: 0.7529 (t0)
REVERT: D   78 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6918 (p90)
  outliers start: 41
  outliers final: 29
  residues processed: 238
  average time/residue: 1.7121
  time to fit residues: 435.6788
Evaluate side-chains
  228 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  142 GLU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  405 SER
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain C residue   69 ASP
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain C residue  170 SER
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue   78 TYR
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   97 THR
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  430 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  170 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    9.9990
   chunk 131 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 136 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 158 optimal weight:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
C 132 ASN
C 135 ASN
C 414 GLN
D  56 ASN
D  84 GLN
D 135 ASN
E 414 GLN
E 472 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.121036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.098152 restraints weight = 14050.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.10
r_work: 0.2822 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13924  Z= 0.253
  Angle     :  0.613   7.802  18797  Z= 0.335
  Chirality :  0.049   0.148   2040
  Planarity :  0.006   0.060   2425
  Dihedral  :  7.104  63.272   1975
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.99 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 22.25 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.21), residues: 1711
  helix:  2.51 (0.16), residues: 950
  sheet: -0.41 (0.31), residues: 283
  loop : -0.01 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 178 
 HIS   0.012   0.002   HIS C 195 
 PHE   0.012   0.002   PHE E 226 
 TYR   0.015   0.002   TYR C 190 
 ARG   0.007   0.001   ARG A  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06240 (  854)
  hydrogen bonds       : angle       3.60795 ( 2469)
  covalent geometry    : bond        0.00621 (13924)
  covalent geometry    : angle       0.61309 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 201
  time to evaluate  : 1.739 
Fit side-chains
REVERT: A  142 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8531 (tt0)
REVERT: A  387 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9045 (tttp)
REVERT: A  397 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8764 (mt)
REVERT: A  438 ASP cc_start: 0.7873 (m-30) cc_final: 0.7648 (m-30)
REVERT: A  459 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8015 (ttm170)
REVERT: B   78 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7118 (p90)
REVERT: C  397 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: C  438 ASP cc_start: 0.7835 (m-30) cc_final: 0.7629 (m-30)
REVERT: C  459 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7983 (ttm170)
REVERT: C  472 ASN cc_start: 0.7943 (t0) cc_final: 0.7606 (t0)
REVERT: D   78 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7155 (p90)
REVERT: D  138 ASP cc_start: 0.8577 (m-30) cc_final: 0.8334 (m-30)
REVERT: D  465 MET cc_start: 0.8602 (mtt) cc_final: 0.8394 (mtt)
REVERT: D  469 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7251 (mpp)
REVERT: E  195 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7281 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8926 (mm110)
REVERT: E  435 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7657 (mp0)
  outliers start: 90
  outliers final: 47
  residues processed: 252
  average time/residue: 2.1425
  time to fit residues: 578.4633
Evaluate side-chains
  255 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 197
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 GLU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  430 ILE
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   78 TYR
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  208 ILE
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  415 GLU
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  446 LYS
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   65 ILE
Chi-restraints excluded: chain E residue   86 ARG
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  187 ILE
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  398 THR
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  431 VAL
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 128 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
C  84 GLN
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.123440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099951 restraints weight = 14722.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.23
r_work: 0.2838 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13924  Z= 0.117
  Angle     :  0.468   8.072  18797  Z= 0.255
  Chirality :  0.040   0.129   2040
  Planarity :  0.004   0.061   2425
  Dihedral  :  5.919  80.635   1949
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.05 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 22.73 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.21), residues: 1711
  helix:  3.02 (0.16), residues: 950
  sheet: -0.33 (0.32), residues: 282
  loop :  0.04 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 385 
 HIS   0.005   0.001   HIS C 195 
 PHE   0.008   0.001   PHE B  63 
 TYR   0.009   0.001   TYR C 190 
 ARG   0.003   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04241 (  854)
  hydrogen bonds       : angle       3.29838 ( 2469)
  covalent geometry    : bond        0.00270 (13924)
  covalent geometry    : angle       0.46842 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 206
  time to evaluate  : 2.198 
Fit side-chains
REVERT: A  438 ASP cc_start: 0.7778 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  459 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8015 (ttm170)
REVERT: B   78 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.6993 (p90)
REVERT: B  469 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6822 (mpp)
REVERT: C  438 ASP cc_start: 0.7771 (m-30) cc_final: 0.7526 (m-30)
REVERT: C  459 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8019 (ttm170)
REVERT: C  472 ASN cc_start: 0.7879 (t0) cc_final: 0.7562 (t0)
REVERT: D   78 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.6977 (p90)
REVERT: D  138 ASP cc_start: 0.8461 (m-30) cc_final: 0.8237 (m-30)
REVERT: E  195 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7053 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8932 (mm110)
REVERT: E  435 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7584 (mp0)
REVERT: F  397 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8493 (mm)
REVERT: F  435 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7564 (mp0)
  outliers start: 70
  outliers final: 30
  residues processed: 246
  average time/residue: 1.7930
  time to fit residues: 471.6113
Evaluate side-chains
  238 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 199
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  469 MET
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   78 TYR
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  397 LEU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 93 optimal weight:    0.5980
   chunk 83 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 173 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 155 optimal weight:    6.9990
   overall best weight:    5.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  57 HIS
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
D  84 GLN
E  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.121646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.097859 restraints weight = 14345.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.22
r_work: 0.2816 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  13924  Z= 0.274
  Angle     :  0.624  11.065  18797  Z= 0.339
  Chirality :  0.049   0.151   2040
  Planarity :  0.005   0.055   2425
  Dihedral  :  5.789  55.809   1940
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.45 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 21.63 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.20), residues: 1711
  helix:  2.54 (0.16), residues: 952
  sheet: -0.35 (0.31), residues: 283
  loop :  0.05 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 385 
 HIS   0.010   0.002   HIS C 195 
 PHE   0.011   0.002   PHE A  63 
 TYR   0.018   0.002   TYR C 190 
 ARG   0.006   0.001   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06318 (  854)
  hydrogen bonds       : angle       3.49820 ( 2469)
  covalent geometry    : bond        0.00673 (13924)
  covalent geometry    : angle       0.62436 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 197
  time to evaluate  : 2.308 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8731 (mt)
REVERT: A  420 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (tptt)
REVERT: A  438 ASP cc_start: 0.7832 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  459 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8008 (ttm170)
REVERT: B   78 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7142 (p90)
REVERT: C  195 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6318 (t70)
REVERT: C  397 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8748 (mt)
REVERT: C  438 ASP cc_start: 0.7730 (m-30) cc_final: 0.7444 (m-30)
REVERT: C  459 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7934 (ttm170)
REVERT: C  470 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7931 (tttt)
REVERT: D  138 ASP cc_start: 0.8456 (m-30) cc_final: 0.8219 (m-30)
REVERT: E   94 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8627 (ttm170)
REVERT: E  195 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7228 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8908 (mm110)
REVERT: E  435 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7526 (mp0)
REVERT: F  397 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8754 (mm)
REVERT: F  435 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7559 (mp0)
  outliers start: 87
  outliers final: 46
  residues processed: 244
  average time/residue: 2.4254
  time to fit residues: 633.9603
Evaluate side-chains
  250 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 192
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   69 ASP
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  171 THR
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  415 GLU
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  446 LYS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   65 ILE
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  397 LEU
Chi-restraints excluded: chain F residue  398 THR
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  431 VAL
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 149 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 160 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 132 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  82 HIS
D  84 GLN
E  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.124249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.101305 restraints weight = 14094.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.13
r_work: 0.2852 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13924  Z= 0.125
  Angle     :  0.485  11.352  18797  Z= 0.261
  Chirality :  0.041   0.127   2040
  Planarity :  0.004   0.058   2425
  Dihedral  :  5.278  57.723   1938
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.46 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 22.66 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.21), residues: 1711
  helix:  2.99 (0.16), residues: 952
  sheet: -0.31 (0.32), residues: 282
  loop :  0.08 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 385 
 HIS   0.005   0.001   HIS C 195 
 PHE   0.009   0.001   PHE B  63 
 TYR   0.009   0.001   TYR C 190 
 ARG   0.006   0.000   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  854)
  hydrogen bonds       : angle       3.23371 ( 2469)
  covalent geometry    : bond        0.00293 (13924)
  covalent geometry    : angle       0.48507 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 200
  time to evaluate  : 1.706 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8777 (mt)
REVERT: A  420 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7987 (tptt)
REVERT: A  438 ASP cc_start: 0.7889 (m-30) cc_final: 0.7599 (m-30)
REVERT: A  459 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8201 (ttm170)
REVERT: B   78 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7095 (p90)
REVERT: B  438 ASP cc_start: 0.7823 (p0) cc_final: 0.7544 (p0)
REVERT: C  195 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6259 (t70)
REVERT: C  397 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8793 (mt)
REVERT: C  438 ASP cc_start: 0.7825 (m-30) cc_final: 0.7570 (m-30)
REVERT: C  459 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8160 (ttm170)
REVERT: D  138 ASP cc_start: 0.8456 (m-30) cc_final: 0.8225 (m-30)
REVERT: E  195 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (mm110)
REVERT: F  435 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7696 (mp0)
  outliers start: 74
  outliers final: 41
  residues processed: 243
  average time/residue: 1.7009
  time to fit residues: 441.8529
Evaluate side-chains
  250 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 200
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 161 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 143 optimal weight:    9.9990
   chunk 168 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 115 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  84 GLN
E  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.123020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.100296 restraints weight = 14786.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.16
r_work: 0.2812 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13924  Z= 0.170
  Angle     :  0.529  11.753  18797  Z= 0.284
  Chirality :  0.043   0.139   2040
  Planarity :  0.004   0.058   2425
  Dihedral  :  5.388  57.291   1938
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.16 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 22.66 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.21), residues: 1711
  helix:  2.93 (0.16), residues: 952
  sheet: -0.35 (0.31), residues: 282
  loop :  0.11 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E 385 
 HIS   0.007   0.001   HIS C 195 
 PHE   0.009   0.001   PHE A  63 
 TYR   0.012   0.002   TYR C 190 
 ARG   0.004   0.000   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05051 (  854)
  hydrogen bonds       : angle       3.27852 ( 2469)
  covalent geometry    : bond        0.00413 (13924)
  covalent geometry    : angle       0.52875 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 200
  time to evaluate  : 1.543 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8730 (mt)
REVERT: A  420 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7935 (tptt)
REVERT: A  438 ASP cc_start: 0.7822 (m-30) cc_final: 0.7484 (m-30)
REVERT: A  459 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8091 (ttm170)
REVERT: B   78 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7108 (p90)
REVERT: B  438 ASP cc_start: 0.7760 (p0) cc_final: 0.7479 (p0)
REVERT: C  195 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6242 (t70)
REVERT: C  397 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8776 (mt)
REVERT: C  438 ASP cc_start: 0.7783 (m-30) cc_final: 0.7495 (m-30)
REVERT: C  459 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8053 (ttm170)
REVERT: D  138 ASP cc_start: 0.8424 (m-30) cc_final: 0.8205 (m-30)
REVERT: D  469 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7129 (mpp)
REVERT: E  195 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7264 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8949 (mm110)
REVERT: F  397 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: F  435 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7586 (mp0)
  outliers start: 78
  outliers final: 45
  residues processed: 240
  average time/residue: 1.6952
  time to fit residues: 435.4342
Evaluate side-chains
  253 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 197
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  397 LEU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 132 optimal weight:    7.9990
   chunk 146 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 137 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.120392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.097104 restraints weight = 14278.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.19
r_work: 0.2778 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13924  Z= 0.213
  Angle     :  0.573  12.051  18797  Z= 0.309
  Chirality :  0.046   0.146   2040
  Planarity :  0.005   0.059   2425
  Dihedral  :  5.569  56.708   1938
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.87 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 22.45 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.20), residues: 1711
  helix:  2.74 (0.16), residues: 954
  sheet: -0.39 (0.31), residues: 282
  loop :  0.08 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E 385 
 HIS   0.009   0.001   HIS C 195 
 PHE   0.010   0.002   PHE C  63 
 TYR   0.015   0.002   TYR C 190 
 ARG   0.004   0.000   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05616 (  854)
  hydrogen bonds       : angle       3.35785 ( 2469)
  covalent geometry    : bond        0.00521 (13924)
  covalent geometry    : angle       0.57275 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 199
  time to evaluate  : 1.565 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.8425 (mtmp) cc_final: 0.8148 (mppt)
REVERT: A  397 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8799 (mt)
REVERT: A  420 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7976 (tptt)
REVERT: A  438 ASP cc_start: 0.7962 (m-30) cc_final: 0.7612 (m-30)
REVERT: A  459 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (ttm170)
REVERT: B   78 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7157 (p90)
REVERT: B  438 ASP cc_start: 0.7799 (p0) cc_final: 0.7487 (p0)
REVERT: C  195 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6297 (t70)
REVERT: C  397 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8821 (mt)
REVERT: C  438 ASP cc_start: 0.7925 (m-30) cc_final: 0.7606 (m-30)
REVERT: C  459 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8200 (ttm170)
REVERT: D  138 ASP cc_start: 0.8529 (m-30) cc_final: 0.8297 (m-30)
REVERT: D  465 MET cc_start: 0.8655 (mtt) cc_final: 0.8407 (mtt)
REVERT: D  469 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7333 (mpp)
REVERT: E  195 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7326 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8987 (mm110)
REVERT: E  458 GLU cc_start: 0.8919 (tt0) cc_final: 0.8610 (tm-30)
REVERT: F  397 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8672 (mm)
REVERT: F  435 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7684 (mp0)
  outliers start: 77
  outliers final: 49
  residues processed: 239
  average time/residue: 1.7202
  time to fit residues: 439.5142
Evaluate side-chains
  254 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 194
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  446 LYS
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  397 LEU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 173 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 127 optimal weight:    2.9990
   chunk 142 optimal weight:   10.0000
   chunk 144 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 137 optimal weight:    9.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.123014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.100387 restraints weight = 14706.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.15
r_work: 0.2809 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13924  Z= 0.171
  Angle     :  0.533  11.594  18797  Z= 0.287
  Chirality :  0.043   0.139   2040
  Planarity :  0.005   0.062   2425
  Dihedral  :  5.460  57.519   1938
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.99 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 22.52 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.21), residues: 1711
  helix:  2.87 (0.16), residues: 952
  sheet: -0.38 (0.31), residues: 282
  loop :  0.06 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP E 385 
 HIS   0.008   0.001   HIS C 195 
 PHE   0.009   0.001   PHE C  63 
 TYR   0.012   0.002   TYR C 190 
 ARG   0.005   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05048 (  854)
  hydrogen bonds       : angle       3.29151 ( 2469)
  covalent geometry    : bond        0.00416 (13924)
  covalent geometry    : angle       0.53269 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 200
  time to evaluate  : 1.711 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8726 (mt)
REVERT: A  420 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7916 (tptt)
REVERT: A  438 ASP cc_start: 0.7820 (m-30) cc_final: 0.7454 (m-30)
REVERT: A  459 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8116 (ttm170)
REVERT: B   78 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7123 (p90)
REVERT: B  438 ASP cc_start: 0.7686 (p0) cc_final: 0.7327 (p0)
REVERT: C  195 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6163 (t70)
REVERT: C  397 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8793 (mt)
REVERT: C  438 ASP cc_start: 0.7840 (m-30) cc_final: 0.7538 (m-30)
REVERT: C  459 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8079 (ttm170)
REVERT: C  470 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7996 (tttt)
REVERT: D  138 ASP cc_start: 0.8414 (m-30) cc_final: 0.8174 (m-30)
REVERT: D  465 MET cc_start: 0.8543 (mtt) cc_final: 0.8281 (mtt)
REVERT: D  469 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7133 (mpp)
REVERT: E  195 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7252 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8952 (mm110)
REVERT: E  458 GLU cc_start: 0.8755 (tt0) cc_final: 0.8416 (tm-30)
REVERT: F  397 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8477 (mm)
REVERT: F  435 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7598 (mp0)
  outliers start: 78
  outliers final: 49
  residues processed: 243
  average time/residue: 1.6668
  time to fit residues: 433.5189
Evaluate side-chains
  257 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 196
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  224 GLU
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  168 ASP
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  446 LYS
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  168 ASP
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  397 LEU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 147 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 152 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  56 ASN
D  84 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.123664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.099470 restraints weight = 14683.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 1.31
r_work: 0.2833 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13924  Z= 0.115
  Angle     :  0.478  12.679  18797  Z= 0.254
  Chirality :  0.040   0.127   2040
  Planarity :  0.004   0.064   2425
  Dihedral  :  5.184  59.210   1938
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.58 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.14 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.21), residues: 1711
  helix:  3.16 (0.16), residues: 954
  sheet: -0.34 (0.31), residues: 282
  loop :  0.09 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 385 
 HIS   0.005   0.001   HIS C 195 
 PHE   0.008   0.001   PHE B  63 
 TYR   0.009   0.001   TYR C 190 
 ARG   0.005   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  854)
  hydrogen bonds       : angle       3.16540 ( 2469)
  covalent geometry    : bond        0.00269 (13924)
  covalent geometry    : angle       0.47765 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 203
  time to evaluate  : 1.657 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8680 (mt)
REVERT: A  420 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7903 (tptt)
REVERT: A  438 ASP cc_start: 0.7829 (m-30) cc_final: 0.7499 (m-30)
REVERT: A  459 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7979 (ttm170)
REVERT: B   78 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7044 (p90)
REVERT: B  438 ASP cc_start: 0.7569 (p0) cc_final: 0.7141 (m-30)
REVERT: C  195 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6038 (t70)
REVERT: C  397 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8722 (mt)
REVERT: C  438 ASP cc_start: 0.7760 (m-30) cc_final: 0.7438 (m-30)
REVERT: C  459 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7961 (ttm170)
REVERT: C  470 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7946 (tttt)
REVERT: D  138 ASP cc_start: 0.8363 (m-30) cc_final: 0.8134 (m-30)
REVERT: D  465 MET cc_start: 0.8390 (mtt) cc_final: 0.8133 (mtt)
REVERT: D  469 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6921 (mpp)
REVERT: E  195 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6942 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (mm110)
REVERT: E  458 GLU cc_start: 0.8673 (tt0) cc_final: 0.8310 (tm-30)
REVERT: F   76 GLU cc_start: 0.8557 (pt0) cc_final: 0.8004 (tp30)
REVERT: F  435 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7541 (mp0)
REVERT: F  437 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8138 (tp-100)
  outliers start: 66
  outliers final: 44
  residues processed: 238
  average time/residue: 1.6483
  time to fit residues: 420.4925
Evaluate side-chains
  251 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 196
  time to evaluate  : 1.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain E residue  428 ILE
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Chi-restraints excluded: chain F residue  435 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
C 414 GLN
D  56 ASN
D  84 GLN
D 472 ASN
E 414 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.123528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.100053 restraints weight = 14671.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.23
r_work: 0.2836 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13924  Z= 0.114
  Angle     :  0.479  12.735  18797  Z= 0.254
  Chirality :  0.040   0.128   2040
  Planarity :  0.004   0.064   2425
  Dihedral  :  4.988  59.667   1936
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.69 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.76 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.21), residues: 1711
  helix:  3.26 (0.16), residues: 954
  sheet: -0.32 (0.31), residues: 282
  loop :  0.10 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 385 
 HIS   0.005   0.001   HIS C 195 
 PHE   0.008   0.001   PHE C  63 
 TYR   0.008   0.001   TYR C 190 
 ARG   0.004   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  854)
  hydrogen bonds       : angle       3.15502 ( 2469)
  covalent geometry    : bond        0.00268 (13924)
  covalent geometry    : angle       0.47912 (18797)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 200
  time to evaluate  : 1.551 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8765 (mt)
REVERT: A  420 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7962 (tptt)
REVERT: A  438 ASP cc_start: 0.7945 (m-30) cc_final: 0.7650 (m-30)
REVERT: A  459 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8121 (ttm170)
REVERT: B   78 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7047 (p90)
REVERT: B  438 ASP cc_start: 0.7650 (p0) cc_final: 0.7243 (m-30)
REVERT: B  462 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7992 (mtm-85)
REVERT: C  195 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6176 (t70)
REVERT: C  397 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8804 (mt)
REVERT: C  414 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8334 (tt0)
REVERT: C  435 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7637 (mp0)
REVERT: C  438 ASP cc_start: 0.7929 (m-30) cc_final: 0.7658 (m-30)
REVERT: C  459 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8122 (ttm170)
REVERT: C  470 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.8001 (tttt)
REVERT: D  138 ASP cc_start: 0.8413 (m-30) cc_final: 0.8199 (m-30)
REVERT: D  465 MET cc_start: 0.8468 (mtt) cc_final: 0.8222 (mtt)
REVERT: D  469 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7012 (mpp)
REVERT: E  195 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7048 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8968 (mm110)
REVERT: E  458 GLU cc_start: 0.8757 (tt0) cc_final: 0.8413 (tm-30)
REVERT: F   76 GLU cc_start: 0.8579 (pt0) cc_final: 0.8110 (tp30)
REVERT: F  437 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8210 (tp-100)
  outliers start: 56
  outliers final: 37
  residues processed: 230
  average time/residue: 1.8291
  time to fit residues: 451.0108
Evaluate side-chains
  248 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 199
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  170 SER
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain C residue  414 GLN
Chi-restraints excluded: chain C residue  421 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  428 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
Chi-restraints excluded: chain E residue  168 ASP
Chi-restraints excluded: chain E residue  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  205 GLN
Chi-restraints excluded: chain E residue  398 THR
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  427 THR
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  224 GLU
Chi-restraints excluded: chain F residue  400 LYS
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  428 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 118 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 161 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
D  56 ASN
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.122127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.097626 restraints weight = 14706.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.32
r_work: 0.2796 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13924  Z= 0.155
  Angle     :  0.523  13.108  18797  Z= 0.279
  Chirality :  0.043   0.137   2040
  Planarity :  0.004   0.062   2425
  Dihedral  :  5.145  59.913   1935
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.75 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 23.14 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.21), residues: 1711
  helix:  3.10 (0.16), residues: 954
  sheet: -0.31 (0.31), residues: 282
  loop :  0.08 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 385 
 HIS   0.007   0.001   HIS C 195 
 PHE   0.009   0.001   PHE A  63 
 TYR   0.011   0.001   TYR C 190 
 ARG   0.005   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04721 (  854)
  hydrogen bonds       : angle       3.23302 ( 2469)
  covalent geometry    : bond        0.00373 (13924)
  covalent geometry    : angle       0.52275 (18797)

===============================================================================
Job complete
usr+sys time: 12960.13 seconds
wall clock time: 231 minutes 31.57 seconds (13891.57 seconds total)