Starting phenix.real_space_refine
on Wed Mar  4 11:10:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_28639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_28639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_28639.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_28639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ew0_28639/03_2026/8ew0_28639.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.04, per 1000 atoms: 0.22
  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: 1.11
  Conformation dependent library (CDL) restraints added in 713.9 milliseconds
  

  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: 0.30
  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: 1.88

  Time building geometry restraints manager: 1.51 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.280
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.680
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (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
 ARG   0.010   0.000   ARG A  66 
 TYR   0.010   0.001   TYR C 190 
 PHE   0.010   0.001   PHE B  63 
 TRP   0.009   0.001   TRP E 385 
 HIS   0.004   0.001   HIS D  82 

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

*********************** 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  : 0.470 
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: 0.7986
  time to fit residues: 202.4673
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  : 0.518 
-------------------------------------------------------------------------------
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 98 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.0270
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    3.3844

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 484 ASN
B 472 ASN
D  56 ASN
D  84 GLN
D 135 ASN
E 414 GLN
E 472 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.121378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.096779 restraints weight = 14785.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.34
r_work: 0.2794 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.0877

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= 0.193
  Angle     :  0.555   7.205  18797  Z= 0.303
  Chirality :  0.045   0.143   2040
  Planarity :  0.005   0.061   2425
  Dihedral  :  6.808  59.449   1975
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.81 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 22.73 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.21), residues: 1711
  helix:  2.73 (0.16), residues: 950
  sheet: -0.38 (0.31), residues: 283
  loop :  0.01 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  66 
 TYR   0.012   0.002   TYR C 190 
 PHE   0.010   0.002   PHE F 220 
 TRP   0.008   0.002   TRP E 385 
 HIS   0.009   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (13924)
  covalent geometry    : angle       0.55529 (18797)
  hydrogen bonds       : bond        0.05534 (  854)
  hydrogen bonds       : angle       3.50519 ( 2469)

*********************** 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
  285 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 204
  time to evaluate  : 0.556 
Fit side-chains
REVERT: A  142 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: A  387 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8926 (tttp)
REVERT: A  438 ASP cc_start: 0.7741 (m-30) cc_final: 0.7505 (m-30)
REVERT: A  459 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7807 (ttm170)
REVERT: B   78 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7105 (p90)
REVERT: C  459 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7824 (ttm170)
REVERT: C  472 ASN cc_start: 0.7820 (t0) cc_final: 0.7516 (t0)
REVERT: D   78 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7100 (p90)
REVERT: D  138 ASP cc_start: 0.8482 (m-30) cc_final: 0.8247 (m-30)
REVERT: E   84 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7637 (mp10)
REVERT: E  195 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.7015 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8871 (mm110)
REVERT: E  435 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7480 (mp0)
  outliers start: 81
  outliers final: 44
  residues processed: 248
  average time/residue: 0.8393
  time to fit residues: 221.4146
Evaluate side-chains
  250 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 197
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
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  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  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 B residue  472 ASN
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  173 GLU
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  430 ILE
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  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 E residue   62 SER
Chi-restraints excluded: chain E residue   65 ILE
Chi-restraints excluded: chain E residue   84 GLN
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  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  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  400 LYS
Chi-restraints excluded: chain F residue  411 MET
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 66 optimal weight:    8.9990
   chunk 165 optimal weight:    6.9990
   chunk 158 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 139 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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  56 ASN
C  84 GLN
C 132 ASN
C 135 ASN
D  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.121172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.097872 restraints weight = 14187.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 1.14
r_work: 0.2800 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  13924  Z= 0.241
  Angle     :  0.594   9.448  18797  Z= 0.325
  Chirality :  0.048   0.147   2040
  Planarity :  0.005   0.060   2425
  Dihedral  :  6.449  81.773   1950
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.93 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 21.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.20), residues: 1711
  helix:  2.57 (0.16), residues: 950
  sheet: -0.37 (0.31), residues: 283
  loop : -0.02 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  79 
 TYR   0.017   0.002   TYR C 190 
 PHE   0.010   0.002   PHE C 421 
 TRP   0.008   0.002   TRP E 385 
 HIS   0.011   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (13924)
  covalent geometry    : angle       0.59442 (18797)
  hydrogen bonds       : bond        0.06019 (  854)
  hydrogen bonds       : angle       3.50203 ( 2469)

*********************** 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
  290 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 197
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8441 (mtp180) cc_final: 0.8221 (mtp180)
REVERT: A  387 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9008 (tttp)
REVERT: A  397 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8799 (mt)
REVERT: A  438 ASP cc_start: 0.7924 (m-30) cc_final: 0.7721 (m-30)
REVERT: A  459 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8120 (ttm170)
REVERT: B   78 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7109 (p90)
REVERT: B  465 MET cc_start: 0.8510 (mtt) cc_final: 0.8282 (mtt)
REVERT: B  469 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7059 (mpp)
REVERT: C  397 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8779 (mt)
REVERT: C  459 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8100 (ttm170)
REVERT: C  472 ASN cc_start: 0.8005 (t0) cc_final: 0.7648 (t0)
REVERT: D  138 ASP cc_start: 0.8527 (m-30) cc_final: 0.8284 (m-30)
REVERT: D  470 LYS cc_start: 0.8405 (tttt) cc_final: 0.8146 (tttt)
REVERT: E  195 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7309 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8939 (mm110)
REVERT: E  435 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (mp0)
REVERT: F  397 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8809 (mm)
REVERT: F  435 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7669 (mp0)
  outliers start: 93
  outliers final: 52
  residues processed: 251
  average time/residue: 0.7771
  time to fit residues: 208.3684
Evaluate side-chains
  259 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 196
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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  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 A residue  469 MET
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue  101 VAL
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 B residue  469 MET
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  173 GLU
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 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  187 ILE
Chi-restraints excluded: chain D residue  198 VAL
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  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   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  400 LYS
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 138 optimal weight:    9.9990
   chunk 98 optimal weight:    0.7980
   chunk 163 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 142 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 117 optimal weight:    8.9990
   chunk 160 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.122144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.097612 restraints weight = 14716.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.33
r_work: 0.2800 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13924  Z= 0.147
  Angle     :  0.504   8.986  18797  Z= 0.273
  Chirality :  0.042   0.133   2040
  Planarity :  0.004   0.062   2425
  Dihedral  :  5.787  55.861   1947
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.69 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 21.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.21), residues: 1711
  helix:  2.87 (0.16), residues: 952
  sheet: -0.30 (0.32), residues: 282
  loop :  0.06 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  66 
 TYR   0.011   0.001   TYR C 190 
 PHE   0.009   0.001   PHE B  63 
 TRP   0.009   0.001   TRP E 385 
 HIS   0.006   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (13924)
  covalent geometry    : angle       0.50414 (18797)
  hydrogen bonds       : bond        0.04756 (  854)
  hydrogen bonds       : angle       3.30998 ( 2469)

*********************** 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
  285 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 201
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7998 (mtp180)
REVERT: A  397 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8670 (mt)
REVERT: A  420 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7980 (tptt)
REVERT: A  438 ASP cc_start: 0.7716 (m-30) cc_final: 0.7423 (m-30)
REVERT: A  459 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7856 (ttm170)
REVERT: B   78 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7077 (p90)
REVERT: C  195 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6271 (t70)
REVERT: C  397 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8703 (mt)
REVERT: C  459 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7860 (ttm170)
REVERT: D  130 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8742 (ttmt)
REVERT: D  138 ASP cc_start: 0.8408 (m-30) cc_final: 0.8174 (m-30)
REVERT: D  414 GLN cc_start: 0.8666 (tt0) cc_final: 0.8433 (tt0)
REVERT: D  470 LYS cc_start: 0.8232 (tttt) cc_final: 0.7974 (tttt)
REVERT: E  195 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7100 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8971 (mm110)
REVERT: E  435 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7447 (mp0)
REVERT: E  462 ARG cc_start: 0.8226 (mtp180) cc_final: 0.8008 (mtp180)
REVERT: F  397 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8448 (mm)
REVERT: F  435 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7473 (mp0)
  outliers start: 84
  outliers final: 45
  residues processed: 248
  average time/residue: 0.8188
  time to fit residues: 216.0689
Evaluate side-chains
  255 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 199
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  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  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 C residue   65 ILE
Chi-restraints excluded: chain C residue   69 ASP
Chi-restraints excluded: chain C residue   71 SER
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  431 VAL
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue  101 VAL
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  415 GLU
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   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  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  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  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  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 171 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 168 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 159 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.8584

-------------------------------------------------------------------------------
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 = 0.3311 r_free = 0.3311 target = 0.122805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.099122 restraints weight = 14857.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.24
r_work: 0.2817 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13924  Z= 0.127
  Angle     :  0.482  11.121  18797  Z= 0.259
  Chirality :  0.041   0.129   2040
  Planarity :  0.004   0.057   2425
  Dihedral  :  5.422  56.082   1943
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.87 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 22.93 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.21), residues: 1711
  helix:  3.09 (0.16), residues: 952
  sheet: -0.32 (0.31), residues: 282
  loop :  0.09 (0.29), residues: 477

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13924)
  covalent geometry    : angle       0.48243 (18797)
  hydrogen bonds       : bond        0.04343 (  854)
  hydrogen bonds       : angle       3.21012 ( 2469)

*********************** 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
  280 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 204
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8745 (mt)
REVERT: A  420 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7950 (tptt)
REVERT: A  438 ASP cc_start: 0.7847 (m-30) cc_final: 0.7525 (m-30)
REVERT: A  459 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8037 (ttm170)
REVERT: B   78 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7095 (p90)
REVERT: C  195 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6392 (t70)
REVERT: C  397 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8785 (mt)
REVERT: C  435 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7679 (mp0)
REVERT: C  459 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8033 (ttm170)
REVERT: D  469 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7007 (mpp)
REVERT: D  470 LYS cc_start: 0.8280 (tttt) cc_final: 0.8023 (tttt)
REVERT: E  195 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7110 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8944 (mm110)
REVERT: F   76 GLU cc_start: 0.8582 (pt0) cc_final: 0.7961 (tp30)
REVERT: F  397 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8362 (mm)
REVERT: F  435 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7604 (mp0)
  outliers start: 76
  outliers final: 44
  residues processed: 244
  average time/residue: 0.8279
  time to fit residues: 214.8390
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  : 0.535 
-------------------------------------------------------------------------------
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  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  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  431 VAL
Chi-restraints excluded: chain C residue   65 ILE
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  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  431 VAL
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain C residue  459 ARG
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  469 MET
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   86 ARG
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  187 ILE
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  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  431 VAL
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 137 optimal weight:   10.0000
   chunk 139 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 74 optimal weight:    9.9990
   chunk 121 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 83 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 154 optimal weight:   10.0000
   chunk 159 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    3.7186

-------------------------------------------------------------------------------
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
D 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.120684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.096135 restraints weight = 14713.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.32
r_work: 0.2784 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13924  Z= 0.202
  Angle     :  0.556  12.248  18797  Z= 0.300
  Chirality :  0.045   0.144   2040
  Planarity :  0.005   0.057   2425
  Dihedral  :  5.428  56.378   1938
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.16 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 22.31 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.21), residues: 1711
  helix:  2.83 (0.16), residues: 952
  sheet: -0.36 (0.31), residues: 282
  loop :  0.07 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  79 
 TYR   0.014   0.002   TYR C 190 
 PHE   0.010   0.002   PHE C  63 
 TRP   0.008   0.002   TRP E 385 
 HIS   0.009   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (13924)
  covalent geometry    : angle       0.55599 (18797)
  hydrogen bonds       : bond        0.05455 (  854)
  hydrogen bonds       : angle       3.34141 ( 2469)

*********************** 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
  286 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 200
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8685 (mt)
REVERT: A  420 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7909 (tptt)
REVERT: A  438 ASP cc_start: 0.7735 (m-30) cc_final: 0.7363 (m-30)
REVERT: A  459 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7885 (ttm170)
REVERT: B   78 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7113 (p90)
REVERT: B  438 ASP cc_start: 0.7759 (p0) cc_final: 0.7492 (p0)
REVERT: C  195 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6161 (t70)
REVERT: C  397 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8718 (mt)
REVERT: C  435 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7579 (mp0)
REVERT: C  459 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7852 (ttm170)
REVERT: D  469 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7043 (mpp)
REVERT: E   94 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8574 (ttm170)
REVERT: E  195 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7159 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8915 (mm110)
REVERT: F  397 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8546 (mm)
REVERT: F  435 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7492 (mp0)
  outliers start: 86
  outliers final: 53
  residues processed: 245
  average time/residue: 0.8076
  time to fit residues: 210.8992
Evaluate side-chains
  262 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 197
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
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  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  101 VAL
Chi-restraints excluded: chain B residue  130 LYS
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   65 ILE
Chi-restraints excluded: chain C residue   69 ASP
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  168 ASP
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  431 VAL
Chi-restraints excluded: chain C residue  435 GLU
Chi-restraints excluded: chain C residue  459 ARG
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue  101 VAL
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 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  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
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  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  397 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 140 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    0.2980
   chunk 104 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 115 optimal weight:   10.0000
   chunk 129 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 141 optimal weight:    2.9990
   overall best weight:    3.2586

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.122816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.100073 restraints weight = 14671.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.16
r_work: 0.2806 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8909
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13924  Z= 0.181
  Angle     :  0.540  12.518  18797  Z= 0.291
  Chirality :  0.044   0.139   2040
  Planarity :  0.005   0.059   2425
  Dihedral  :  5.399  56.957   1938
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.75 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 22.59 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.20), residues: 1711
  helix:  2.89 (0.16), residues: 949
  sheet: -0.38 (0.31), residues: 282
  loop :  0.03 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 419 
 TYR   0.013   0.002   TYR C 190 
 PHE   0.009   0.001   PHE C  63 
 TRP   0.009   0.002   TRP E 385 
 HIS   0.008   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (13924)
  covalent geometry    : angle       0.54039 (18797)
  hydrogen bonds       : bond        0.05161 (  854)
  hydrogen bonds       : angle       3.30701 ( 2469)

*********************** 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
  280 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 196
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8738 (mt)
REVERT: A  420 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7895 (tptt)
REVERT: A  438 ASP cc_start: 0.7842 (m-30) cc_final: 0.7489 (m-30)
REVERT: A  459 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (ttm170)
REVERT: B   78 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7095 (p90)
REVERT: B   84 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7622 (mp10)
REVERT: B  438 ASP cc_start: 0.7717 (p0) cc_final: 0.7409 (p0)
REVERT: C  195 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6109 (t70)
REVERT: C  397 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8770 (mt)
REVERT: C  435 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7658 (mp0)
REVERT: C  459 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8044 (ttm170)
REVERT: D  465 MET cc_start: 0.8568 (mtt) cc_final: 0.8267 (mtt)
REVERT: D  469 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7143 (mpp)
REVERT: E  195 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7259 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8952 (mm110)
REVERT: E  458 GLU cc_start: 0.8766 (tt0) cc_final: 0.8439 (tm-30)
REVERT: F  397 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8550 (mm)
REVERT: F  435 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7565 (mp0)
  outliers start: 84
  outliers final: 56
  residues processed: 245
  average time/residue: 0.7975
  time to fit residues: 208.3518
Evaluate side-chains
  263 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 194
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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  374 ASN
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  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   84 GLN
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   65 ILE
Chi-restraints excluded: chain C residue   69 ASP
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue  168 ASP
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   65 ILE
Chi-restraints excluded: chain D residue  101 VAL
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  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 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  101 VAL
Chi-restraints excluded: chain E residue  130 LYS
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  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  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  431 VAL
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 166 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 143 optimal weight:    9.9990
   chunk 170 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 169 optimal weight:    7.9990
   chunk 94 optimal weight:    9.9990
   chunk 99 optimal weight:    0.0570
   chunk 171 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0980
   overall best weight:    1.0100

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.127862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.105875 restraints weight = 14485.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.13
r_work: 0.2876 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13924  Z= 0.100
  Angle     :  0.457  12.465  18797  Z= 0.243
  Chirality :  0.039   0.128   2040
  Planarity :  0.004   0.061   2425
  Dihedral  :  5.036  58.942   1938
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.69 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.83 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.21), residues: 1711
  helix:  3.34 (0.16), residues: 949
  sheet: -0.37 (0.31), residues: 282
  loop :  0.06 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  66 
 TYR   0.007   0.001   TYR C 190 
 PHE   0.007   0.001   PHE B  63 
 TRP   0.011   0.001   TRP E 385 
 HIS   0.004   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (13924)
  covalent geometry    : angle       0.45686 (18797)
  hydrogen bonds       : bond        0.03684 (  854)
  hydrogen bonds       : angle       3.13133 ( 2469)

*********************** 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
  263 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 197
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8752 (mt)
REVERT: A  420 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7904 (tptt)
REVERT: A  438 ASP cc_start: 0.7846 (m-30) cc_final: 0.7536 (m-30)
REVERT: A  459 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8059 (ttm170)
REVERT: B   78 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7039 (p90)
REVERT: B   84 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7514 (mp10)
REVERT: B  438 ASP cc_start: 0.7649 (p0) cc_final: 0.7254 (p0)
REVERT: B  465 MET cc_start: 0.8341 (mtt) cc_final: 0.8058 (mtt)
REVERT: B  469 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6723 (mpp)
REVERT: C  195 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6019 (t70)
REVERT: C  435 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7543 (mp0)
REVERT: C  459 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8073 (ttm170)
REVERT: D  465 MET cc_start: 0.8522 (mtt) cc_final: 0.8269 (mtt)
REVERT: D  469 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6848 (mpp)
REVERT: E   94 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8266 (ttm170)
REVERT: E  130 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8789 (ttmt)
REVERT: E  195 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6974 (OUTLIER)
REVERT: E  458 GLU cc_start: 0.8728 (tt0) cc_final: 0.8380 (tm-30)
REVERT: F   76 GLU cc_start: 0.8512 (pt0) cc_final: 0.8078 (tp30)
REVERT: F  437 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8262 (tp-100)
  outliers start: 66
  outliers final: 34
  residues processed: 233
  average time/residue: 0.8023
  time to fit residues: 199.4164
Evaluate side-chains
  239 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
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   84 GLN
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  469 MET
Chi-restraints excluded: chain C residue   71 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  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  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  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  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  414 GLN
Chi-restraints excluded: chain F residue  431 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 23 optimal weight:    0.0370
   chunk 33 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 110 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.9262

-------------------------------------------------------------------------------
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**
B 472 ASN
C  84 GLN
C 414 GLN
D  84 GLN
D 472 ASN
** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.125395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.102172 restraints weight = 14742.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.22
r_work: 0.2867 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13924  Z= 0.096
  Angle     :  0.453  12.263  18797  Z= 0.240
  Chirality :  0.039   0.129   2040
  Planarity :  0.004   0.062   2425
  Dihedral  :  4.865  59.110   1937
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.40 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.38 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.21), residues: 1711
  helix:  3.50 (0.16), residues: 949
  sheet: -0.34 (0.31), residues: 282
  loop :  0.08 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  86 
 TYR   0.006   0.001   TYR C 190 
 PHE   0.007   0.001   PHE C  63 
 TRP   0.010   0.001   TRP E 385 
 HIS   0.004   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (13924)
  covalent geometry    : angle       0.45323 (18797)
  hydrogen bonds       : bond        0.03551 (  854)
  hydrogen bonds       : angle       3.08717 ( 2469)

*********************** 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
  259 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 201
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8774 (mt)
REVERT: A  403 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8120 (ttp-110)
REVERT: A  420 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7880 (tptt)
REVERT: A  438 ASP cc_start: 0.7911 (m-30) cc_final: 0.7640 (m-30)
REVERT: A  459 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8089 (ttm170)
REVERT: B   78 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7038 (p90)
REVERT: B   84 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7536 (mp10)
REVERT: B  438 ASP cc_start: 0.7658 (p0) cc_final: 0.7224 (m-30)
REVERT: C  195 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6017 (t70)
REVERT: C  435 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7569 (mp0)
REVERT: C  459 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8109 (ttm170)
REVERT: E  195 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6951 (OUTLIER)
REVERT: E  458 GLU cc_start: 0.8744 (tt0) cc_final: 0.8393 (tm-30)
REVERT: F   76 GLU cc_start: 0.8554 (pt0) cc_final: 0.8129 (tp30)
REVERT: F  176 MET cc_start: 0.9242 (mmp) cc_final: 0.8730 (mmp)
REVERT: F  437 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8218 (tp-100)
  outliers start: 58
  outliers final: 33
  residues processed: 231
  average time/residue: 0.8031
  time to fit residues: 197.9968
Evaluate side-chains
  237 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 196
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  397 LEU
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  459 ARG
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   78 TYR
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  130 LYS
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 C residue   71 SER
Chi-restraints excluded: chain C residue  195 HIS
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  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  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 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  195 HIS
Chi-restraints excluded: chain E residue  198 VAL
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  414 GLN
Chi-restraints excluded: chain F residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 128 optimal weight:    5.9990
   chunk 156 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 141 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 109 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 114 optimal weight:    9.9990
   chunk 153 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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**
B 472 ASN
C  84 GLN
C 414 GLN
D  84 GLN
D 472 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.123565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.099266 restraints weight = 14647.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.31
r_work: 0.2824 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13924  Z= 0.130
  Angle     :  0.499  12.601  18797  Z= 0.264
  Chirality :  0.041   0.131   2040
  Planarity :  0.004   0.068   2425
  Dihedral  :  5.043  58.933   1937
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.58 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.21), residues: 1711
  helix:  3.35 (0.16), residues: 951
  sheet: -0.35 (0.31), residues: 282
  loop :  0.11 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  86 
 TYR   0.010   0.001   TYR F  78 
 PHE   0.008   0.001   PHE C  63 
 TRP   0.008   0.001   TRP E 385 
 HIS   0.006   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13924)
  covalent geometry    : angle       0.49862 (18797)
  hydrogen bonds       : bond        0.04273 (  854)
  hydrogen bonds       : angle       3.16299 ( 2469)

********************** 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
  247 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 196
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8714 (mt)
REVERT: A  420 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7861 (tptt)
REVERT: A  438 ASP cc_start: 0.7815 (m-30) cc_final: 0.7500 (m-30)
REVERT: A  459 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7974 (ttm170)
REVERT: B   78 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7062 (p90)
REVERT: B  438 ASP cc_start: 0.7640 (p0) cc_final: 0.7154 (m-30)
REVERT: C  195 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6050 (t70)
REVERT: C  435 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7446 (mp0)
REVERT: C  459 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7972 (ttm170)
REVERT: E  195 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7029 (OUTLIER)
REVERT: E  205 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8934 (mm110)
REVERT: E  458 GLU cc_start: 0.8690 (tt0) cc_final: 0.8329 (tm-30)
REVERT: F   76 GLU cc_start: 0.8528 (pt0) cc_final: 0.8015 (tp30)
REVERT: F  437 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8085 (tp-100)
REVERT: F  458 GLU cc_start: 0.8617 (tt0) cc_final: 0.8268 (tm-30)
  outliers start: 51
  outliers final: 33
  residues processed: 227
  average time/residue: 0.8021
  time to fit residues: 194.3691
Evaluate side-chains
  236 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 195
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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  420 LYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  428 ILE
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  415 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   71 SER
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  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  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 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  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  411 MET
Chi-restraints excluded: chain F residue  414 GLN
Chi-restraints excluded: chain F residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 142 optimal weight:    9.9990
   chunk 144 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 125 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3325 r_free = 0.3325 target = 0.123873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099605 restraints weight = 14692.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.31
r_work: 0.2847 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13924  Z= 0.123
  Angle     :  0.492  12.139  18797  Z= 0.260
  Chirality :  0.041   0.129   2040
  Planarity :  0.004   0.069   2425
  Dihedral  :  5.011  58.146   1937
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.58 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.86 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.21), residues: 1711
  helix:  3.33 (0.16), residues: 951
  sheet: -0.35 (0.31), residues: 282
  loop :  0.09 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  86 
 TYR   0.009   0.001   TYR C 190 
 PHE   0.008   0.001   PHE C  63 
 TRP   0.009   0.001   TRP E 385 
 HIS   0.005   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13924)
  covalent geometry    : angle       0.49213 (18797)
  hydrogen bonds       : bond        0.04138 (  854)
  hydrogen bonds       : angle       3.17332 ( 2469)

===============================================================================
Job complete
usr+sys time: 5228.88 seconds
wall clock time: 89 minutes 46.01 seconds (5386.01 seconds total)