Starting phenix.real_space_refine
on Mon Jul 28 23:52:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u5j_26352/07_2025/7u5j_26352.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.069
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      48      5.16       5
     C    6628      2.51       5
     N    1860      2.21       5
     O    2268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10804
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2630
          Classifications: {'peptide': 344}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "B"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 68
          Classifications: {'water': 68}
          Link IDs: {None: 67}
    Chain: "C"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 73
          Classifications: {'water': 73}
          Link IDs: {None: 72}
    Chain: "D"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 73
          Classifications: {'water': 73}
          Link IDs: {None: 72}
  Time building chain proxies: 7.09, per 1000 atoms: 0.66
  Number of scatterers: 10804
  At special positions: 0
  Unit cell: (95.23, 80.25, 103.79, 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      48     16.00
     O    2268      8.00
     N    1860      7.00
     C    6628      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2528

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      53.5% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 24
    Processing helix  chain 'A' and resid 36 through 47
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 67 through 71
      removed outlier: 3.932A  pdb=" N   VAL A  70 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 86
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 130 through 141
    Processing helix  chain 'A' and resid 160 through 180
    Processing helix  chain 'A' and resid 198 through 220
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 245 through 261
    Processing helix  chain 'A' and resid 276 through 289
    Processing helix  chain 'A' and resid 307 through 315
    Processing helix  chain 'A' and resid 320 through 339
      removed outlier: 4.097A  pdb=" N   ALA A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 24
    Processing helix  chain 'B' and resid 36 through 47
    Processing helix  chain 'B' and resid 52 through 64
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 3.920A  pdb=" N   VAL B  70 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 86
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 180
    Processing helix  chain 'B' and resid 198 through 220
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 245 through 261
    Processing helix  chain 'B' and resid 276 through 289
    Processing helix  chain 'B' and resid 307 through 315
    Processing helix  chain 'B' and resid 320 through 339
      removed outlier: 4.088A  pdb=" N   ALA B 334 " --> pdb=" O   LYS B 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 36 through 47
    Processing helix  chain 'C' and resid 52 through 64
    Processing helix  chain 'C' and resid 67 through 71
      removed outlier: 3.928A  pdb=" N   VAL C  70 " --> pdb=" O   ASP C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 86
    Processing helix  chain 'C' and resid 93 through 102
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 180
    Processing helix  chain 'C' and resid 198 through 220
    Processing helix  chain 'C' and resid 223 through 227
    Processing helix  chain 'C' and resid 245 through 261
    Processing helix  chain 'C' and resid 276 through 289
    Processing helix  chain 'C' and resid 307 through 315
    Processing helix  chain 'C' and resid 320 through 339
      removed outlier: 4.095A  pdb=" N   ALA C 334 " --> pdb=" O   LYS C 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 36 through 47
    Processing helix  chain 'D' and resid 52 through 64
    Processing helix  chain 'D' and resid 67 through 71
      removed outlier: 3.926A  pdb=" N   VAL D  70 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 86
    Processing helix  chain 'D' and resid 93 through 102
    Processing helix  chain 'D' and resid 130 through 141
    Processing helix  chain 'D' and resid 160 through 180
    Processing helix  chain 'D' and resid 198 through 220
    Processing helix  chain 'D' and resid 223 through 227
    Processing helix  chain 'D' and resid 245 through 261
    Processing helix  chain 'D' and resid 276 through 289
    Processing helix  chain 'D' and resid 307 through 315
    Processing helix  chain 'D' and resid 320 through 339
      removed outlier: 4.110A  pdb=" N   ALA D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.129A  pdb=" N   GLY A  29 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ILE A  78 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU A  31 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL A 105 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ALA A 146 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ILE A 107 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   TRP A 148 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ASP A 144 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   ILE A 186 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA A 146 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLU A 188 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   TRP A 148 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLU A 190 " --> pdb=" O   TRP A 148 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   CYS A 150 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   LEU A 192 " --> pdb=" O   CYS A 150 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   LEU A 152 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 115
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.127A  pdb=" N   GLY B  29 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE B  78 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU B  31 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL B 105 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ALA B 146 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ILE B 107 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   TRP B 148 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ASP B 144 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ILE B 186 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   GLU B 188 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   TRP B 148 " --> pdb=" O   GLU B 188 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   GLU B 190 " --> pdb=" O   TRP B 148 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   CYS B 150 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   LEU B 192 " --> pdb=" O   CYS B 150 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   LEU B 152 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU B 229 " --> pdb=" O   THR B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 115
    Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.135A  pdb=" N   GLY C  29 " --> pdb=" O   GLY C  76 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE C  78 " --> pdb=" O   GLY C  29 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU C  31 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL C 105 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ALA C 146 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ILE C 107 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   TRP C 148 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ASP C 144 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   ILE C 186 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA C 146 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   GLU C 188 " --> pdb=" O   ALA C 146 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP C 148 " --> pdb=" O   GLU C 188 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   GLU C 190 " --> pdb=" O   TRP C 148 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   CYS C 150 " --> pdb=" O   GLU C 190 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   LEU C 192 " --> pdb=" O   CYS C 150 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   LEU C 152 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LEU C 229 " --> pdb=" O   THR C 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 115
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.134A  pdb=" N   GLY D  29 " --> pdb=" O   GLY D  76 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE D  78 " --> pdb=" O   GLY D  29 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU D  31 " --> pdb=" O   ILE D  78 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   VAL D 105 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ALA D 146 " --> pdb=" O   VAL D 105 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ILE D 107 " --> pdb=" O   ALA D 146 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   TRP D 148 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASP D 144 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   ILE D 186 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA D 146 " --> pdb=" O   ILE D 186 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   GLU D 188 " --> pdb=" O   ALA D 146 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP D 148 " --> pdb=" O   GLU D 188 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   GLU D 190 " --> pdb=" O   TRP D 148 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   CYS D 150 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   LEU D 192 " --> pdb=" O   CYS D 150 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LEU D 152 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   LEU D 229 " --> pdb=" O   THR D 269 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 115

    568 hydrogen bonds defined for protein.
    1656 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: 3.52

  Time building geometry restraints manager: 3.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3516
        1.34 -     1.46: 1636
        1.46 -     1.57: 5512
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 10724
  Sorted by residual:
  bond pdb=" C   ASN A  71 "
       pdb=" N   PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.017 1.24e-02 6.50e+03 1.93e+00
  bond pdb=" C   ASN D  71 "
       pdb=" N   PRO D  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.017 1.24e-02 6.50e+03 1.79e+00
  bond pdb=" C   ASN B  71 "
       pdb=" N   PRO B  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.016 1.24e-02 6.50e+03 1.76e+00
  bond pdb=" C   ASN C  71 "
       pdb=" N   PRO C  72 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.016 1.24e-02 6.50e+03 1.67e+00
  bond pdb=" CA  PHE A  58 "
       pdb=" CB  PHE A  58 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.68e-02 3.54e+03 9.90e-01
  ... (remaining 10719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 13697
        1.05 -     2.10: 674
        2.10 -     3.15: 134
        3.15 -     4.20: 23
        4.20 -     5.25: 8
  Bond angle restraints: 14536
  Sorted by residual:
  angle pdb=" CA  PHE D  58 "
        pdb=" CB  PHE D  58 "
        pdb=" CG  PHE D  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.26   -2.46 1.00e+00 1.00e+00 6.03e+00
  angle pdb=" CA  PHE B  58 "
        pdb=" CB  PHE B  58 "
        pdb=" CG  PHE B  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.25   -2.45 1.00e+00 1.00e+00 6.01e+00
  angle pdb=" CA  PHE A  58 "
        pdb=" CB  PHE A  58 "
        pdb=" CG  PHE A  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.23   -2.43 1.00e+00 1.00e+00 5.91e+00
  angle pdb=" CA  PHE C  58 "
        pdb=" CB  PHE C  58 "
        pdb=" CG  PHE C  58 "
      ideal   model   delta    sigma   weight residual
     113.80  116.14   -2.34 1.00e+00 1.00e+00 5.50e+00
  angle pdb=" C   ARG D  57 "
        pdb=" N   PHE D  58 "
        pdb=" CA  PHE D  58 "
      ideal   model   delta    sigma   weight residual
     121.14  117.09    4.05 1.75e+00 3.27e-01 5.35e+00
  ... (remaining 14531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.97: 5826
       11.97 -    23.94: 526
       23.94 -    35.91: 153
       35.91 -    47.88: 34
       47.88 -    59.85: 5
  Dihedral angle restraints: 6544
    sinusoidal: 2596
      harmonic: 3948
  Sorted by residual:
  dihedral pdb=" CA  THR A 260 "
           pdb=" C   THR A 260 "
           pdb=" N   VAL A 261 "
           pdb=" CA  VAL A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.23  -15.77     0      5.00e+00 4.00e-02 9.94e+00
  dihedral pdb=" CA  THR C 260 "
           pdb=" C   THR C 260 "
           pdb=" N   VAL C 261 "
           pdb=" CA  VAL C 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.32  -15.68     0      5.00e+00 4.00e-02 9.84e+00
  dihedral pdb=" CA  THR B 260 "
           pdb=" C   THR B 260 "
           pdb=" N   VAL B 261 "
           pdb=" CA  VAL B 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.32  -15.68     0      5.00e+00 4.00e-02 9.84e+00
  ... (remaining 6541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1108
       0.033 -    0.065: 338
       0.065 -    0.098: 141
       0.098 -    0.131: 53
       0.131 -    0.164: 4
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  PHE C  58 "
            pdb=" N   PHE C  58 "
            pdb=" C   PHE C  58 "
            pdb=" CB  PHE C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.69e-01
  chirality pdb=" CA  PHE B  58 "
            pdb=" N   PHE B  58 "
            pdb=" C   PHE B  58 "
            pdb=" CB  PHE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  PHE A  58 "
            pdb=" N   PHE A  58 "
            pdb=" C   PHE A  58 "
            pdb=" CB  PHE A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  58 "   -0.017 2.00e-02 2.50e+03   1.49e-02 3.87e+00
        pdb=" CG  PHE C  58 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  58 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  58 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  58 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  58 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  58 "    0.017 2.00e-02 2.50e+03   1.48e-02 3.83e+00
        pdb=" CG  PHE D  58 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  58 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  58 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  58 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  58 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  58 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  58 "   -0.016 2.00e-02 2.50e+03   1.47e-02 3.77e+00
        pdb=" CG  PHE B  58 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  58 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  58 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  58 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  58 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1480
        2.75 -     3.29: 10766
        3.29 -     3.83: 19952
        3.83 -     4.36: 23880
        4.36 -     4.90: 39095
  Nonbonded interactions: 95173
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  61 "
            pdb=" OG1 THR B  65 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   GLN C  61 "
            pdb=" OG1 THR C  65 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   GLN A  61 "
            pdb=" OG1 THR A  65 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLN D  61 "
            pdb=" OG1 THR D  65 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LYS C 289 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.260 3.040
  ... (remaining 95168 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.170
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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      :  0.004   0.038  10724  Z= 0.158
  Angle     :  0.543   5.247  14536  Z= 0.301
  Chirality :  0.041   0.164   1644
  Planarity :  0.005   0.039   1892
  Dihedral  : 10.541  59.847   4016
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  4.30 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.22), residues: 1368
  helix:  1.07 (0.19), residues: 708
  sheet: -1.58 (0.35), residues: 192
  loop : -0.34 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 148 
 HIS   0.004   0.001   HIS D  21 
 PHE   0.034   0.003   PHE C  58 
 TYR   0.017   0.002   TYR D 214 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14935 (  568)
  hydrogen bonds       : angle       5.78328 ( 1656)
  covalent geometry    : bond        0.00361 (10724)
  covalent geometry    : angle       0.54261 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLN cc_start: 0.7589 (mt0) cc_final: 0.7186 (mt0)
REVERT: A  174 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: A  232 ASN cc_start: 0.8152 (p0) cc_final: 0.7818 (p0)
REVERT: A  251 MET cc_start: 0.7485 (mmm) cc_final: 0.6677 (mmp)
REVERT: B   11 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6541 (mm-30)
REVERT: B   86 GLN cc_start: 0.7605 (mt0) cc_final: 0.7203 (mt0)
REVERT: B  174 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: B  251 MET cc_start: 0.7541 (mmm) cc_final: 0.6715 (mmp)
REVERT: C   11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6600 (mm-30)
REVERT: C   86 GLN cc_start: 0.7546 (mt0) cc_final: 0.7202 (mt0)
REVERT: C  251 MET cc_start: 0.7478 (mmm) cc_final: 0.7129 (mmp)
REVERT: D   11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6583 (mm-30)
REVERT: D   86 GLN cc_start: 0.7636 (mt0) cc_final: 0.7265 (mt0)
REVERT: D  174 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8521 (t80)
REVERT: D  251 MET cc_start: 0.7483 (mmm) cc_final: 0.7119 (mmp)
  outliers start: 24
  outliers final: 16
  residues processed: 205
  average time/residue: 1.3103
  time to fit residues: 292.5066
Evaluate side-chains
  174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A 169 ASN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  55 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
C  55 ASN
C 169 ASN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 HIS
C 275 GLN
D  55 ASN
D 169 ASN
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 220 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.206240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.154989 restraints weight = 11632.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.25
r_work: 0.3543 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10724  Z= 0.159
  Angle     :  0.535   5.463  14536  Z= 0.285
  Chirality :  0.041   0.159   1644
  Planarity :  0.005   0.036   1892
  Dihedral  :  6.368  59.446   1510
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  :  9.59 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.22), residues: 1368
  helix:  1.40 (0.19), residues: 744
  sheet: -2.01 (0.37), residues: 160
  loop : -0.14 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 148 
 HIS   0.004   0.001   HIS A  21 
 PHE   0.031   0.003   PHE C  58 
 TYR   0.013   0.002   TYR D 302 
 ARG   0.005   0.001   ARG D  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  568)
  hydrogen bonds       : angle       4.53459 ( 1656)
  covalent geometry    : bond        0.00373 (10724)
  covalent geometry    : angle       0.53466 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 192
  time to evaluate  : 1.240 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.8317 (tptm) cc_final: 0.8097 (tptp)
REVERT: A  232 ASN cc_start: 0.8301 (p0) cc_final: 0.7992 (p0)
REVERT: A  247 GLU cc_start: 0.7181 (mp0) cc_final: 0.6857 (mm-30)
REVERT: A  251 MET cc_start: 0.7632 (mmm) cc_final: 0.7298 (mmm)
REVERT: B   11 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6850 (mm-30)
REVERT: B   86 GLN cc_start: 0.7985 (mt0) cc_final: 0.7581 (mt0)
REVERT: B  247 GLU cc_start: 0.7157 (mp0) cc_final: 0.6952 (mm-30)
REVERT: B  251 MET cc_start: 0.7693 (mmm) cc_final: 0.7395 (tpt)
REVERT: C   11 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6831 (mm-30)
REVERT: D   11 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6850 (mm-30)
REVERT: D   86 GLN cc_start: 0.7982 (mt0) cc_final: 0.7736 (mt0)
REVERT: D  247 GLU cc_start: 0.7120 (mp0) cc_final: 0.6796 (mm-30)
REVERT: D  251 MET cc_start: 0.7670 (mmm) cc_final: 0.7339 (mmm)
  outliers start: 33
  outliers final: 22
  residues processed: 210
  average time/residue: 1.1456
  time to fit residues: 264.7694
Evaluate side-chains
  190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 ASN
B  81 HIS
B 169 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
C  71 ASN
C  81 HIS
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  71 ASN
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 246 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.206824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.155929 restraints weight = 11746.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.23
r_work: 0.3552 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10724  Z= 0.149
  Angle     :  0.523   5.799  14536  Z= 0.275
  Chirality :  0.041   0.160   1644
  Planarity :  0.005   0.035   1892
  Dihedral  :  6.207  58.450   1508
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 10.22 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.22), residues: 1368
  helix:  1.68 (0.18), residues: 720
  sheet: -2.22 (0.36), residues: 160
  loop : -0.15 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 148 
 HIS   0.005   0.001   HIS B 246 
 PHE   0.028   0.003   PHE C  58 
 TYR   0.011   0.002   TYR D 302 
 ARG   0.007   0.001   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  568)
  hydrogen bonds       : angle       4.33723 ( 1656)
  covalent geometry    : bond        0.00353 (10724)
  covalent geometry    : angle       0.52323 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 181
  time to evaluate  : 1.938 
Fit side-chains
REVERT: A   86 GLN cc_start: 0.7925 (mt0) cc_final: 0.7549 (mt0)
REVERT: A  156 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7763 (tt0)
REVERT: A  174 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8577 (t80)
REVERT: A  232 ASN cc_start: 0.8296 (p0) cc_final: 0.8014 (p0)
REVERT: A  251 MET cc_start: 0.7646 (mmm) cc_final: 0.7305 (mmp)
REVERT: B   11 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6897 (mm-30)
REVERT: B   86 GLN cc_start: 0.7880 (mt0) cc_final: 0.7502 (mt0)
REVERT: B  174 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8558 (t80)
REVERT: B  251 MET cc_start: 0.7694 (mmm) cc_final: 0.7375 (tpt)
REVERT: C   11 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6905 (mm-30)
REVERT: C   71 ASN cc_start: 0.7341 (m-40) cc_final: 0.7108 (m-40)
REVERT: C   99 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7953 (mmtp)
REVERT: D   11 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6910 (mm-30)
REVERT: D   86 GLN cc_start: 0.7986 (mt0) cc_final: 0.7572 (mt0)
REVERT: D  174 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8550 (t80)
REVERT: D  251 MET cc_start: 0.7674 (mmm) cc_final: 0.7360 (mmp)
  outliers start: 32
  outliers final: 21
  residues processed: 202
  average time/residue: 1.0139
  time to fit residues: 224.3563
Evaluate side-chains
  189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 47 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 GLN
B  81 HIS
B 169 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 GLN
C  81 HIS
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 275 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.206140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.154747 restraints weight = 11668.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.50
r_work: 0.3519 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10724  Z= 0.176
  Angle     :  0.548   5.481  14536  Z= 0.288
  Chirality :  0.042   0.172   1644
  Planarity :  0.005   0.035   1892
  Dihedral  :  6.316  58.475   1508
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 10.84 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.22), residues: 1368
  helix:  1.69 (0.18), residues: 720
  sheet: -2.33 (0.37), residues: 160
  loop : -0.29 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 148 
 HIS   0.004   0.001   HIS B 246 
 PHE   0.029   0.003   PHE B  58 
 TYR   0.014   0.002   TYR D 302 
 ARG   0.008   0.001   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  568)
  hydrogen bonds       : angle       4.33125 ( 1656)
  covalent geometry    : bond        0.00418 (10724)
  covalent geometry    : angle       0.54821 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  174 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8537 (t80)
REVERT: A  232 ASN cc_start: 0.8324 (p0) cc_final: 0.8071 (p0)
REVERT: A  247 GLU cc_start: 0.7230 (mp0) cc_final: 0.6896 (mm-30)
REVERT: B   11 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7081 (mm-30)
REVERT: B   86 GLN cc_start: 0.7967 (mt0) cc_final: 0.7566 (mt0)
REVERT: B  174 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8583 (t80)
REVERT: B  251 MET cc_start: 0.7687 (mmm) cc_final: 0.7382 (tpt)
REVERT: C   11 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7087 (mm-30)
REVERT: C   99 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7938 (mmtp)
REVERT: C  156 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (tt0)
REVERT: C  247 GLU cc_start: 0.7243 (mp0) cc_final: 0.6951 (mm-30)
REVERT: D   11 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7052 (mm-30)
REVERT: D   86 GLN cc_start: 0.7968 (mt0) cc_final: 0.7646 (mt0)
REVERT: D  174 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8538 (t80)
REVERT: D  247 GLU cc_start: 0.7262 (mp0) cc_final: 0.6917 (mm-30)
  outliers start: 39
  outliers final: 25
  residues processed: 200
  average time/residue: 1.0159
  time to fit residues: 223.9138
Evaluate side-chains
  190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  289 LYS
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 90 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 120 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 HIS
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.208110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.156902 restraints weight = 11699.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.22
r_work: 0.3581 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10724  Z= 0.135
  Angle     :  0.521   6.394  14536  Z= 0.272
  Chirality :  0.041   0.160   1644
  Planarity :  0.005   0.040   1892
  Dihedral  :  6.186  58.674   1508
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 12.01 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.22), residues: 1368
  helix:  1.89 (0.18), residues: 720
  sheet: -2.05 (0.51), residues: 96
  loop : -0.45 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 148 
 HIS   0.003   0.001   HIS A  21 
 PHE   0.028   0.003   PHE C  58 
 TYR   0.015   0.002   TYR D 302 
 ARG   0.009   0.001   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  568)
  hydrogen bonds       : angle       4.19982 ( 1656)
  covalent geometry    : bond        0.00320 (10724)
  covalent geometry    : angle       0.52077 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A   86 GLN cc_start: 0.7990 (mt0) cc_final: 0.7576 (mt0)
REVERT: A  174 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8670 (t80)
REVERT: A  232 ASN cc_start: 0.8304 (p0) cc_final: 0.8033 (p0)
REVERT: A  247 GLU cc_start: 0.7328 (mp0) cc_final: 0.7108 (mm-30)
REVERT: B   11 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7114 (mm-30)
REVERT: B   31 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7284 (tp)
REVERT: B   86 GLN cc_start: 0.8011 (mt0) cc_final: 0.7624 (mt0)
REVERT: B  174 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8687 (t80)
REVERT: B  247 GLU cc_start: 0.7346 (mp0) cc_final: 0.7140 (mm-30)
REVERT: B  251 MET cc_start: 0.7731 (mmm) cc_final: 0.7372 (tpt)
REVERT: C   11 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7139 (mm-30)
REVERT: C   31 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7271 (tp)
REVERT: C   81 HIS cc_start: 0.7051 (t-170) cc_final: 0.6837 (t70)
REVERT: C  156 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7871 (tt0)
REVERT: D   11 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7087 (mm-30)
REVERT: D   31 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7320 (tp)
REVERT: D   86 GLN cc_start: 0.8088 (mt0) cc_final: 0.7788 (mt0)
REVERT: D  174 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8664 (t80)
  outliers start: 40
  outliers final: 26
  residues processed: 211
  average time/residue: 1.4856
  time to fit residues: 349.0216
Evaluate side-chains
  198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0770
   chunk 59 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.207915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.156599 restraints weight = 11746.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.21
r_work: 0.3570 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10724  Z= 0.142
  Angle     :  0.528   6.780  14536  Z= 0.276
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.041   1892
  Dihedral  :  6.199  58.678   1508
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.72 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.22), residues: 1368
  helix:  1.96 (0.18), residues: 720
  sheet: -2.32 (0.38), residues: 160
  loop : -0.23 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 148 
 HIS   0.006   0.001   HIS C  81 
 PHE   0.028   0.003   PHE B  58 
 TYR   0.018   0.002   TYR D 302 
 ARG   0.011   0.001   ARG D  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  568)
  hydrogen bonds       : angle       4.18807 ( 1656)
  covalent geometry    : bond        0.00339 (10724)
  covalent geometry    : angle       0.52823 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7313 (tp)
REVERT: A   86 GLN cc_start: 0.7986 (mt0) cc_final: 0.7574 (mt0)
REVERT: A  174 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8664 (t80)
REVERT: A  232 ASN cc_start: 0.8308 (p0) cc_final: 0.8025 (p0)
REVERT: A  247 GLU cc_start: 0.7377 (mp0) cc_final: 0.7128 (mm-30)
REVERT: B   11 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7123 (mm-30)
REVERT: B   31 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7228 (tp)
REVERT: B   86 GLN cc_start: 0.8023 (mt0) cc_final: 0.7619 (mt0)
REVERT: B  174 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8663 (t80)
REVERT: B  251 MET cc_start: 0.7794 (mmm) cc_final: 0.7438 (tpt)
REVERT: C   11 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7128 (mm-30)
REVERT: C   31 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7284 (tp)
REVERT: C  156 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7879 (tt0)
REVERT: C  247 GLU cc_start: 0.7497 (mp0) cc_final: 0.7160 (mm-30)
REVERT: D   11 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7096 (mm-30)
REVERT: D   31 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7291 (tp)
REVERT: D   86 GLN cc_start: 0.8120 (mt0) cc_final: 0.7811 (mt0)
REVERT: D  174 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8655 (t80)
REVERT: D  247 GLU cc_start: 0.7393 (mp0) cc_final: 0.7118 (mm-30)
  outliers start: 43
  outliers final: 28
  residues processed: 207
  average time/residue: 0.9779
  time to fit residues: 224.7036
Evaluate side-chains
  206 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 2.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  105 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  101 LYS
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 123 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0770
   chunk 81 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.208662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.157494 restraints weight = 11895.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.23
r_work: 0.3575 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10724  Z= 0.131
  Angle     :  0.534   7.326  14536  Z= 0.276
  Chirality :  0.040   0.161   1644
  Planarity :  0.005   0.046   1892
  Dihedral  :  6.137  59.129   1508
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.53 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.22), residues: 1368
  helix:  2.09 (0.18), residues: 720
  sheet: -2.01 (0.51), residues: 96
  loop : -0.41 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 148 
 HIS   0.003   0.001   HIS A  21 
 PHE   0.028   0.003   PHE C  58 
 TYR   0.026   0.002   TYR B 138 
 ARG   0.011   0.001   ARG D  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  568)
  hydrogen bonds       : angle       4.15115 ( 1656)
  covalent geometry    : bond        0.00314 (10724)
  covalent geometry    : angle       0.53392 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 176
  time to evaluate  : 2.164 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7216 (tp)
REVERT: A   86 GLN cc_start: 0.7915 (mt0) cc_final: 0.7642 (mt0)
REVERT: A  174 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8633 (t80)
REVERT: A  232 ASN cc_start: 0.8190 (p0) cc_final: 0.7877 (p0)
REVERT: A  247 GLU cc_start: 0.7316 (mp0) cc_final: 0.7067 (mm-30)
REVERT: B   11 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6994 (mm-30)
REVERT: B   31 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (tp)
REVERT: B   86 GLN cc_start: 0.7953 (mt0) cc_final: 0.7562 (mt0)
REVERT: B  174 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8628 (t80)
REVERT: B  247 GLU cc_start: 0.7258 (mp0) cc_final: 0.7034 (mm-30)
REVERT: B  251 MET cc_start: 0.7755 (mmm) cc_final: 0.7415 (tpt)
REVERT: C   11 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7096 (mm-30)
REVERT: C   31 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7178 (tp)
REVERT: C  156 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (tp30)
REVERT: C  247 GLU cc_start: 0.7485 (mp0) cc_final: 0.7111 (mm-30)
REVERT: D   11 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: D   31 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7144 (tp)
REVERT: D   86 GLN cc_start: 0.8067 (mt0) cc_final: 0.7747 (mt0)
REVERT: D  138 TYR cc_start: 0.8273 (m-10) cc_final: 0.8009 (m-80)
REVERT: D  174 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (t80)
REVERT: D  247 GLU cc_start: 0.7226 (mp0) cc_final: 0.6938 (mm-30)
  outliers start: 42
  outliers final: 26
  residues processed: 207
  average time/residue: 1.2684
  time to fit residues: 290.7421
Evaluate side-chains
  198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 2.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 118 optimal weight:    0.6980
   chunk 99 optimal weight:   20.0000
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.207280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.155703 restraints weight = 11696.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.23
r_work: 0.3554 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10724  Z= 0.159
  Angle     :  0.564   7.428  14536  Z= 0.290
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.051   1892
  Dihedral  :  6.255  58.994   1508
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.43 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.22), residues: 1368
  helix:  2.02 (0.18), residues: 720
  sheet: -2.39 (0.37), residues: 160
  loop : -0.28 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 148 
 HIS   0.004   0.001   HIS C  21 
 PHE   0.028   0.003   PHE C  58 
 TYR   0.030   0.002   TYR C 138 
 ARG   0.013   0.001   ARG A  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  568)
  hydrogen bonds       : angle       4.19519 ( 1656)
  covalent geometry    : bond        0.00382 (10724)
  covalent geometry    : angle       0.56421 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 166
  time to evaluate  : 2.051 
Fit side-chains
REVERT: A   86 GLN cc_start: 0.7960 (mt0) cc_final: 0.7663 (mt0)
REVERT: A  174 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8674 (t80)
REVERT: A  232 ASN cc_start: 0.8351 (p0) cc_final: 0.8089 (p0)
REVERT: B   11 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: B   31 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7316 (tp)
REVERT: B   86 GLN cc_start: 0.7920 (mt0) cc_final: 0.7527 (mt0)
REVERT: B  174 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8667 (t80)
REVERT: B  247 GLU cc_start: 0.7371 (mp0) cc_final: 0.7123 (mm-30)
REVERT: B  251 MET cc_start: 0.7753 (mmm) cc_final: 0.7380 (mmp)
REVERT: C   11 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7161 (mm-30)
REVERT: C   31 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7255 (tp)
REVERT: C  156 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7898 (tt0)
REVERT: D   11 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7199 (mm-30)
REVERT: D   31 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7249 (tp)
REVERT: D   86 GLN cc_start: 0.8123 (mt0) cc_final: 0.7819 (mt0)
REVERT: D  174 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (t80)
  outliers start: 37
  outliers final: 25
  residues processed: 194
  average time/residue: 1.5815
  time to fit residues: 337.0439
Evaluate side-chains
  197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 2.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 8 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 101 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0470
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 167 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 GLN
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 307 GLN
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.209754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.158640 restraints weight = 11778.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.24
r_work: 0.3587 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10724  Z= 0.124
  Angle     :  0.546   8.125  14536  Z= 0.280
  Chirality :  0.040   0.162   1644
  Planarity :  0.005   0.054   1892
  Dihedral  :  6.133  59.947   1508
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.78 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1368
  helix:  2.14 (0.18), residues: 720
  sheet: -2.77 (0.34), residues: 188
  loop : -0.03 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 148 
 HIS   0.004   0.001   HIS C  81 
 PHE   0.027   0.003   PHE C  58 
 TYR   0.033   0.002   TYR A 138 
 ARG   0.014   0.001   ARG C  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03578 (  568)
  hydrogen bonds       : angle       4.12281 ( 1656)
  covalent geometry    : bond        0.00296 (10724)
  covalent geometry    : angle       0.54565 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 2.000 
Fit side-chains
REVERT: A  138 TYR cc_start: 0.8339 (m-80) cc_final: 0.8119 (m-80)
REVERT: A  174 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8668 (t80)
REVERT: A  232 ASN cc_start: 0.8191 (p0) cc_final: 0.7878 (p0)
REVERT: A  247 GLU cc_start: 0.7474 (mp0) cc_final: 0.7203 (mm-30)
REVERT: B   11 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7174 (mm-30)
REVERT: B   31 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7351 (tp)
REVERT: B  174 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (t80)
REVERT: B  251 MET cc_start: 0.7777 (mmm) cc_final: 0.7426 (tpt)
REVERT: C   11 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7166 (mm-30)
REVERT: C   31 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7234 (tp)
REVERT: C  247 GLU cc_start: 0.7428 (mp0) cc_final: 0.7102 (mm-30)
REVERT: D   11 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7163 (mm-30)
REVERT: D   31 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7264 (tp)
REVERT: D   86 GLN cc_start: 0.8130 (mt0) cc_final: 0.7691 (mt0)
REVERT: D  174 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8653 (t80)
REVERT: D  247 GLU cc_start: 0.7449 (mp0) cc_final: 0.7162 (mm-30)
  outliers start: 36
  outliers final: 26
  residues processed: 196
  average time/residue: 1.2983
  time to fit residues: 282.7082
Evaluate side-chains
  189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   62 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0060
   chunk 82 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 GLN
C 167 ASN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.208464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.157275 restraints weight = 11704.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.24
r_work: 0.3575 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10724  Z= 0.141
  Angle     :  0.561   7.935  14536  Z= 0.289
  Chirality :  0.041   0.161   1644
  Planarity :  0.005   0.056   1892
  Dihedral  :  6.200  59.718   1508
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.41 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.22), residues: 1368
  helix:  2.10 (0.18), residues: 720
  sheet: -2.81 (0.33), residues: 188
  loop : -0.07 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 148 
 HIS   0.004   0.001   HIS C  81 
 PHE   0.028   0.003   PHE C  58 
 TYR   0.031   0.003   TYR A 302 
 ARG   0.015   0.001   ARG C  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  568)
  hydrogen bonds       : angle       4.16730 ( 1656)
  covalent geometry    : bond        0.00341 (10724)
  covalent geometry    : angle       0.56115 (14536)

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

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

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2736 Ramachandran restraints generated.
    1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 1.175 
Fit side-chains
REVERT: A  174 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8695 (t80)
REVERT: A  232 ASN cc_start: 0.8286 (p0) cc_final: 0.7993 (p0)
REVERT: A  247 GLU cc_start: 0.7508 (mp0) cc_final: 0.7209 (mm-30)
REVERT: B   11 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7192 (mm-30)
REVERT: B   31 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7349 (tp)
REVERT: B   81 HIS cc_start: 0.7175 (t70) cc_final: 0.6840 (t-90)
REVERT: B  138 TYR cc_start: 0.8394 (m-80) cc_final: 0.8192 (m-80)
REVERT: B  174 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8694 (t80)
REVERT: B  247 GLU cc_start: 0.7398 (mp0) cc_final: 0.7141 (mm-30)
REVERT: B  251 MET cc_start: 0.7739 (mmm) cc_final: 0.7370 (tpt)
REVERT: C   11 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7211 (mm-30)
REVERT: C   31 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7248 (tp)
REVERT: C   81 HIS cc_start: 0.7164 (t70) cc_final: 0.6743 (t-90)
REVERT: C  247 GLU cc_start: 0.7443 (mp0) cc_final: 0.7115 (mm-30)
REVERT: D   11 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7149 (mm-30)
REVERT: D   31 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7220 (tp)
REVERT: D   86 GLN cc_start: 0.8110 (mt0) cc_final: 0.7676 (mt0)
REVERT: D  174 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8681 (t80)
REVERT: D  247 GLU cc_start: 0.7487 (mp0) cc_final: 0.7170 (mm-30)
  outliers start: 33
  outliers final: 25
  residues processed: 187
  average time/residue: 0.9592
  time to fit residues: 198.8154
Evaluate side-chains
  192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 161
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  296 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain D residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0000
   chunk 112 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0970
   chunk 117 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   overall best weight:    0.4382

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 GLN
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.210291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.159304 restraints weight = 11749.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.25
r_work: 0.3595 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10724  Z= 0.121
  Angle     :  0.546   8.306  14536  Z= 0.281
  Chirality :  0.040   0.161   1644
  Planarity :  0.005   0.055   1892
  Dihedral  :  6.065  59.985   1506
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.59 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.23), residues: 1368
  helix:  2.17 (0.18), residues: 720
  sheet: -2.80 (0.34), residues: 188
  loop : -0.01 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 314 
 HIS   0.004   0.001   HIS C  81 
 PHE   0.027   0.003   PHE C  58 
 TYR   0.032   0.003   TYR D 302 
 ARG   0.014   0.001   ARG D  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  568)
  hydrogen bonds       : angle       4.15109 ( 1656)
  covalent geometry    : bond        0.00293 (10724)
  covalent geometry    : angle       0.54628 (14536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9084.46 seconds
wall clock time: 168 minutes 51.98 seconds (10131.98 seconds total)