Starting phenix.real_space_refine
on Mon Jun 23 06:07:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jmi_36422/06_2025/8jmi_36422_neut_trim.cif"
  }
  resolution = 2.6
  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=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C    8872      2.51       5
     N    2212      2.21       5
     O    2264      1.98       5
     H   13812      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 27256
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "B"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "C"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "D"
      Number of atoms: 6791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 6791
          Classifications: {'peptide': 407}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390}
    Chain: "E"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 12.58, per 1000 atoms: 0.46
  Number of scatterers: 27256
  At special positions: 0
  Unit cell: (116.25, 116.25, 103.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     O    2264      8.00
     N    2212      7.00
     C    8872      6.00
     H   13812      1.00
    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
  Links applied
    ALPHA1-4
      " BGC E   1 " - " GLC E   2 "
      " BGC F   1 " - " GLC F   2 "
      " BGC G   1 " - " GLC G   2 "
      " BGC H   1 " - " GLC H   2 "
  Time building additional restraints: 7.49
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3136

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      79.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 73
      Proline residue:  A  65  - end of helix
      removed outlier: 3.703A  pdb=" N   VAL A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 95 through 123
    Processing helix  chain 'A' and resid 125 through 164
      removed outlier: 4.015A  pdb=" N   VAL A 130 " --> pdb=" O   ALA A 126 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   GLY A 131 " --> pdb=" O   LYS A 127 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 177 through 214
    Processing helix  chain 'A' and resid 223 through 232
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 242 through 287
      removed outlier: 4.479A  pdb=" N   ASP A 264 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 339
      removed outlier: 3.570A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   SER A 321 " --> pdb=" O   SER A 317 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   LEU A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 387
      removed outlier: 3.901A  pdb=" N   ILE A 375 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ASN A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLY A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   LEU A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY A 384 " --> pdb=" O   LYS A 380 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 408
    Processing helix  chain 'A' and resid 421 through 440
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 3.822A  pdb=" N   GLY A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 73
      Proline residue:  B  65  - end of helix
      removed outlier: 3.704A  pdb=" N   VAL B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
    Processing helix  chain 'B' and resid 95 through 123
    Processing helix  chain 'B' and resid 125 through 164
      removed outlier: 4.030A  pdb=" N   VAL B 130 " --> pdb=" O   ALA B 126 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   GLY B 131 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU B 132 " --> pdb=" O   ASN B 128 " (cutoff:3.500A)
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 177 through 214
    Processing helix  chain 'B' and resid 223 through 232
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 242 through 287
      removed outlier: 4.479A  pdb=" N   ASP B 264 " --> pdb=" O   TRP B 260 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 339
      removed outlier: 3.570A  pdb=" N   PHE B 298 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   SER B 321 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   LEU B 322 " --> pdb=" O   ALA B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 387
      removed outlier: 3.900A  pdb=" N   ILE B 375 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ASN B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLY B 382 " --> pdb=" O   GLU B 378 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   LEU B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLY B 384 " --> pdb=" O   LYS B 380 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL B 385 " --> pdb=" O   ARG B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 408
    Processing helix  chain 'B' and resid 421 through 440
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 3.821A  pdb=" N   GLY B 450 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 73
      Proline residue:  C  65  - end of helix
      removed outlier: 3.703A  pdb=" N   VAL C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 89
    Processing helix  chain 'C' and resid 95 through 123
    Processing helix  chain 'C' and resid 125 through 164
      removed outlier: 4.016A  pdb=" N   VAL C 130 " --> pdb=" O   ALA C 126 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   GLY C 131 " --> pdb=" O   LYS C 127 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU C 132 " --> pdb=" O   ASN C 128 " (cutoff:3.500A)
      Proline residue:  C 153  - end of helix
    Processing helix  chain 'C' and resid 165 through 168
    Processing helix  chain 'C' and resid 177 through 214
    Processing helix  chain 'C' and resid 223 through 232
    Processing helix  chain 'C' and resid 232 through 237
    Processing helix  chain 'C' and resid 242 through 287
      removed outlier: 4.478A  pdb=" N   ASP C 264 " --> pdb=" O   TRP C 260 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG C 277 " --> pdb=" O   GLY C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 339
      removed outlier: 3.573A  pdb=" N   PHE C 298 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   SER C 321 " --> pdb=" O   SER C 317 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   LEU C 322 " --> pdb=" O   ALA C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 387
      removed outlier: 3.893A  pdb=" N   ILE C 375 " --> pdb=" O   THR C 371 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ASN C 376 " --> pdb=" O   ALA C 372 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY C 382 " --> pdb=" O   GLU C 378 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   LEU C 383 " --> pdb=" O   SER C 379 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY C 384 " --> pdb=" O   LYS C 380 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL C 385 " --> pdb=" O   ARG C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 408
    Processing helix  chain 'C' and resid 421 through 440
    Processing helix  chain 'C' and resid 443 through 450
      removed outlier: 3.822A  pdb=" N   GLY C 450 " --> pdb=" O   ASN C 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 73
      Proline residue:  D  65  - end of helix
      removed outlier: 3.704A  pdb=" N   VAL D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 89
    Processing helix  chain 'D' and resid 95 through 123
    Processing helix  chain 'D' and resid 125 through 164
      removed outlier: 4.030A  pdb=" N   VAL D 130 " --> pdb=" O   ALA D 126 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   GLY D 131 " --> pdb=" O   LYS D 127 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU D 132 " --> pdb=" O   ASN D 128 " (cutoff:3.500A)
      Proline residue:  D 153  - end of helix
    Processing helix  chain 'D' and resid 165 through 168
    Processing helix  chain 'D' and resid 177 through 214
    Processing helix  chain 'D' and resid 223 through 232
    Processing helix  chain 'D' and resid 232 through 237
    Processing helix  chain 'D' and resid 242 through 287
      removed outlier: 4.478A  pdb=" N   ASP D 264 " --> pdb=" O   TRP D 260 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG D 277 " --> pdb=" O   GLY D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 339
      removed outlier: 3.568A  pdb=" N   PHE D 298 " --> pdb=" O   CYS D 294 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   SER D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   LEU D 322 " --> pdb=" O   ALA D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 387
      removed outlier: 3.895A  pdb=" N   ILE D 375 " --> pdb=" O   THR D 371 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASN D 376 " --> pdb=" O   ALA D 372 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLY D 382 " --> pdb=" O   GLU D 378 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LEU D 383 " --> pdb=" O   SER D 379 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY D 384 " --> pdb=" O   LYS D 380 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL D 385 " --> pdb=" O   ARG D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 395 through 408
    Processing helix  chain 'D' and resid 421 through 440
    Processing helix  chain 'D' and resid 443 through 450
      removed outlier: 3.822A  pdb=" N   GLY D 450 " --> pdb=" O   ASN D 446 " (cutoff:3.500A)

    988 hydrogen bonds defined for protein.
    2928 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: 11.12

  Time building geometry restraints manager: 8.94 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13772
        1.03 -     1.23: 41
        1.23 -     1.42: 5787
        1.42 -     1.61: 7840
        1.61 -     1.81: 152
  Bond restraints: 27592
  Sorted by residual:
  bond pdb=" C3  BGC H   1 "
       pdb=" O3  BGC H   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.492 -0.084 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C3  BGC E   1 "
       pdb=" O3  BGC E   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.491 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C3  BGC F   1 "
       pdb=" O3  BGC F   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.491 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C3  BGC G   1 "
       pdb=" O3  BGC G   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.490 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" C1  GLC G   2 "
       pdb=" O5  GLC G   2 "
    ideal  model  delta    sigma   weight residual
    1.402  1.474 -0.072 2.00e-02 2.50e+03 1.31e+01
  ... (remaining 27587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 46800
        1.10 -     2.20: 2780
        2.20 -     3.30: 159
        3.30 -     4.40: 65
        4.40 -     5.50: 20
  Bond angle restraints: 49824
  Sorted by residual:
  angle pdb=" C   TYR D 262 "
        pdb=" N   MET D 263 "
        pdb=" CA  MET D 263 "
      ideal   model   delta    sigma   weight residual
     120.44  118.00    2.44 1.30e+00 5.92e-01 3.51e+00
  angle pdb=" C   TRP C 152 "
        pdb=" CA  TRP C 152 "
        pdb=" CB  TRP C 152 "
      ideal   model   delta    sigma   weight residual
     112.76  109.33    3.43 1.86e+00 2.89e-01 3.40e+00
  angle pdb=" C   TYR B 262 "
        pdb=" N   MET B 263 "
        pdb=" CA  MET B 263 "
      ideal   model   delta    sigma   weight residual
     120.44  118.05    2.39 1.30e+00 5.92e-01 3.39e+00
  angle pdb=" C   TRP B 152 "
        pdb=" CA  TRP B 152 "
        pdb=" CB  TRP B 152 "
      ideal   model   delta    sigma   weight residual
     112.76  109.34    3.42 1.86e+00 2.89e-01 3.39e+00
  angle pdb=" C   TRP A 152 "
        pdb=" CA  TRP A 152 "
        pdb=" CB  TRP A 152 "
      ideal   model   delta    sigma   weight residual
     112.76  109.34    3.42 1.86e+00 2.89e-01 3.38e+00
  ... (remaining 49819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 11648
       17.55 -    35.11: 1021
       35.11 -    52.66: 322
       52.66 -    70.21: 80
       70.21 -    87.76: 9
  Dihedral angle restraints: 13080
    sinusoidal: 7076
      harmonic: 6004
  Sorted by residual:
  dihedral pdb=" CB  MET D  98 "
           pdb=" CG  MET D  98 "
           pdb=" SD  MET D  98 "
           pdb=" CE  MET D  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.50  -59.50     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET B  98 "
           pdb=" CG  MET B  98 "
           pdb=" SD  MET B  98 "
           pdb=" CE  MET B  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.54  -59.46     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  ARG A 286 "
           pdb=" CG  ARG A 286 "
           pdb=" CD  ARG A 286 "
           pdb=" NE  ARG A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.46   59.46     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 13077 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1508
       0.027 -    0.055: 381
       0.055 -    0.082: 214
       0.082 -    0.109: 62
       0.109 -    0.137: 15
  Chirality restraints: 2180
  Sorted by residual:
  chirality pdb=" C1  GLC E   2 "
            pdb=" O4  BGC E   1 "
            pdb=" C2  GLC E   2 "
            pdb=" O5  GLC E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.38    0.02 2.00e-02 2.50e+03 1.21e+00
  chirality pdb=" C1  GLC G   2 "
            pdb=" O4  BGC G   1 "
            pdb=" C2  GLC G   2 "
            pdb=" O5  GLC G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.38    0.02 2.00e-02 2.50e+03 1.11e+00
  chirality pdb=" CA  ILE B 218 "
            pdb=" N   ILE B 218 "
            pdb=" C   ILE B 218 "
            pdb=" CB  ILE B 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  ... (remaining 2177 not shown)

  Planarity restraints: 3836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 142 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.08e+00
        pdb=" C   TYR B 142 "    0.030 2.00e-02 2.50e+03
        pdb=" O   TYR B 142 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B 143 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 142 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   TYR C 142 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR C 142 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL C 143 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 142 "   -0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   TYR D 142 "    0.030 2.00e-02 2.50e+03
        pdb=" O   TYR D 142 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL D 143 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 3833 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 2173
        2.21 -     2.81: 58534
        2.81 -     3.41: 80688
        3.41 -     4.00: 104783
        4.00 -     4.60: 161104
  Nonbonded interactions: 407282
  Sorted by model distance:
  nonbonded pdb="HH22 ARG B 346 "
            pdb=" O   GLN B 452 "
     model   vdw
     1.616 2.450
  nonbonded pdb="HH22 ARG D 346 "
            pdb=" O   GLN D 452 "
     model   vdw
     1.617 2.450
  nonbonded pdb="HH22 ARG A 346 "
            pdb=" O   GLN A 452 "
     model   vdw
     1.617 2.450
  nonbonded pdb="HH22 ARG C 346 "
            pdb=" O   GLN C 452 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" HH  TYR A 208 "
            pdb=" OD1 ASN A 226 "
     model   vdw
     1.648 2.450
  ... (remaining 407277 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'H'
}
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:             0.850
  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:             0.440
  Extract box with map and model:          1.080
  Check model and map are aligned:         0.200
  Set scattering table:                    0.250
  Process input model:                     57.240
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.140
  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:             0.020
  Load rotamer database and sin/cos tables:14.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   75.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
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   0.084  13784  Z= 0.219
  Angle     :  0.546   5.497  18712  Z= 0.286
  Chirality :  0.035   0.137   2180
  Planarity :  0.004   0.033   2276
  Dihedral  : 15.877  87.765   5160
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 16.64 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.21), residues: 1620
  helix:  2.29 (0.15), residues: 1192
  sheet:  None (None), residues: 0
  loop : -0.03 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 152 
 HIS   0.001   0.000   HIS D 118 
 PHE   0.010   0.001   PHE B  66 
 TYR   0.011   0.001   TYR D 241 
 ARG   0.002   0.000   ARG B  82 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.05675 (    4)
  link_ALPHA1-4        : angle       3.68477 (   12)
  hydrogen bonds       : bond        0.10592 (  988)
  hydrogen bonds       : angle       5.46274 ( 2928)
  covalent geometry    : bond        0.00417 (13780)
  covalent geometry    : angle       0.53804 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 211
  time to evaluate  : 2.060 
Fit side-chains
  outliers start: 13
  outliers final: 13
  residues processed: 224
  average time/residue: 3.2595
  time to fit residues: 790.0913
Evaluate side-chains
  215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 2.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  307 LYS
Chi-restraints excluded: chain D residue  398 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 253 ASN
B 441 GLN
C 441 GLN
D 253 ASN
D 441 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.136342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.101588 restraints weight = 38443.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.34
r_work: 0.2975 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.0579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022  13784  Z= 0.176
  Angle     :  0.515   5.090  18712  Z= 0.280
  Chirality :  0.037   0.132   2180
  Planarity :  0.004   0.034   2276
  Dihedral  :  5.152  47.181   2017
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 16.51 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.20), residues: 1620
  helix:  2.75 (0.14), residues: 1172
  sheet:  None (None), residues: 0
  loop : -0.16 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 355 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.013   0.002   PHE D  66 
 TYR   0.013   0.002   TYR C 241 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00095 (    4)
  link_ALPHA1-4        : angle       1.20953 (   12)
  hydrogen bonds       : bond        0.05245 (  988)
  hydrogen bonds       : angle       4.16093 ( 2928)
  covalent geometry    : bond        0.00368 (13780)
  covalent geometry    : angle       0.51431 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 199
  time to evaluate  : 2.002 
Fit side-chains
REVERT: A  214 MET cc_start: 0.6291 (ptp) cc_final: 0.6065 (ptp)
REVERT: B  214 MET cc_start: 0.6295 (ptp) cc_final: 0.6068 (ptp)
REVERT: C  214 MET cc_start: 0.6286 (ptp) cc_final: 0.6058 (ptp)
REVERT: D  214 MET cc_start: 0.6205 (ptp) cc_final: 0.5990 (ptp)
  outliers start: 10
  outliers final: 7
  residues processed: 208
  average time/residue: 3.3662
  time to fit residues: 756.0170
Evaluate side-chains
  200 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 2.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  391 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 90 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
B 253 ASN
B 441 GLN
C 441 GLN
D 229 GLN
D 253 ASN
D 441 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.137536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.103145 restraints weight = 38624.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.33
r_work: 0.2872 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.0714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13784  Z= 0.124
  Angle     :  0.473   5.458  18712  Z= 0.254
  Chirality :  0.035   0.139   2180
  Planarity :  0.003   0.031   2276
  Dihedral  :  3.527  15.854   1988
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 17.19 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  3.10 (0.20), residues: 1620
  helix:  2.85 (0.14), residues: 1192
  sheet:  None (None), residues: 0
  loop : -0.35 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 355 
 HIS   0.002   0.001   HIS A  60 
 PHE   0.011   0.001   PHE D  64 
 TYR   0.013   0.001   TYR D 241 
 ARG   0.004   0.000   ARG C 346 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00100 (    4)
  link_ALPHA1-4        : angle       1.18346 (   12)
  hydrogen bonds       : bond        0.04766 (  988)
  hydrogen bonds       : angle       4.02475 ( 2928)
  covalent geometry    : bond        0.00243 (13780)
  covalent geometry    : angle       0.47217 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 202
  time to evaluate  : 2.153 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8093 (pt0) cc_final: 0.7880 (pt0)
REVERT: B  172 GLU cc_start: 0.8014 (pt0) cc_final: 0.7805 (pt0)
REVERT: C  172 GLU cc_start: 0.8006 (pt0) cc_final: 0.7768 (pt0)
REVERT: D  172 GLU cc_start: 0.8003 (pt0) cc_final: 0.7740 (pt0)
  outliers start: 3
  outliers final: 0
  residues processed: 204
  average time/residue: 3.3210
  time to fit residues: 731.1610
Evaluate side-chains
  198 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 2.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 153 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
B  71 GLN
B 253 ASN
B 329 ASN
C 229 GLN
C 329 ASN
C 441 GLN
D  71 GLN
D 253 ASN
D 329 ASN
D 441 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.133984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.099410 restraints weight = 38770.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.33
r_work: 0.2815 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13784  Z= 0.239
  Angle     :  0.551   5.167  18712  Z= 0.302
  Chirality :  0.039   0.130   2180
  Planarity :  0.004   0.034   2276
  Dihedral  :  3.941  17.933   1988
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.78 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.20), residues: 1620
  helix:  2.66 (0.14), residues: 1176
  sheet:  None (None), residues: 0
  loop : -0.43 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 355 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.017   0.002   PHE A 419 
 TYR   0.015   0.002   TYR C 276 
 ARG   0.003   0.001   ARG D 346 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00289 (    4)
  link_ALPHA1-4        : angle       1.39546 (   12)
  hydrogen bonds       : bond        0.05439 (  988)
  hydrogen bonds       : angle       4.15372 ( 2928)
  covalent geometry    : bond        0.00525 (13780)
  covalent geometry    : angle       0.55004 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 201
  time to evaluate  : 2.067 
Fit side-chains
REVERT: A  310 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: C  172 GLU cc_start: 0.8034 (pt0) cc_final: 0.7793 (pt0)
REVERT: C  310 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8494 (mt-10)
REVERT: D  310 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8496 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 211
  average time/residue: 3.1254
  time to fit residues: 715.0649
Evaluate side-chains
  208 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 196
  time to evaluate  : 1.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
B 253 ASN
C 441 GLN
D 229 GLN
D 253 ASN
D 441 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.134418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.099944 restraints weight = 38460.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.32
r_work: 0.2823 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  13784  Z= 0.192
  Angle     :  0.526   5.411  18712  Z= 0.285
  Chirality :  0.037   0.134   2180
  Planarity :  0.004   0.035   2276
  Dihedral  :  3.914  18.545   1988
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.03 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.20), residues: 1620
  helix:  2.64 (0.14), residues: 1172
  sheet:  None (None), residues: 0
  loop : -0.50 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 355 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.014   0.002   PHE C  66 
 TYR   0.014   0.002   TYR C 276 
 ARG   0.003   0.000   ARG D 346 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00165 (    4)
  link_ALPHA1-4        : angle       1.30148 (   12)
  hydrogen bonds       : bond        0.05176 (  988)
  hydrogen bonds       : angle       4.10821 ( 2928)
  covalent geometry    : bond        0.00410 (13780)
  covalent geometry    : angle       0.52513 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 2.271 
Fit side-chains
  outliers start: 21
  outliers final: 10
  residues processed: 218
  average time/residue: 3.6461
  time to fit residues: 871.4375
Evaluate side-chains
  210 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 2.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 134 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
A 329 ASN
C 229 GLN
D 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.133102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.098460 restraints weight = 38659.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.34
r_work: 0.2800 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  13784  Z= 0.254
  Angle     :  0.564   5.344  18712  Z= 0.308
  Chirality :  0.040   0.130   2180
  Planarity :  0.005   0.037   2276
  Dihedral  :  4.105  20.944   1988
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.29 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.20), residues: 1620
  helix:  2.48 (0.14), residues: 1196
  sheet:  None (None), residues: 0
  loop : -0.57 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 355 
 HIS   0.004   0.001   HIS B  60 
 PHE   0.018   0.002   PHE A 419 
 TYR   0.015   0.002   TYR B 276 
 ARG   0.003   0.001   ARG D 284 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00185 (    4)
  link_ALPHA1-4        : angle       1.52245 (   12)
  hydrogen bonds       : bond        0.05482 (  988)
  hydrogen bonds       : angle       4.20264 ( 2928)
  covalent geometry    : bond        0.00561 (13780)
  covalent geometry    : angle       0.56300 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 2.251 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7730 (pt0)
REVERT: A  253 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8239 (m-40)
REVERT: A  310 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8511 (mt-10)
REVERT: B  172 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7718 (pt0)
REVERT: C  172 GLU cc_start: 0.8063 (pt0) cc_final: 0.7843 (pm20)
REVERT: C  249 ILE cc_start: 0.8306 (mm) cc_final: 0.7939 (mm)
REVERT: C  253 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8255 (m-40)
REVERT: D  310 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8502 (mt-10)
  outliers start: 23
  outliers final: 16
  residues processed: 218
  average time/residue: 3.3726
  time to fit residues: 797.4284
Evaluate side-chains
  222 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 2.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Chi-restraints excluded: chain D residue  398 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 153 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.099321 restraints weight = 38442.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.32
r_work: 0.2815 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  13784  Z= 0.207
  Angle     :  0.539   5.661  18712  Z= 0.293
  Chirality :  0.038   0.133   2180
  Planarity :  0.004   0.037   2276
  Dihedral  :  4.051  19.526   1988
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.35 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.20), residues: 1620
  helix:  2.53 (0.14), residues: 1196
  sheet:  None (None), residues: 0
  loop : -0.58 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 355 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.016   0.002   PHE D 419 
 TYR   0.015   0.002   TYR C 276 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00176 (    4)
  link_ALPHA1-4        : angle       1.34830 (   12)
  hydrogen bonds       : bond        0.05269 (  988)
  hydrogen bonds       : angle       4.16376 ( 2928)
  covalent geometry    : bond        0.00446 (13780)
  covalent geometry    : angle       0.53760 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 2.002 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (pt0)
REVERT: A  249 ILE cc_start: 0.8354 (mm) cc_final: 0.8115 (mm)
REVERT: A  253 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8169 (m-40)
REVERT: A  310 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8497 (mt-10)
REVERT: B  172 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7703 (pt0)
REVERT: C  249 ILE cc_start: 0.8314 (mm) cc_final: 0.7971 (mm)
REVERT: C  253 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (m-40)
REVERT: C  287 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7486 (mttt)
REVERT: D  172 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7704 (pt0)
  outliers start: 23
  outliers final: 14
  residues processed: 220
  average time/residue: 3.4754
  time to fit residues: 830.2846
Evaluate side-chains
  220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 201
  time to evaluate  : 2.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Chi-restraints excluded: chain D residue  398 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 135 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 229 GLN
D 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.132983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.098648 restraints weight = 38384.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.32
r_work: 0.2810 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  13784  Z= 0.242
  Angle     :  0.561   6.305  18712  Z= 0.306
  Chirality :  0.039   0.131   2180
  Planarity :  0.005   0.037   2276
  Dihedral  :  4.136  19.446   1988
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.83 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.20), residues: 1620
  helix:  2.46 (0.14), residues: 1196
  sheet:  None (None), residues: 0
  loop : -0.57 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 355 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.018   0.002   PHE A 419 
 TYR   0.015   0.002   TYR C 232 
 ARG   0.003   0.001   ARG D 284 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00226 (    4)
  link_ALPHA1-4        : angle       1.44747 (   12)
  hydrogen bonds       : bond        0.05417 (  988)
  hydrogen bonds       : angle       4.21084 ( 2928)
  covalent geometry    : bond        0.00531 (13780)
  covalent geometry    : angle       0.56003 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 2.224 
Fit side-chains
REVERT: A  249 ILE cc_start: 0.8370 (mm) cc_final: 0.8126 (mm)
REVERT: A  253 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8241 (m-40)
REVERT: A  310 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8495 (mt-10)
REVERT: C  172 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7631 (pt0)
REVERT: C  253 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8197 (m-40)
REVERT: D  172 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7725 (pt0)
REVERT: D  310 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8488 (mt-10)
  outliers start: 25
  outliers final: 18
  residues processed: 224
  average time/residue: 3.1751
  time to fit residues: 770.4955
Evaluate side-chains
  225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 2.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  172 GLU
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  391 SER
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Chi-restraints excluded: chain D residue  398 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 135 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 123 optimal weight:    4.9990
   chunk 150 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.133734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.099439 restraints weight = 38565.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.32
r_work: 0.2818 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  13784  Z= 0.189
  Angle     :  0.533   6.243  18712  Z= 0.290
  Chirality :  0.037   0.133   2180
  Planarity :  0.004   0.037   2276
  Dihedral  :  4.042  17.553   1988
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.03 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.20), residues: 1620
  helix:  2.53 (0.14), residues: 1196
  sheet:  None (None), residues: 0
  loop : -0.57 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 355 
 HIS   0.004   0.001   HIS C  60 
 PHE   0.016   0.002   PHE A 419 
 TYR   0.014   0.002   TYR C 276 
 ARG   0.003   0.000   ARG D 346 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00139 (    4)
  link_ALPHA1-4        : angle       1.29831 (   12)
  hydrogen bonds       : bond        0.05174 (  988)
  hydrogen bonds       : angle       4.16474 ( 2928)
  covalent geometry    : bond        0.00400 (13780)
  covalent geometry    : angle       0.53210 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 205
  time to evaluate  : 3.902 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.8114 (pm20) cc_final: 0.7750 (pt0)
REVERT: A  249 ILE cc_start: 0.8355 (mm) cc_final: 0.8111 (mm)
REVERT: A  253 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8162 (m-40)
REVERT: A  310 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8489 (mt-10)
REVERT: B  172 GLU cc_start: 0.8117 (pm20) cc_final: 0.7732 (pt0)
REVERT: C  249 ILE cc_start: 0.8300 (mm) cc_final: 0.7953 (mm)
REVERT: C  253 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8182 (m-40)
REVERT: D  172 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7696 (pt0)
  outliers start: 21
  outliers final: 15
  residues processed: 221
  average time/residue: 3.7726
  time to fit residues: 915.9244
Evaluate side-chains
  218 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 2.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  368 VAL
Chi-restraints excluded: chain D residue  391 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 150 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 141 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0970
   chunk 159 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 112 optimal weight:    3.9990
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.101574 restraints weight = 38335.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.32
r_work: 0.2852 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  13784  Z= 0.126
  Angle     :  0.493   6.438  18712  Z= 0.266
  Chirality :  0.036   0.139   2180
  Planarity :  0.004   0.037   2276
  Dihedral  :  3.770  15.002   1988
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.26 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.20), residues: 1620
  helix:  2.65 (0.14), residues: 1212
  sheet:  None (None), residues: 0
  loop : -0.72 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 355 
 HIS   0.002   0.001   HIS C  60 
 PHE   0.011   0.001   PHE C  66 
 TYR   0.012   0.002   TYR B 232 
 ARG   0.003   0.000   ARG C 161 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00063 (    4)
  link_ALPHA1-4        : angle       1.08792 (   12)
  hydrogen bonds       : bond        0.04742 (  988)
  hydrogen bonds       : angle       4.07528 ( 2928)
  covalent geometry    : bond        0.00243 (13780)
  covalent geometry    : angle       0.49257 (18700)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 211
  time to evaluate  : 2.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.8044 (pm20) cc_final: 0.7802 (pm20)
REVERT: A  253 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8115 (m-40)
REVERT: B  172 GLU cc_start: 0.8046 (pm20) cc_final: 0.7807 (pm20)
REVERT: C  249 ILE cc_start: 0.8312 (mm) cc_final: 0.7979 (mm)
REVERT: C  253 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8128 (m-40)
REVERT: D  172 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7670 (pt0)
  outliers start: 9
  outliers final: 5
  residues processed: 218
  average time/residue: 3.2760
  time to fit residues: 774.2212
Evaluate side-chains
  209 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 201
  time to evaluate  : 2.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain D residue  156 VAL
Chi-restraints excluded: chain D residue  172 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 154 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 156 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0030
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
B  71 GLN
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 ASN
D  71 GLN
D 253 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.136188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.101771 restraints weight = 38376.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.34
r_work: 0.2857 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13784  Z= 0.127
  Angle     :  0.491   6.404  18712  Z= 0.264
  Chirality :  0.036   0.135   2180
  Planarity :  0.004   0.036   2276
  Dihedral  :  3.681  14.945   1988
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 17.53 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.20), residues: 1620
  helix:  2.75 (0.14), residues: 1188
  sheet:  None (None), residues: 0
  loop : -0.64 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 355 
 HIS   0.002   0.001   HIS B  60 
 PHE   0.011   0.001   PHE C  66 
 TYR   0.013   0.002   TYR A 232 
 ARG   0.003   0.000   ARG C 180 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00077 (    4)
  link_ALPHA1-4        : angle       1.04262 (   12)
  hydrogen bonds       : bond        0.04697 (  988)
  hydrogen bonds       : angle       4.03363 ( 2928)
  covalent geometry    : bond        0.00249 (13780)
  covalent geometry    : angle       0.49076 (18700)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 21859.16 seconds
wall clock time: 378 minutes 26.55 seconds (22706.55 seconds total)