Starting phenix.real_space_refine
on Sun Jun  8 15:25:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wut_32841/06_2025/7wut_32841.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 128 atoms to isotropic.
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      76      5.16       5
     C    6100      2.51       5
     N    1728      2.21       5
     O    1828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9732
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "B"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "C"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "D"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 6.00, per 1000 atoms: 0.62
  Number of scatterers: 9732
  At special positions: 0
  Unit cell: (114.84, 85.8, 85.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    1828      8.00
     N    1728      7.00
     C    6100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 179 " - pdb=" SG  CYS C 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 280 " - pdb=" SG  CYS C 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  55 " - pdb=" SG  CYS D 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 179 " - pdb=" SG  CYS D 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 280 " - pdb=" SG  CYS D 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 313 " - pdb=" SG  CYS D 316 " distance=2.03

  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      17.4% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 51
      removed outlier: 4.326A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 78
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 256
    Processing helix  chain 'B' and resid 38 through 51
      removed outlier: 4.313A  pdb=" N   LEU B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 79
      Proline residue:  B  73  - end of helix
      removed outlier: 3.596A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 83
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 252 through 256
    Processing helix  chain 'C' and resid 38 through 51
      removed outlier: 4.290A  pdb=" N   LEU C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 79
      Proline residue:  C  73  - end of helix
      removed outlier: 3.587A  pdb=" N   LEU C  79 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 83
    Processing helix  chain 'C' and resid 144 through 146
      No H-bonds generated for 'chain 'C' and resid 144 through 146'
    Processing helix  chain 'C' and resid 226 through 230
    Processing helix  chain 'C' and resid 244 through 248
    Processing helix  chain 'C' and resid 252 through 256
    Processing helix  chain 'D' and resid 38 through 51
      removed outlier: 4.288A  pdb=" N   LEU D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 79
      Proline residue:  D  73  - end of helix
      removed outlier: 3.588A  pdb=" N   LEU D  79 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 83
    Processing helix  chain 'D' and resid 144 through 146
      No H-bonds generated for 'chain 'D' and resid 144 through 146'
    Processing helix  chain 'D' and resid 226 through 230
    Processing helix  chain 'D' and resid 244 through 248
    Processing helix  chain 'D' and resid 252 through 256
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57
      removed outlier: 6.812A  pdb=" N   GLY A  56 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 331
      removed outlier: 4.041A  pdb=" N   ASP A 276 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A 324 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE A 277 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 8.978A  pdb=" N   GLU A 213 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG A 192 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG C 192 " --> pdb=" O   LYS C 189 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER C 216 " --> pdb=" O   TRP C 201 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ALA C 205 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ILE C 212 " --> pdb=" O   ALA C 205 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   GLU C 213 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE C 277 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG C 324 " --> pdb=" O   GLU C 274 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASP C 276 " --> pdb=" O   ARG C 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287
      removed outlier: 6.973A  pdb=" N   VAL A 286 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57
      removed outlier: 6.775A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154
    Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 331
      removed outlier: 4.046A  pdb=" N   ASP B 276 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG B 324 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE B 277 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLU B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER B 216 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG B 192 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG D 192 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER D 216 " --> pdb=" O   TRP D 201 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ALA D 205 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   ILE D 212 " --> pdb=" O   ALA D 205 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLU D 213 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE D 277 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG D 324 " --> pdb=" O   GLU D 274 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ASP D 276 " --> pdb=" O   ARG D 322 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 287
      removed outlier: 6.972A  pdb=" N   VAL B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57
      removed outlier: 6.765A  pdb=" N   GLY C  56 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 154
    Processing sheet with id=AB2, first strand: chain 'C' and resid 286 through 287
      removed outlier: 6.984A  pdb=" N   VAL C 286 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 57
      removed outlier: 6.770A  pdb=" N   GLY D  56 " --> pdb=" O   ALA D 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'D' and resid 153 through 154
    Processing sheet with id=AB5, first strand: chain 'D' and resid 286 through 287
      removed outlier: 6.977A  pdb=" N   VAL D 286 " --> pdb=" O   CYS D 313 " (cutoff:3.500A)

    213 hydrogen bonds defined for protein.
    492 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 3.01 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: 3226
        1.34 -     1.46: 2163
        1.46 -     1.58: 4467
        1.58 -     1.69: 0
        1.69 -     1.81: 108
  Bond restraints: 9964
  Sorted by residual:
  bond pdb=" N   GLN C  31 "
       pdb=" CA  GLN C  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.11e+00
  bond pdb=" N   GLN B  31 "
       pdb=" CA  GLN B  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.08e+00
  bond pdb=" N   GLN D  31 "
       pdb=" CA  GLN D  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.06e+00
  bond pdb=" N   GLN A  31 "
       pdb=" CA  GLN A  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.05e+00
  bond pdb=" N   GLU A 156 "
       pdb=" CA  GLU A 156 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 1.99e+00
  ... (remaining 9959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 13158
        2.10 -     4.21: 274
        4.21 -     6.31: 48
        6.31 -     8.41: 17
        8.41 -    10.52: 23
  Bond angle restraints: 13520
  Sorted by residual:
  angle pdb=" C   VAL B 155 "
        pdb=" N   GLU B 156 "
        pdb=" CA  GLU B 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.51   -9.81 1.80e+00 3.09e-01 2.97e+01
  angle pdb=" C   VAL D 155 "
        pdb=" N   GLU D 156 "
        pdb=" CA  GLU D 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.50   -9.80 1.80e+00 3.09e-01 2.97e+01
  angle pdb=" C   VAL C 155 "
        pdb=" N   GLU C 156 "
        pdb=" CA  GLU C 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.48   -9.78 1.80e+00 3.09e-01 2.95e+01
  angle pdb=" C   GLU A  30 "
        pdb=" N   GLN A  31 "
        pdb=" CA  GLN A  31 "
      ideal   model   delta    sigma   weight residual
     121.70  131.45   -9.75 1.80e+00 3.09e-01 2.94e+01
  angle pdb=" C   GLU C  30 "
        pdb=" N   GLN C  31 "
        pdb=" CA  GLN C  31 "
      ideal   model   delta    sigma   weight residual
     121.70  131.44   -9.74 1.80e+00 3.09e-01 2.93e+01
  ... (remaining 13515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 5050
       15.62 -    31.23: 678
       31.23 -    46.85: 199
       46.85 -    62.47: 73
       62.47 -    78.08: 16
  Dihedral angle restraints: 6016
    sinusoidal: 2392
      harmonic: 3624
  Sorted by residual:
  dihedral pdb=" CB  CYS D 313 "
           pdb=" SG  CYS D 313 "
           pdb=" SG  CYS D 316 "
           pdb=" CB  CYS D 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.82   54.18     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 316 "
           pdb=" CB  CYS B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.89   54.11     1      1.00e+01 1.00e-02 3.97e+01
  dihedral pdb=" CB  CYS A 313 "
           pdb=" SG  CYS A 313 "
           pdb=" SG  CYS A 316 "
           pdb=" CB  CYS A 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.05   53.95     1      1.00e+01 1.00e-02 3.95e+01
  ... (remaining 6013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 959
       0.035 -    0.070: 339
       0.070 -    0.105: 119
       0.105 -    0.141: 54
       0.141 -    0.176: 9
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  THR C  72 "
            pdb=" N   THR C  72 "
            pdb=" C   THR C  72 "
            pdb=" CB  THR C  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CA  THR B  72 "
            pdb=" N   THR B  72 "
            pdb=" C   THR B  72 "
            pdb=" CB  THR B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  THR D  72 "
            pdb=" N   THR D  72 "
            pdb=" C   THR D  72 "
            pdb=" CB  THR D  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 1477 not shown)

  Planarity restraints: 1740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  72 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO D  73 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D  73 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  73 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  72 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.05e+00
        pdb=" N   PRO C  73 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C  73 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  73 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  72 "   -0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO A  73 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1737 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 333
        2.69 -     3.24: 9875
        3.24 -     3.80: 15637
        3.80 -     4.35: 19508
        4.35 -     4.90: 31111
  Nonbonded interactions: 76464
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  23 "
            pdb=" OG  SER B 185 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OD2 ASP A  23 "
            pdb=" OG  SER A 185 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OD2 ASP C  23 "
            pdb=" OG  SER C 185 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD2 ASP D  23 "
            pdb=" OG  SER D 185 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG1 THR B 300 "
            pdb=" O   CYS B 329 "
     model   vdw
     2.267 3.040
  ... (remaining 76459 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.340
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9984  Z= 0.144
  Angle     :  0.832  10.516  13560  Z= 0.417
  Chirality :  0.046   0.176   1480
  Planarity :  0.004   0.036   1740
  Dihedral  : 16.782  78.083   3612
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.30 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 32.13 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.82 (0.24), residues: 1248
  helix:  0.09 (0.48), residues: 128
  sheet:  0.00 (0.77), residues: 60
  loop : -1.61 (0.20), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 225 
 HIS   0.004   0.001   HIS A 254 
 PHE   0.005   0.001   PHE A 217 
 TYR   0.006   0.001   TYR D 256 
 ARG   0.006   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28396 (  213)
  hydrogen bonds       : angle      11.01054 (  492)
  SS BOND              : bond        0.00152 (   20)
  SS BOND              : angle       0.56574 (   40)
  covalent geometry    : bond        0.00294 ( 9964)
  covalent geometry    : angle       0.83254 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8745 (t0) cc_final: 0.7851 (t70)
REVERT: A  241 MET cc_start: 0.8010 (mmm) cc_final: 0.7703 (mtt)
REVERT: B   86 LEU cc_start: 0.8778 (pp) cc_final: 0.8501 (tp)
REVERT: C   86 LEU cc_start: 0.8739 (pp) cc_final: 0.8499 (tp)
REVERT: D   86 LEU cc_start: 0.8729 (pp) cc_final: 0.8488 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1737
  time to fit residues: 20.5703
Evaluate side-chains
  73 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.0370
   chunk 93 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:   50.0000
   chunk 112 optimal weight:    7.9990
   overall best weight:    5.4066

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.111500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.074925 restraints weight = 33947.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.077829 restraints weight = 18464.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.079826 restraints weight = 12876.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9984  Z= 0.280
  Angle     :  0.869   9.805  13560  Z= 0.452
  Chirality :  0.048   0.182   1480
  Planarity :  0.005   0.033   1740
  Dihedral  :  5.651  34.398   1342
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.34 %
    Favored  : 85.34 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 28.81 %
    Favored  : 64.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.24), residues: 1248
  helix: -0.07 (0.45), residues: 144
  sheet: -0.60 (0.60), residues: 92
  loop : -1.73 (0.20), residues: 1012

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 225 
 HIS   0.004   0.001   HIS D 195 
 PHE   0.010   0.001   PHE D 217 
 TYR   0.009   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05841 (  213)
  hydrogen bonds       : angle       8.05263 (  492)
  SS BOND              : bond        0.00516 (   20)
  SS BOND              : angle       0.71640 (   40)
  covalent geometry    : bond        0.00594 ( 9964)
  covalent geometry    : angle       0.86908 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 69
  time to evaluate  : 1.083 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8795 (p0)
REVERT: A  195 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8215 (m90)
REVERT: A  227 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8984 (mmmt)
REVERT: B  190 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8796 (p0)
REVERT: B  195 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8196 (m90)
REVERT: B  227 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8863 (mmmt)
REVERT: B  242 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8978 (mm)
REVERT: B  310 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: C   42 LEU cc_start: 0.9536 (tt) cc_final: 0.9044 (mp)
REVERT: C  190 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8805 (p0)
REVERT: C  195 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8229 (m90)
REVERT: C  242 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8986 (mm)
REVERT: C  260 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (m-10)
REVERT: C  310 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (pp20)
REVERT: D   42 LEU cc_start: 0.9531 (tt) cc_final: 0.9037 (mp)
REVERT: D  190 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8700 (p0)
REVERT: D  195 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8204 (m90)
REVERT: D  227 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8959 (mmmt)
  outliers start: 64
  outliers final: 22
  residues processed: 114
  average time/residue: 0.1758
  time to fit residues: 30.3501
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 70
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LYS
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  260 TYR
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  264 THR
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 94 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** 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 = 0.4316 r_free = 0.4316 target = 0.116876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.090401 restraints weight = 39795.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.092538 restraints weight = 23116.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.094000 restraints weight = 16375.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9984  Z= 0.248
  Angle     :  0.858   9.660  13560  Z= 0.445
  Chirality :  0.047   0.172   1480
  Planarity :  0.004   0.035   1740
  Dihedral  :  5.719  33.291   1342
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.82 %
    Favored  : 84.86 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 29.98 %
    Favored  : 63.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.99 (0.24), residues: 1248
  helix:  0.13 (0.45), residues: 144
  sheet: -1.12 (0.57), residues: 104
  loop : -1.72 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 225 
 HIS   0.005   0.001   HIS D 254 
 PHE   0.010   0.002   PHE D 217 
 TYR   0.010   0.001   TYR A 323 
 ARG   0.004   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  213)
  hydrogen bonds       : angle       7.71387 (  492)
  SS BOND              : bond        0.00445 (   20)
  SS BOND              : angle       0.70807 (   40)
  covalent geometry    : bond        0.00523 ( 9964)
  covalent geometry    : angle       0.85871 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 77
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8707 (p0)
REVERT: A  195 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8280 (m90)
REVERT: A  227 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8906 (mmmt)
REVERT: A  238 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8575 (mt-10)
REVERT: A  242 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: A  323 TYR cc_start: 0.7294 (m-80) cc_final: 0.6342 (m-80)
REVERT: B  190 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8712 (p0)
REVERT: B  195 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8292 (m90)
REVERT: B  227 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8911 (mmmt)
REVERT: B  238 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8559 (mt-10)
REVERT: B  241 MET cc_start: 0.8684 (mmm) cc_final: 0.8081 (mtt)
REVERT: B  242 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8973 (mm)
REVERT: B  310 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (pp20)
REVERT: B  333 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7891 (ptp)
REVERT: C   42 LEU cc_start: 0.9560 (tt) cc_final: 0.9037 (mp)
REVERT: C  190 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8724 (p0)
REVERT: C  195 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8321 (m90)
REVERT: C  227 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9016 (mmmm)
REVERT: C  238 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8579 (mt-10)
REVERT: C  242 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: C  310 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8546 (pp20)
REVERT: C  333 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (ptp)
REVERT: D  190 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8702 (p0)
REVERT: D  195 HIS cc_start: 0.8749 (OUTLIER) cc_final: 0.8304 (m90)
REVERT: D  227 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8890 (mmmt)
REVERT: D  238 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8598 (mt-10)
REVERT: D  242 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8924 (mm)
REVERT: D  323 TYR cc_start: 0.7294 (m-80) cc_final: 0.6346 (m-80)
  outliers start: 66
  outliers final: 29
  residues processed: 131
  average time/residue: 0.1763
  time to fit residues: 34.7161
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 70
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LYS
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 72 optimal weight:   50.0000
   chunk 96 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 112 optimal weight:    0.7980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** 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 = 0.4292 r_free = 0.4292 target = 0.107196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.075811 restraints weight = 30779.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.078843 restraints weight = 16045.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.080900 restraints weight = 11008.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9984  Z= 0.152
  Angle     :  0.814  10.480  13560  Z= 0.417
  Chirality :  0.047   0.174   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.289  22.367   1340
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.62 %
    Favored  : 86.06 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 31.15 %
    Favored  : 64.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.86 (0.25), residues: 1248
  helix:  0.38 (0.48), residues: 144
  sheet: -1.34 (0.55), residues: 100
  loop : -1.61 (0.20), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 225 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.009   0.001   PHE D 277 
 TYR   0.013   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03900 (  213)
  hydrogen bonds       : angle       7.28267 (  492)
  SS BOND              : bond        0.00240 (   20)
  SS BOND              : angle       0.65857 (   40)
  covalent geometry    : bond        0.00318 ( 9964)
  covalent geometry    : angle       0.81410 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 77
  time to evaluate  : 1.072 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9072 (t0) cc_final: 0.8513 (t70)
REVERT: A  190 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8647 (p0)
REVERT: A  242 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: A  323 TYR cc_start: 0.7397 (m-80) cc_final: 0.6459 (m-80)
REVERT: B  184 MET cc_start: 0.7604 (mmm) cc_final: 0.7258 (mtp)
REVERT: B  190 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8624 (p0)
REVERT: B  241 MET cc_start: 0.8471 (mmm) cc_final: 0.7850 (mtt)
REVERT: B  310 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8454 (pp20)
REVERT: B  333 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7756 (ptp)
REVERT: C  190 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8620 (p0)
REVERT: C  310 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8456 (pp20)
REVERT: C  333 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (ptp)
REVERT: D  190 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8645 (p0)
REVERT: D  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8966 (mm)
  outliers start: 45
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1522
  time to fit residues: 27.3886
Evaluate side-chains
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 94 optimal weight:    0.5980
   chunk 116 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 120 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 108 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.112847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.075054 restraints weight = 34347.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.078018 restraints weight = 17915.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.079945 restraints weight = 12317.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9984  Z= 0.201
  Angle     :  0.827  10.270  13560  Z= 0.425
  Chirality :  0.047   0.172   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.346  21.729   1340
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.70 %
    Favored  : 85.98 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 29.49 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.86 (0.25), residues: 1248
  helix:  0.48 (0.49), residues: 144
  sheet: -1.29 (0.56), residues: 104
  loop : -1.64 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 225 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.010   0.001   PHE D 217 
 TYR   0.008   0.001   TYR D 323 
 ARG   0.003   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  213)
  hydrogen bonds       : angle       7.26892 (  492)
  SS BOND              : bond        0.00451 (   20)
  SS BOND              : angle       0.75213 (   40)
  covalent geometry    : bond        0.00426 ( 9964)
  covalent geometry    : angle       0.82708 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 72
  time to evaluate  : 1.182 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8708 (p0)
REVERT: A  238 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8650 (mt-10)
REVERT: A  242 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: A  275 MET cc_start: 0.8753 (mmp) cc_final: 0.8336 (mmt)
REVERT: A  323 TYR cc_start: 0.7408 (m-80) cc_final: 0.6845 (m-80)
REVERT: B  227 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8842 (mmmt)
REVERT: B  242 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9025 (mm)
REVERT: B  310 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (pp20)
REVERT: B  333 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7526 (ptp)
REVERT: C   26 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7490 (t-90)
REVERT: C  227 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8905 (mmmm)
REVERT: C  242 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9030 (mm)
REVERT: C  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8464 (pp20)
REVERT: C  333 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7619 (ptp)
REVERT: D  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8965 (mm)
REVERT: D  275 MET cc_start: 0.8746 (mmp) cc_final: 0.8317 (mmt)
REVERT: D  323 TYR cc_start: 0.7389 (m-80) cc_final: 0.6784 (m-80)
  outliers start: 60
  outliers final: 34
  residues processed: 118
  average time/residue: 0.1751
  time to fit residues: 31.8497
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 70
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    0.0370
   chunk 77 optimal weight:    7.9990
   chunk 116 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 123 optimal weight:    9.9990
   chunk 104 optimal weight:   20.0000
   chunk 111 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    3.8066

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 ASN
C  65 ASN
D  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.111223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.073406 restraints weight = 34636.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.076436 restraints weight = 18358.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.078431 restraints weight = 12756.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9984  Z= 0.211
  Angle     :  0.834  10.142  13560  Z= 0.429
  Chirality :  0.047   0.170   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.444  21.847   1340
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 15.14 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 29.30 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.86 (0.25), residues: 1248
  helix:  0.52 (0.48), residues: 144
  sheet: -1.19 (0.50), residues: 124
  loop : -1.66 (0.21), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.011   0.002   PHE D 217 
 TYR   0.012   0.001   TYR C 323 
 ARG   0.003   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  213)
  hydrogen bonds       : angle       7.18875 (  492)
  SS BOND              : bond        0.00354 (   20)
  SS BOND              : angle       0.77983 (   40)
  covalent geometry    : bond        0.00448 ( 9964)
  covalent geometry    : angle       0.83444 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 77
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7083 (t-90)
REVERT: A  238 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8637 (mt-10)
REVERT: A  242 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: A  275 MET cc_start: 0.8811 (mmp) cc_final: 0.8407 (mmt)
REVERT: A  323 TYR cc_start: 0.7428 (m-80) cc_final: 0.6848 (m-80)
REVERT: B  190 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8683 (p0)
REVERT: B  227 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8851 (mmmt)
REVERT: B  242 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: B  310 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8457 (pp20)
REVERT: B  323 TYR cc_start: 0.7208 (m-80) cc_final: 0.6642 (m-80)
REVERT: B  333 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7461 (ptp)
REVERT: C   26 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7472 (t-90)
REVERT: C  190 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8682 (p0)
REVERT: C  227 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8928 (mmmm)
REVERT: C  241 MET cc_start: 0.8823 (mmm) cc_final: 0.8437 (mtt)
REVERT: C  242 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8961 (mm)
REVERT: C  310 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8452 (pp20)
REVERT: C  333 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7789 (ptp)
REVERT: D  190 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8684 (p0)
REVERT: D  242 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: D  275 MET cc_start: 0.8787 (mmp) cc_final: 0.8343 (mmt)
REVERT: D  323 TYR cc_start: 0.7427 (m-80) cc_final: 0.6831 (m-80)
  outliers start: 62
  outliers final: 40
  residues processed: 125
  average time/residue: 0.1659
  time to fit residues: 32.1566
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 70
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 28 optimal weight:    9.9990
   overall best weight:    1.7944

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.113449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.075825 restraints weight = 34368.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.079008 restraints weight = 18050.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.081135 restraints weight = 12466.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9984  Z= 0.151
  Angle     :  0.821  10.117  13560  Z= 0.415
  Chirality :  0.046   0.172   1480
  Planarity :  0.004   0.030   1740
  Dihedral  :  5.223  22.249   1340
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.02 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.57 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.66 (0.25), residues: 1248
  helix:  0.78 (0.53), residues: 128
  sheet: -1.32 (0.49), residues: 124
  loop : -1.45 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 225 
 HIS   0.002   0.001   HIS B 229 
 PHE   0.009   0.001   PHE C 277 
 TYR   0.014   0.001   TYR C 323 
 ARG   0.003   0.000   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  213)
  hydrogen bonds       : angle       7.03121 (  492)
  SS BOND              : bond        0.00223 (   20)
  SS BOND              : angle       0.66194 (   40)
  covalent geometry    : bond        0.00321 ( 9964)
  covalent geometry    : angle       0.82092 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 78
  time to evaluate  : 1.211 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9104 (t0) cc_final: 0.8206 (t70)
REVERT: A  190 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8629 (p0)
REVERT: A  242 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9038 (mm)
REVERT: A  275 MET cc_start: 0.8931 (mmp) cc_final: 0.8571 (mmt)
REVERT: A  323 TYR cc_start: 0.7357 (m-80) cc_final: 0.6757 (m-80)
REVERT: B  136 ASP cc_start: 0.9070 (t0) cc_final: 0.8226 (t70)
REVERT: B  190 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (p0)
REVERT: B  242 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: B  310 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8385 (pp20)
REVERT: B  333 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7494 (ptp)
REVERT: C   26 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7452 (t-90)
REVERT: C  190 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8677 (p0)
REVERT: C  227 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8753 (mmmm)
REVERT: C  241 MET cc_start: 0.8549 (mmm) cc_final: 0.8195 (mtt)
REVERT: C  242 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9024 (mm)
REVERT: C  310 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8426 (pp20)
REVERT: C  333 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (ptp)
REVERT: D  136 ASP cc_start: 0.9085 (t0) cc_final: 0.8234 (t70)
REVERT: D  190 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8641 (p0)
REVERT: D  241 MET cc_start: 0.8355 (mtt) cc_final: 0.7848 (mtt)
REVERT: D  242 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9035 (mm)
REVERT: D  275 MET cc_start: 0.8878 (mmp) cc_final: 0.8482 (mmt)
REVERT: D  323 TYR cc_start: 0.7379 (m-80) cc_final: 0.6763 (m-80)
  outliers start: 44
  outliers final: 27
  residues processed: 114
  average time/residue: 0.1665
  time to fit residues: 29.7417
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 76
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 105 optimal weight:    0.0570
   chunk 113 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    2.1704

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

Flipped N/Q/H residues before XYZ refinement:
B  77 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.114441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.075959 restraints weight = 34591.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.079165 restraints weight = 17986.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.081238 restraints weight = 12361.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9984  Z= 0.159
  Angle     :  0.829  10.266  13560  Z= 0.416
  Chirality :  0.047   0.170   1480
  Planarity :  0.004   0.029   1740
  Dihedral  :  5.147  22.130   1340
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.42 %
    Favored  : 85.26 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 29.98 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.72 (0.25), residues: 1248
  helix:  0.51 (0.51), residues: 128
  sheet: -1.33 (0.48), residues: 124
  loop : -1.46 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 225 
 HIS   0.003   0.001   HIS B 229 
 PHE   0.009   0.001   PHE D 217 
 TYR   0.014   0.001   TYR C 323 
 ARG   0.002   0.000   ARG A 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (  213)
  hydrogen bonds       : angle       6.99849 (  492)
  SS BOND              : bond        0.00250 (   20)
  SS BOND              : angle       0.62231 (   40)
  covalent geometry    : bond        0.00338 ( 9964)
  covalent geometry    : angle       0.82956 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 77
  time to evaluate  : 1.434 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7037 (t-90)
REVERT: A  136 ASP cc_start: 0.9066 (t0) cc_final: 0.8237 (t70)
REVERT: A  190 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8702 (p0)
REVERT: A  242 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: A  323 TYR cc_start: 0.7302 (m-80) cc_final: 0.6639 (m-80)
REVERT: B   26 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7498 (t-90)
REVERT: B  136 ASP cc_start: 0.9027 (t0) cc_final: 0.8234 (t70)
REVERT: B  190 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8679 (p0)
REVERT: B  242 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9016 (mm)
REVERT: B  275 MET cc_start: 0.8488 (mmp) cc_final: 0.8196 (mmp)
REVERT: B  310 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8472 (pp20)
REVERT: B  333 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7528 (ptp)
REVERT: C   26 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7484 (t-90)
REVERT: C  136 ASP cc_start: 0.9096 (t0) cc_final: 0.8570 (t70)
REVERT: C  190 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8672 (p0)
REVERT: C  227 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8862 (mmmm)
REVERT: C  241 MET cc_start: 0.8695 (mmm) cc_final: 0.7970 (mtt)
REVERT: C  242 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9023 (mm)
REVERT: C  310 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: C  333 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7568 (ptp)
REVERT: D  136 ASP cc_start: 0.9019 (t0) cc_final: 0.8230 (t70)
REVERT: D  190 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8637 (p0)
REVERT: D  242 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9020 (mm)
REVERT: D  275 MET cc_start: 0.8889 (mmp) cc_final: 0.8462 (mmt)
REVERT: D  323 TYR cc_start: 0.7340 (m-80) cc_final: 0.6796 (m-80)
  outliers start: 47
  outliers final: 30
  residues processed: 116
  average time/residue: 0.1855
  time to fit residues: 34.1973
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 77
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 99 optimal weight:    0.6980
   chunk 25 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 49 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   chunk 119 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.113258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.075574 restraints weight = 34632.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.078752 restraints weight = 18387.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.080862 restraints weight = 12780.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9984  Z= 0.165
  Angle     :  0.827  10.285  13560  Z= 0.415
  Chirality :  0.047   0.169   1480
  Planarity :  0.004   0.029   1740
  Dihedral  :  5.152  22.124   1340
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.34 %
    Favored  : 85.34 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 29.20 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.71 (0.25), residues: 1248
  helix:  0.37 (0.50), residues: 132
  sheet: -1.32 (0.48), residues: 124
  loop : -1.44 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.010   0.001   PHE D 217 
 TYR   0.009   0.001   TYR D 323 
 ARG   0.003   0.000   ARG D 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03324 (  213)
  hydrogen bonds       : angle       6.93318 (  492)
  SS BOND              : bond        0.00266 (   20)
  SS BOND              : angle       0.60867 (   40)
  covalent geometry    : bond        0.00351 ( 9964)
  covalent geometry    : angle       0.82746 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 77
  time to evaluate  : 1.248 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7037 (t-90)
REVERT: A  136 ASP cc_start: 0.9065 (t0) cc_final: 0.8276 (t70)
REVERT: A  190 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8727 (p0)
REVERT: A  242 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8971 (mm)
REVERT: A  323 TYR cc_start: 0.7549 (m-80) cc_final: 0.6930 (m-80)
REVERT: B   26 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7519 (t-90)
REVERT: B  136 ASP cc_start: 0.9028 (t0) cc_final: 0.8250 (t70)
REVERT: B  190 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8671 (p0)
REVERT: B  242 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9004 (mm)
REVERT: B  275 MET cc_start: 0.8712 (mmp) cc_final: 0.8439 (mmt)
REVERT: B  310 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8466 (pp20)
REVERT: B  333 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7629 (ptp)
REVERT: C   26 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7488 (t-90)
REVERT: C  190 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8676 (p0)
REVERT: C  227 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (mmmm)
REVERT: C  241 MET cc_start: 0.8710 (mmm) cc_final: 0.8002 (mtt)
REVERT: C  242 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9020 (mm)
REVERT: C  310 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: C  333 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7550 (ptp)
REVERT: D  136 ASP cc_start: 0.9030 (t0) cc_final: 0.8506 (t70)
REVERT: D  190 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8634 (p0)
REVERT: D  242 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8962 (mm)
REVERT: D  323 TYR cc_start: 0.7567 (m-80) cc_final: 0.6925 (m-80)
  outliers start: 52
  outliers final: 34
  residues processed: 120
  average time/residue: 0.1625
  time to fit residues: 30.7161
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 77
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 117 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 31 optimal weight:   30.0000
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.114553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.076077 restraints weight = 34431.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.079295 restraints weight = 17887.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.081416 restraints weight = 12240.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9984  Z= 0.157
  Angle     :  0.823  10.390  13560  Z= 0.413
  Chirality :  0.046   0.169   1480
  Planarity :  0.004   0.028   1740
  Dihedral  :  5.101  22.209   1340
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.86 %
    Favored  : 85.82 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 29.39 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.71 (0.25), residues: 1248
  helix:  0.36 (0.50), residues: 132
  sheet: -1.38 (0.47), residues: 124
  loop : -1.42 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.017   0.001   TYR C 323 
 ARG   0.003   0.000   ARG D 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 (  213)
  hydrogen bonds       : angle       6.85152 (  492)
  SS BOND              : bond        0.00248 (   20)
  SS BOND              : angle       0.59902 (   40)
  covalent geometry    : bond        0.00333 ( 9964)
  covalent geometry    : angle       0.82399 (13520)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 77
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7040 (t-90)
REVERT: A  136 ASP cc_start: 0.9026 (t0) cc_final: 0.8261 (t70)
REVERT: A  190 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8710 (p0)
REVERT: A  242 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: B  136 ASP cc_start: 0.8976 (t0) cc_final: 0.8196 (t70)
REVERT: B  190 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8685 (p0)
REVERT: B  242 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9009 (mm)
REVERT: B  275 MET cc_start: 0.8417 (mmp) cc_final: 0.8164 (mmp)
REVERT: B  310 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: B  333 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7628 (ptp)
REVERT: C   26 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7473 (t-90)
REVERT: C  136 ASP cc_start: 0.9062 (t0) cc_final: 0.8562 (t70)
REVERT: C  190 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8663 (p0)
REVERT: C  227 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8868 (mmmm)
REVERT: C  241 MET cc_start: 0.8689 (mmm) cc_final: 0.7955 (mtt)
REVERT: C  242 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9007 (mm)
REVERT: C  310 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: C  333 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7554 (ptp)
REVERT: D  136 ASP cc_start: 0.8985 (t0) cc_final: 0.8199 (t70)
REVERT: D  190 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8692 (p0)
REVERT: D  242 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8989 (mm)
REVERT: D  323 TYR cc_start: 0.7421 (m-80) cc_final: 0.6814 (m-80)
  outliers start: 52
  outliers final: 33
  residues processed: 122
  average time/residue: 0.1748
  time to fit residues: 33.0885
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 76
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 70 optimal weight:    0.0000
   chunk 26 optimal weight:    9.9990
   chunk 120 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 112 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0980
   chunk 110 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
C  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.115893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.078714 restraints weight = 33933.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.082068 restraints weight = 17957.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.084280 restraints weight = 12344.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9984  Z= 0.134
  Angle     :  0.816  10.707  13560  Z= 0.405
  Chirality :  0.046   0.171   1480
  Planarity :  0.004   0.028   1740
  Dihedral  :  4.906  22.398   1340
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 12.90 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 31.64 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.67 (0.25), residues: 1248
  helix:  0.15 (0.49), residues: 132
  sheet: -1.12 (0.47), residues: 116
  loop : -1.40 (0.21), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 225 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.010   0.001   PHE A 277 
 TYR   0.016   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03095 (  213)
  hydrogen bonds       : angle       6.69693 (  492)
  SS BOND              : bond        0.00156 (   20)
  SS BOND              : angle       0.55439 (   40)
  covalent geometry    : bond        0.00279 ( 9964)
  covalent geometry    : angle       0.81617 (13520)

===============================================================================
Job complete
usr+sys time: 3292.25 seconds
wall clock time: 58 minutes 10.30 seconds (3490.30 seconds total)