Starting phenix.real_space_refine
on Fri Feb 14 03:15:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wut_32841/02_2025/7wut_32841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wut_32841/02_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_32841/02_2025/7wut_32841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wut_32841/02_2025/7wut_32841.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wut_32841/02_2025/7wut_32841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wut_32841/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.82, per 1000 atoms: 0.60
  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: 2.37
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.23
  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: 2.64

  Time building geometry restraints manager: 2.73 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:             0.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.030
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.980
-------------------------------------------------------------------------------
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   9964  Z= 0.193
  Angle     :  0.833  10.516  13520  Z= 0.418
  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 

*********************** 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  : 1.215 
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: 0.1731
  time to fit residues: 20.4336
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  : 1.251 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 72 optimal weight:   50.0000
   chunk 112 optimal weight:    7.9990
   overall best weight:    4.8066

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.113040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.075457 restraints weight = 33569.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.078326 restraints weight = 17793.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.080248 restraints weight = 12291.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9964  Z= 0.359
  Angle     :  0.852   9.870  13520  Z= 0.443
  Chirality :  0.047   0.178   1480
  Planarity :  0.004   0.032   1740
  Dihedral  :  5.537  34.528   1342
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.18 %
    Favored  : 85.50 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 29.20 %
    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: -1.95 (0.24), residues: 1248
  helix: -0.05 (0.45), residues: 144
  sheet: -1.13 (0.57), residues: 100
  loop : -1.65 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 225 
 HIS   0.005   0.001   HIS B 254 
 PHE   0.010   0.001   PHE D 217 
 TYR   0.009   0.001   TYR A 323 
 ARG   0.004   0.000   ARG A 294 

*********************** 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
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 73
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8773 (p0)
REVERT: A  195 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8122 (m90)
REVERT: A  227 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8973 (mmmt)
REVERT: A  310 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (pp20)
REVERT: B  190 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8759 (p0)
REVERT: B  195 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8179 (m90)
REVERT: B  227 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8983 (mmmt)
REVERT: B  242 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: B  310 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: C  190 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8781 (p0)
REVERT: C  195 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8147 (m90)
REVERT: C  242 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8985 (mm)
REVERT: C  310 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8468 (pp20)
REVERT: D  190 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8738 (p0)
REVERT: D  195 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.8122 (m90)
REVERT: D  227 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8933 (mmmt)
REVERT: D  310 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8474 (pp20)
  outliers start: 58
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1734
  time to fit residues: 29.8521
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 77
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 TYR
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  310 GLU
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  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  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  310 GLU
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:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 94 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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**
** C  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 = 0.4236 r_free = 0.4236 target = 0.104363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.073771 restraints weight = 31367.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.076483 restraints weight = 16940.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.078278 restraints weight = 11770.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9964  Z= 0.326
  Angle     :  0.847   9.718  13520  Z= 0.438
  Chirality :  0.047   0.172   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.625  33.048   1342
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.58 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 28.61 %
    Favored  : 64.75 %
  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: -1.93 (0.24), residues: 1248
  helix:  0.12 (0.45), residues: 144
  sheet: -0.87 (0.58), residues: 100
  loop : -1.69 (0.20), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 225 
 HIS   0.004   0.001   HIS C 195 
 PHE   0.009   0.001   PHE D 217 
 TYR   0.010   0.001   TYR A 323 
 ARG   0.004   0.000   ARG A 294 

*********************** 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
  148 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 80
  time to evaluate  : 1.125 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8713 (p0)
REVERT: A  195 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8273 (m90)
REVERT: A  227 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8903 (mmmt)
REVERT: A  238 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8588 (mt-10)
REVERT: A  242 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: A  310 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8507 (pp20)
REVERT: A  323 TYR cc_start: 0.7274 (m-80) cc_final: 0.6321 (m-80)
REVERT: B  190 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8716 (p0)
REVERT: B  195 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8276 (m90)
REVERT: B  227 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8910 (mmmt)
REVERT: B  238 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8578 (mt-10)
REVERT: B  241 MET cc_start: 0.8640 (mmm) cc_final: 0.8064 (mtt)
REVERT: B  242 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8985 (mm)
REVERT: B  310 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8503 (pp20)
REVERT: B  323 TYR cc_start: 0.7260 (m-80) cc_final: 0.6301 (m-80)
REVERT: B  333 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8055 (ptp)
REVERT: C  190 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8728 (p0)
REVERT: C  195 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8298 (m90)
REVERT: C  227 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9024 (mmmm)
REVERT: C  242 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8975 (mm)
REVERT: C  310 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8513 (pp20)
REVERT: C  323 TYR cc_start: 0.7284 (m-80) cc_final: 0.6326 (m-80)
REVERT: C  333 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7838 (ptp)
REVERT: D  190 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8721 (p0)
REVERT: D  195 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8271 (m90)
REVERT: D  227 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8888 (mmmt)
REVERT: D  238 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8602 (mt-10)
REVERT: D  242 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8904 (mm)
REVERT: D  310 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8500 (pp20)
REVERT: D  323 TYR cc_start: 0.7286 (m-80) cc_final: 0.6334 (m-80)
  outliers start: 68
  outliers final: 29
  residues processed: 137
  average time/residue: 0.1921
  time to fit residues: 38.7227
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 74
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
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  310 GLU
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  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  242 ILE
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   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  310 GLU
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:    8.9990
   chunk 64 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 72 optimal weight:   50.0000
   chunk 96 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.111620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.074974 restraints weight = 33788.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.077936 restraints weight = 18282.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.079925 restraints weight = 12775.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9964  Z= 0.330
  Angle     :  0.853  10.407  13520  Z= 0.441
  Chirality :  0.047   0.171   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.569  21.705   1340
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 15.71 %
    Favored  : 83.97 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 28.52 %
    Favored  : 64.55 %
  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: -1.92 (0.25), residues: 1248
  helix:  0.42 (0.47), residues: 144
  sheet: -1.00 (0.59), residues: 104
  loop : -1.72 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 225 
 HIS   0.004   0.001   HIS C 254 
 PHE   0.011   0.002   PHE B 217 
 TYR   0.009   0.001   TYR C 323 
 ARG   0.003   0.000   ARG A 294 

*********************** 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
  149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 78
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A  195 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8252 (m90)
REVERT: A  227 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8869 (mmtt)
REVERT: A  238 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8615 (mt-10)
REVERT: A  242 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8978 (mm)
REVERT: A  260 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8193 (m-10)
REVERT: A  275 MET cc_start: 0.8764 (mmp) cc_final: 0.8334 (mmt)
REVERT: A  310 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8478 (pp20)
REVERT: A  323 TYR cc_start: 0.7368 (m-80) cc_final: 0.6715 (m-80)
REVERT: B  184 MET cc_start: 0.7665 (mmm) cc_final: 0.7400 (mtp)
REVERT: B  190 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8723 (p0)
REVERT: B  195 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8246 (m90)
REVERT: B  227 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8905 (mmmt)
REVERT: B  241 MET cc_start: 0.8744 (mmm) cc_final: 0.8221 (mtt)
REVERT: B  242 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: B  260 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8203 (m-10)
REVERT: B  275 MET cc_start: 0.8758 (mmp) cc_final: 0.8319 (mmt)
REVERT: B  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8513 (pp20)
REVERT: B  323 TYR cc_start: 0.7367 (m-80) cc_final: 0.6708 (m-80)
REVERT: B  333 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7818 (ptp)
REVERT: C  195 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8286 (m90)
REVERT: C  227 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8930 (mmmm)
REVERT: C  238 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (mt-10)
REVERT: C  242 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: C  275 MET cc_start: 0.8757 (mmp) cc_final: 0.8331 (mmt)
REVERT: C  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (pp20)
REVERT: C  323 TYR cc_start: 0.7371 (m-80) cc_final: 0.6690 (m-80)
REVERT: C  333 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7830 (ptp)
REVERT: D  190 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8725 (p0)
REVERT: D  195 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8341 (m90)
REVERT: D  238 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (mt-10)
REVERT: D  241 MET cc_start: 0.8468 (mtt) cc_final: 0.7989 (mtt)
REVERT: D  242 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8959 (mm)
REVERT: D  275 MET cc_start: 0.8773 (mmp) cc_final: 0.8318 (mmt)
REVERT: D  310 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: D  323 TYR cc_start: 0.7370 (m-80) cc_final: 0.6705 (m-80)
  outliers start: 71
  outliers final: 35
  residues processed: 135
  average time/residue: 0.1743
  time to fit residues: 36.0566
Evaluate side-chains
  134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 75
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
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  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  212 ILE
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  260 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  310 GLU
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  242 ILE
Chi-restraints excluded: chain B residue  260 TYR
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   40 SER
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  194 VAL
Chi-restraints excluded: chain C residue  195 HIS
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  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
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   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  232 TRP
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  310 GLU
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:   20.0000
   chunk 57 optimal weight:    8.9990
   chunk 94 optimal weight:   20.0000
   chunk 116 optimal weight:    6.9990
   chunk 104 optimal weight:   20.0000
   chunk 120 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4235 r_free = 0.4235 target = 0.105201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.071917 restraints weight = 30909.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.074725 restraints weight = 16862.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.076590 restraints weight = 11792.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9964  Z= 0.354
  Angle     :  0.868  10.218  13520  Z= 0.448
  Chirality :  0.048   0.170   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.665  21.736   1340
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 15.14 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 27.54 %
    Favored  : 65.04 %
  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: -1.97 (0.25), residues: 1248
  helix:  0.60 (0.49), residues: 144
  sheet: -0.96 (0.60), residues: 104
  loop : -1.80 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 225 
 HIS   0.005   0.001   HIS C 254 
 PHE   0.012   0.002   PHE D 217 
 TYR   0.008   0.001   TYR B 323 
 ARG   0.004   0.000   ARG D 257 

*********************** 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
  151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 75
  time to evaluate  : 1.238 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7573 (t-90)
REVERT: A  190 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8733 (p0)
REVERT: A  195 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8269 (m90)
REVERT: A  227 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8917 (mmmt)
REVERT: A  238 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8683 (mt-10)
REVERT: A  242 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8972 (mm)
REVERT: A  260 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8323 (m-10)
REVERT: A  275 MET cc_start: 0.8873 (mmp) cc_final: 0.8457 (mmt)
REVERT: A  310 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8433 (pp20)
REVERT: A  323 TYR cc_start: 0.7336 (m-80) cc_final: 0.6685 (m-80)
REVERT: B  195 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8265 (m90)
REVERT: B  227 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8857 (mmmt)
REVERT: B  238 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8694 (mt-10)
REVERT: B  242 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: B  275 MET cc_start: 0.8869 (mmp) cc_final: 0.8444 (mmt)
REVERT: B  310 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8428 (pp20)
REVERT: B  323 TYR cc_start: 0.7274 (m-80) cc_final: 0.6595 (m-80)
REVERT: B  333 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7756 (ptp)
REVERT: C   26 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7381 (t-90)
REVERT: C  190 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8713 (p0)
REVERT: C  195 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8304 (m90)
REVERT: C  227 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8845 (mmmm)
REVERT: C  238 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8688 (mt-10)
REVERT: C  242 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8990 (mm)
REVERT: C  275 MET cc_start: 0.8873 (mmp) cc_final: 0.8385 (mmt)
REVERT: C  310 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8414 (pp20)
REVERT: C  323 TYR cc_start: 0.7341 (m-80) cc_final: 0.6389 (m-80)
REVERT: C  333 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7816 (ptp)
REVERT: D  195 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8302 (m90)
REVERT: D  227 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8946 (mmmm)
REVERT: D  238 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8701 (mt-10)
REVERT: D  242 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8982 (mm)
REVERT: D  275 MET cc_start: 0.8896 (mmp) cc_final: 0.8373 (mmt)
REVERT: D  310 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (pp20)
REVERT: D  323 TYR cc_start: 0.7332 (m-80) cc_final: 0.6391 (m-80)
  outliers start: 76
  outliers final: 40
  residues processed: 138
  average time/residue: 0.1773
  time to fit residues: 37.5512
Evaluate side-chains
  139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 72
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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  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  212 ILE
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  260 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  195 HIS
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  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   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  195 HIS
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  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
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   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  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  310 GLU
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:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 116 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0050
   chunk 111 optimal weight:    1.9990
   chunk 44 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   overall best weight:    3.6000

-------------------------------------------------------------------------------
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
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.105417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.073777 restraints weight = 31419.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.076674 restraints weight = 16446.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.078679 restraints weight = 11270.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9964  Z= 0.290
  Angle     :  0.844  10.163  13520  Z= 0.434
  Chirality :  0.047   0.171   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.547  21.972   1340
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.90 %
    Favored  : 84.78 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 28.42 %
    Favored  : 65.04 %
  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: -1.95 (0.25), residues: 1248
  helix:  0.66 (0.49), residues: 144
  sheet: -0.95 (0.60), residues: 104
  loop : -1.80 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 225 
 HIS   0.004   0.001   HIS C 254 
 PHE   0.012   0.002   PHE D 217 
 TYR   0.009   0.001   TYR D 323 
 ARG   0.003   0.000   ARG D 257 

*********************** 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
  145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 78
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8685 (p0)
REVERT: A  241 MET cc_start: 0.8136 (mtt) cc_final: 0.7617 (mtt)
REVERT: A  242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: A  275 MET cc_start: 0.8846 (mmp) cc_final: 0.8410 (mmt)
REVERT: A  310 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8475 (pp20)
REVERT: A  323 TYR cc_start: 0.7449 (m-80) cc_final: 0.6824 (m-80)
REVERT: B  190 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8687 (p0)
REVERT: B  227 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8861 (mmmt)
REVERT: B  238 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8646 (mt-10)
REVERT: B  242 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9017 (mm)
REVERT: B  275 MET cc_start: 0.8826 (mmp) cc_final: 0.8415 (mmt)
REVERT: B  310 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8473 (pp20)
REVERT: B  323 TYR cc_start: 0.7416 (m-80) cc_final: 0.6801 (m-80)
REVERT: B  333 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7455 (ptp)
REVERT: C   26 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7470 (t-90)
REVERT: C  190 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8689 (p0)
REVERT: C  195 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (m90)
REVERT: C  227 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8919 (mmmm)
REVERT: C  238 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8649 (mt-10)
REVERT: C  242 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9019 (mm)
REVERT: C  275 MET cc_start: 0.8845 (mmp) cc_final: 0.8353 (mmt)
REVERT: C  310 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8482 (pp20)
REVERT: C  323 TYR cc_start: 0.7431 (m-80) cc_final: 0.6520 (m-80)
REVERT: C  333 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7570 (ptp)
REVERT: D  190 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8694 (p0)
REVERT: D  227 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8836 (mmmm)
REVERT: D  238 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (mt-10)
REVERT: D  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: D  275 MET cc_start: 0.8847 (mmp) cc_final: 0.8429 (mmt)
REVERT: D  310 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: D  323 TYR cc_start: 0.7463 (m-80) cc_final: 0.6543 (m-80)
  outliers start: 67
  outliers final: 38
  residues processed: 133
  average time/residue: 0.1787
  time to fit residues: 36.5481
Evaluate side-chains
  134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 74
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
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  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  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   87 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  212 ILE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  238 GLU
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  195 HIS
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  238 GLU
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   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  227 LYS
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  310 GLU
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:    6.9990
   chunk 120 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 104 optimal weight:    9.9990
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 8 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    3.6586

-------------------------------------------------------------------------------
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
D  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.112961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.075686 restraints weight = 34225.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.078632 restraints weight = 17951.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.080595 restraints weight = 12378.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9964  Z= 0.292
  Angle     :  0.846  10.058  13520  Z= 0.433
  Chirality :  0.047   0.169   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.515  22.044   1340
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.26 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 28.52 %
    Favored  : 64.55 %
  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: -1.94 (0.25), residues: 1248
  helix:  0.69 (0.49), residues: 144
  sheet: -0.94 (0.60), residues: 104
  loop : -1.79 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 225 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.011   0.002   PHE B 217 
 TYR   0.009   0.001   TYR B 323 
 ARG   0.003   0.000   ARG D 257 

*********************** 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
  148 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 77
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7538 (t-90)
REVERT: A  190 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (p0)
REVERT: A  238 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8691 (mt-10)
REVERT: A  241 MET cc_start: 0.8351 (mtt) cc_final: 0.7827 (mtt)
REVERT: A  242 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8994 (mm)
REVERT: A  275 MET cc_start: 0.8960 (mmp) cc_final: 0.8576 (mmt)
REVERT: A  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8438 (pp20)
REVERT: A  323 TYR cc_start: 0.7414 (m-80) cc_final: 0.6788 (m-80)
REVERT: B   26 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7560 (t-90)
REVERT: B  190 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8678 (p0)
REVERT: B  225 TRP cc_start: 0.7982 (t-100) cc_final: 0.7762 (t-100)
REVERT: B  227 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8781 (mmmm)
REVERT: B  238 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8685 (mt-10)
REVERT: B  242 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9030 (mm)
REVERT: B  275 MET cc_start: 0.8914 (mmp) cc_final: 0.8628 (mmt)
REVERT: B  310 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8435 (pp20)
REVERT: B  323 TYR cc_start: 0.7430 (m-80) cc_final: 0.6814 (m-80)
REVERT: B  333 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7486 (ptp)
REVERT: C   26 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7464 (t-90)
REVERT: C  190 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8701 (p0)
REVERT: C  195 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8310 (m90)
REVERT: C  227 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8854 (mmmm)
REVERT: C  238 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8683 (mt-10)
REVERT: C  242 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9032 (mm)
REVERT: C  275 MET cc_start: 0.8955 (mmp) cc_final: 0.8535 (mmt)
REVERT: C  310 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8430 (pp20)
REVERT: C  323 TYR cc_start: 0.7442 (m-80) cc_final: 0.6567 (m-80)
REVERT: C  333 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7481 (ptp)
REVERT: D  190 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8696 (p0)
REVERT: D  227 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8796 (mmmm)
REVERT: D  238 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8703 (mt-10)
REVERT: D  242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9001 (mm)
REVERT: D  245 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8746 (ttmt)
REVERT: D  275 MET cc_start: 0.8950 (mmp) cc_final: 0.8647 (mmt)
REVERT: D  310 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8428 (pp20)
REVERT: D  323 TYR cc_start: 0.7450 (m-80) cc_final: 0.6615 (m-80)
  outliers start: 71
  outliers final: 43
  residues processed: 136
  average time/residue: 0.1697
  time to fit residues: 34.8726
Evaluate side-chains
  142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 73
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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  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  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
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  310 GLU
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   72 THR
Chi-restraints excluded: chain B residue   87 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  212 ILE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  236 VAL
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   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  195 HIS
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  236 VAL
Chi-restraints excluded: chain C residue  238 GLU
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   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  227 LYS
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  245 LYS
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  310 GLU
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:    0.7980
   chunk 76 optimal weight:    0.0010
   chunk 114 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 113 optimal weight:    0.8980
   chunk 50 optimal weight:    0.1980
   chunk 97 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   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  65 ASN
B  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.115995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.077749 restraints weight = 34447.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.080992 restraints weight = 17728.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.083123 restraints weight = 12021.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9964  Z= 0.202
  Angle     :  0.818  10.207  13520  Z= 0.412
  Chirality :  0.046   0.171   1480
  Planarity :  0.004   0.033   1740
  Dihedral  :  5.141  22.531   1340
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.30 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 32.13 %
    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: -1.77 (0.24), residues: 1248
  helix:  0.61 (0.51), residues: 128
  sheet: -0.64 (0.59), residues: 92
  loop : -1.61 (0.20), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 225 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.008   0.001   PHE D 217 
 TYR   0.011   0.001   TYR C 323 
 ARG   0.004   0.000   ARG C  62 

*********************** 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
  109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7566 (t-90)
REVERT: A  136 ASP cc_start: 0.9092 (t0) cc_final: 0.8293 (t70)
REVERT: A  190 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (p0)
REVERT: A  238 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8667 (mt-10)
REVERT: A  242 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9019 (mm)
REVERT: A  310 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8504 (pp20)
REVERT: A  321 LEU cc_start: 0.7172 (mt) cc_final: 0.5963 (tp)
REVERT: B   26 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7515 (t-90)
REVERT: B  136 ASP cc_start: 0.9034 (t0) cc_final: 0.8247 (t70)
REVERT: B  190 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8632 (p0)
REVERT: B  238 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8731 (mt-10)
REVERT: B  275 MET cc_start: 0.8846 (mmp) cc_final: 0.8638 (mmt)
REVERT: B  310 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8496 (pp20)
REVERT: B  333 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7558 (ptp)
REVERT: C   26 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7516 (t-90)
REVERT: C  136 ASP cc_start: 0.9007 (t0) cc_final: 0.8156 (t70)
REVERT: C  190 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8640 (p0)
REVERT: C  238 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8699 (mt-10)
REVERT: C  310 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: C  321 LEU cc_start: 0.7121 (mt) cc_final: 0.5934 (tp)
REVERT: C  333 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7636 (ptp)
REVERT: D  136 ASP cc_start: 0.8973 (t0) cc_final: 0.8119 (t70)
REVERT: D  190 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8649 (p0)
REVERT: D  310 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (pp20)
  outliers start: 35
  outliers final: 17
  residues processed: 102
  average time/residue: 0.1709
  time to fit residues: 27.6125
Evaluate side-chains
  107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 HIS
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  190 ASP
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  310 GLU
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   87 THR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  238 GLU
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   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  238 GLU
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   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  310 GLU
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:    9.9990
   chunk 63 optimal weight:    0.0980
   chunk 94 optimal weight:   30.0000
   chunk 99 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    3.8188

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.111489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.073859 restraints weight = 35008.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.076907 restraints weight = 18729.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.078841 restraints weight = 13057.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9964  Z= 0.296
  Angle     :  0.837  10.135  13520  Z= 0.426
  Chirality :  0.047   0.168   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.327  22.080   1340
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.58 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 32.32 %
    Favored  : 63.96 %
  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: -1.84 (0.25), residues: 1248
  helix:  0.79 (0.52), residues: 128
  sheet: -1.20 (0.50), residues: 124
  loop : -1.64 (0.20), residues: 996

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   0.011   0.001   PHE C 217 
 TYR   0.009   0.001   TYR C 323 
 ARG   0.003   0.000   ARG C 257 

*********************** 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
  111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 73
  time to evaluate  : 1.140 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7510 (t-90)
REVERT: A  190 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8670 (p0)
REVERT: A  238 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8698 (mt-10)
REVERT: A  242 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: A  310 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8480 (pp20)
REVERT: A  323 TYR cc_start: 0.7409 (m-80) cc_final: 0.6882 (m-80)
REVERT: B   26 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7514 (t-90)
REVERT: B  190 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8689 (p0)
REVERT: B  238 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8707 (mt-10)
REVERT: B  241 MET cc_start: 0.8064 (mtt) cc_final: 0.7665 (mtt)
REVERT: B  310 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8451 (pp20)
REVERT: B  323 TYR cc_start: 0.7166 (m-80) cc_final: 0.6391 (m-80)
REVERT: B  333 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7451 (ptp)
REVERT: C   26 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7507 (t-90)
REVERT: C  190 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8670 (p0)
REVERT: C  238 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8663 (mt-10)
REVERT: C  241 MET cc_start: 0.8059 (mtt) cc_final: 0.7756 (mtt)
REVERT: C  310 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8493 (pp20)
REVERT: C  323 TYR cc_start: 0.7540 (m-80) cc_final: 0.6996 (m-80)
REVERT: C  333 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7476 (ptp)
REVERT: D  190 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8751 (p0)
REVERT: D  310 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8491 (pp20)
REVERT: D  323 TYR cc_start: 0.7540 (m-80) cc_final: 0.7004 (m-80)
  outliers start: 38
  outliers final: 19
  residues processed: 104
  average time/residue: 0.1738
  time to fit residues: 27.8231
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
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  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
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   87 THR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  238 GLU
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   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  238 GLU
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   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  310 GLU
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:    0.2980
   chunk 33 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 117 optimal weight:    0.1980
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 31 optimal weight:   30.0000
   chunk 20 optimal weight:    4.9990
   overall best weight:    3.4986

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.111510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.073632 restraints weight = 35057.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.076668 restraints weight = 18681.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.078659 restraints weight = 13017.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9964  Z= 0.284
  Angle     :  0.844  10.515  13520  Z= 0.429
  Chirality :  0.047   0.169   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.383  22.108   1340
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.34 %
    Favored  : 85.34 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 31.84 %
    Favored  : 64.06 %
  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:  0.62 (0.51), residues: 132
  sheet: -1.15 (0.51), residues: 124
  loop : -1.65 (0.20), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.012   0.002   PHE B 217 
 TYR   0.011   0.001   TYR A 323 
 ARG   0.004   0.000   ARG A 257 

********************** 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
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 73
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A   26 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7518 (t-90)
REVERT: A  190 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8666 (p0)
REVERT: A  238 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8679 (mt-10)
REVERT: A  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: A  310 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: A  323 TYR cc_start: 0.7400 (m-80) cc_final: 0.6878 (m-80)
REVERT: B   26 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7566 (t-90)
REVERT: B   66 LEU cc_start: 0.9321 (mm) cc_final: 0.8938 (pp)
REVERT: B  183 LEU cc_start: 0.8301 (tp) cc_final: 0.7435 (pp)
REVERT: B  190 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8726 (p0)
REVERT: B  238 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8705 (mt-10)
REVERT: B  310 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8459 (pp20)
REVERT: B  323 TYR cc_start: 0.7201 (m-80) cc_final: 0.6614 (m-80)
REVERT: B  333 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7451 (ptp)
REVERT: C   26 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7447 (t-90)
REVERT: C  190 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8662 (p0)
REVERT: C  195 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8304 (m90)
REVERT: C  238 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (mt-10)
REVERT: C  241 MET cc_start: 0.8050 (mtt) cc_final: 0.7702 (mtt)
REVERT: C  310 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8457 (pp20)
REVERT: C  323 TYR cc_start: 0.7425 (m-80) cc_final: 0.6733 (m-80)
REVERT: C  333 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7451 (ptp)
REVERT: D  190 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8731 (p0)
REVERT: D  310 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (pp20)
REVERT: D  323 TYR cc_start: 0.7418 (m-80) cc_final: 0.6743 (m-80)
  outliers start: 42
  outliers final: 24
  residues processed: 109
  average time/residue: 0.1666
  time to fit residues: 28.2645
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 73
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
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  232 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
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   87 THR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  238 GLU
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  195 HIS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  238 GLU
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   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  310 GLU
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:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 120 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 112 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   chunk 83 optimal weight:    0.1980
   chunk 110 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 97 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.112068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.074124 restraints weight = 34748.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.077179 restraints weight = 18522.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.079232 restraints weight = 12905.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9964  Z= 0.261
  Angle     :  0.839  10.487  13520  Z= 0.424
  Chirality :  0.047   0.170   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.318  21.988   1340
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.66 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 31.25 %
    Favored  : 63.96 %
  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: -1.85 (0.24), residues: 1248
  helix:  0.65 (0.51), residues: 132
  sheet: -1.18 (0.51), residues: 124
  loop : -1.64 (0.20), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.011   0.002   PHE C 277 
 TYR   0.011   0.001   TYR A 323 
 ARG   0.004   0.000   ARG C 257 

===============================================================================
Job complete
usr+sys time: 3067.29 seconds
wall clock time: 55 minutes 52.68 seconds (3352.68 seconds total)