Starting phenix.real_space_refine
on Tue Feb 11 22:58:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sqg_25384/02_2025/7sqg_25384.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4296      2.51       5
     N    1083      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6630
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.01, per 1000 atoms: 0.76
  Number of scatterers: 6630
  At special positions: 0
  Unit cell: (83.426, 82.6, 125.552, 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      27     16.00
     O    1224      8.00
     N    1083      7.00
     C    4296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG A 404 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG B 404 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG C 404 " - " ASN C 155 "
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 995.8 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 9 sheets defined
      34.6% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 98
      removed outlier: 3.563A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 334
    Processing helix  chain 'B' and resid 66 through 98
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 334
    Processing helix  chain 'C' and resid 66 through 98
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER C 225 " --> pdb=" O   GLN C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP A 287 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU A 181 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN A 148 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   CYS A 128 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157
      removed outlier: 3.743A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE B 236 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP B 287 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU B 181 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU B 125 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN B 148 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   CYS B 128 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157
      removed outlier: 3.741A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE C 236 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP C 287 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   GLU C 181 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG C 188 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   LEU C 125 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN C 148 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   CYS C 128 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157
      removed outlier: 3.733A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1179 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: 2.16

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2049
        1.34 -     1.46: 1202
        1.46 -     1.57: 3505
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 6798
  Sorted by residual:
  bond pdb=" N   GLU A 224 "
       pdb=" CA  GLU A 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.032 1.25e-02 6.40e+03 6.43e+00
  bond pdb=" N   ARG C  93 "
       pdb=" CA  ARG C  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.36e+00
  bond pdb=" N   GLU C 224 "
       pdb=" CA  GLU C 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.15e+00
  bond pdb=" N   ARG B  93 "
       pdb=" CA  ARG B  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.15e+00
  bond pdb=" N   GLU B 224 "
       pdb=" CA  GLU B 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.14e+00
  ... (remaining 6793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 8460
        0.97 -     1.94: 559
        1.94 -     2.91: 161
        2.91 -     3.88: 32
        3.88 -     4.84: 10
  Bond angle restraints: 9222
  Sorted by residual:
  angle pdb=" C   ARG A 259 "
        pdb=" N   GLN A 260 "
        pdb=" CA  GLN A 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.15    4.84 1.41e+00 5.03e-01 1.18e+01
  angle pdb=" C   ARG C 259 "
        pdb=" N   GLN C 260 "
        pdb=" CA  GLN C 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.15    4.84 1.41e+00 5.03e-01 1.18e+01
  angle pdb=" C   ARG B 259 "
        pdb=" N   GLN B 260 "
        pdb=" CA  GLN B 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.23    4.76 1.41e+00 5.03e-01 1.14e+01
  angle pdb=" CA  ARG B  93 "
        pdb=" C   ARG B  93 "
        pdb=" O   ARG B  93 "
      ideal   model   delta    sigma   weight residual
     120.82  117.99    2.83 1.05e+00 9.07e-01 7.29e+00
  angle pdb=" CA  ARG C  93 "
        pdb=" C   ARG C  93 "
        pdb=" O   ARG C  93 "
      ideal   model   delta    sigma   weight residual
     120.82  118.00    2.82 1.05e+00 9.07e-01 7.22e+00
  ... (remaining 9217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.51: 3910
       21.51 -    43.02: 199
       43.02 -    64.53: 63
       64.53 -    86.03: 7
       86.03 -   107.54: 24
  Dihedral angle restraints: 4203
    sinusoidal: 1806
      harmonic: 2397
  Sorted by residual:
  dihedral pdb=" CA  PHE A 236 "
           pdb=" C   PHE A 236 "
           pdb=" N   ARG A 237 "
           pdb=" CA  ARG A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE B 236 "
           pdb=" C   PHE B 236 "
           pdb=" N   ARG B 237 "
           pdb=" CA  ARG B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE C 236 "
           pdb=" C   PHE C 236 "
           pdb=" N   ARG C 237 "
           pdb=" CA  ARG C 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.94   24.06     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 4200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 721
       0.041 -    0.083: 231
       0.083 -    0.124: 86
       0.124 -    0.166: 8
       0.166 -    0.207: 4
  Chirality restraints: 1050
  Sorted by residual:
  chirality pdb=" CA  LEU A 169 "
            pdb=" N   LEU A 169 "
            pdb=" C   LEU A 169 "
            pdb=" CB  LEU A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  LEU B 169 "
            pdb=" N   LEU B 169 "
            pdb=" C   LEU B 169 "
            pdb=" CB  LEU B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  LEU C 169 "
            pdb=" N   LEU C 169 "
            pdb=" C   LEU C 169 "
            pdb=" CB  LEU C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1047 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 118 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   LEU C 118 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU C 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C 119 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 118 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   LEU B 118 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU B 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR B 119 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 118 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   LEU A 118 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 119 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 2643
        2.92 -     3.41: 5865
        3.41 -     3.91: 11062
        3.91 -     4.40: 11948
        4.40 -     4.90: 20624
  Nonbonded interactions: 52142
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 150 "
            pdb=" OE1 GLN A 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG1 THR C 150 "
            pdb=" OE1 GLN C 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG1 THR B 150 "
            pdb=" OE1 GLN B 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG  SER C 197 "
            pdb=" OE1 GLN C 279 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" OG  SER A 197 "
            pdb=" OE1 GLN A 279 "
     model   vdw
     2.440 3.040
  ... (remaining 52137 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.530
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:12.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6798  Z= 0.266
  Angle     :  0.605   4.844   9222  Z= 0.340
  Chirality :  0.047   0.207   1050
  Planarity :  0.004   0.033   1158
  Dihedral  : 17.267 107.543   2643
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.30), residues: 804
  helix:  3.12 (0.28), residues: 273
  sheet:  0.75 (0.29), residues: 318
  loop : -1.86 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 304 
 HIS   0.001   0.001   HIS A  98 
 PHE   0.020   0.002   PHE A 219 
 TYR   0.009   0.001   TYR A 201 
 ARG   0.003   0.000   ARG A 110 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.7274 (ttt) cc_final: 0.6970 (ttt)
REVERT: A   94 GLU cc_start: 0.7009 (tp30) cc_final: 0.6807 (tp30)
REVERT: A  106 LYS cc_start: 0.7670 (tttp) cc_final: 0.7363 (tttp)
REVERT: A  143 GLN cc_start: 0.7727 (mm110) cc_final: 0.7497 (mm110)
REVERT: A  147 MET cc_start: 0.7523 (mtm) cc_final: 0.7285 (mtp)
REVERT: A  166 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7694 (mttm)
REVERT: A  180 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6806 (mtp180)
REVERT: A  294 LYS cc_start: 0.7529 (mttt) cc_final: 0.7281 (mttt)
REVERT: A  304 TRP cc_start: 0.7393 (m100) cc_final: 0.7012 (m100)
REVERT: B   94 GLU cc_start: 0.7036 (tp30) cc_final: 0.6790 (tp30)
REVERT: B   98 HIS cc_start: 0.8294 (m90) cc_final: 0.8075 (m-70)
REVERT: B  180 ARG cc_start: 0.7003 (mtp180) cc_final: 0.6686 (mtp180)
REVERT: B  197 SER cc_start: 0.8098 (p) cc_final: 0.7657 (p)
REVERT: B  219 PHE cc_start: 0.7931 (t80) cc_final: 0.7657 (t80)
REVERT: B  224 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6921 (mm-30)
REVERT: B  247 THR cc_start: 0.7494 (m) cc_final: 0.7187 (t)
REVERT: B  275 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6944 (mmmm)
REVERT: C   92 PHE cc_start: 0.7508 (t80) cc_final: 0.6960 (t80)
REVERT: C  124 GLN cc_start: 0.7490 (pt0) cc_final: 0.7262 (pt0)
REVERT: C  148 ASN cc_start: 0.6303 (t0) cc_final: 0.6057 (p0)
REVERT: C  176 GLU cc_start: 0.7333 (mp0) cc_final: 0.6829 (mp0)
REVERT: C  179 LYS cc_start: 0.8267 (mtpp) cc_final: 0.8010 (mtmt)
REVERT: C  188 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7048 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6424 (tm-30)
REVERT: C  197 SER cc_start: 0.8136 (p) cc_final: 0.7731 (p)
REVERT: C  219 PHE cc_start: 0.7989 (t80) cc_final: 0.7659 (t80)
REVERT: C  271 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7444 (mtm-85)
REVERT: C  304 TRP cc_start: 0.7634 (m100) cc_final: 0.7103 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 1.6817
  time to fit residues: 453.9147
Evaluate side-chains
  236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.0670
   chunk 61 optimal weight:    0.0000
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0970
   chunk 32 optimal weight:    0.0470
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.1818

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 172 GLN
A 208 GLN
A 293 GLN
A 296 GLN
B 172 GLN
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN
B 296 GLN
C  98 HIS
C 186 GLN
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.139203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121484 restraints weight = 9577.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.30
r_work: 0.3496 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6798  Z= 0.174
  Angle     :  0.562   6.321   9222  Z= 0.282
  Chirality :  0.044   0.188   1050
  Planarity :  0.003   0.027   1158
  Dihedral  : 13.226  83.237   1125
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.35 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.29), residues: 804
  helix:  3.39 (0.28), residues: 258
  sheet:  1.21 (0.29), residues: 297
  loop : -1.27 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 304 
 HIS   0.008   0.002   HIS C  98 
 PHE   0.021   0.002   PHE A 219 
 TYR   0.007   0.001   TYR C 111 
 ARG   0.004   0.001   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 228
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8420 (tttp) cc_final: 0.8179 (ttmm)
REVERT: A  147 MET cc_start: 0.7764 (mtm) cc_final: 0.7514 (mtp)
REVERT: A  175 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7527 (mtp85)
REVERT: A  176 GLU cc_start: 0.8031 (mp0) cc_final: 0.7301 (mp0)
REVERT: A  180 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7667 (mtp180)
REVERT: A  181 GLU cc_start: 0.8075 (tt0) cc_final: 0.7611 (tt0)
REVERT: A  206 SER cc_start: 0.8569 (m) cc_final: 0.8363 (t)
REVERT: A  268 ILE cc_start: 0.8182 (mt) cc_final: 0.7929 (mt)
REVERT: A  304 TRP cc_start: 0.8373 (m100) cc_final: 0.8150 (m100)
REVERT: B  219 PHE cc_start: 0.8285 (t80) cc_final: 0.7796 (t80)
REVERT: B  271 ARG cc_start: 0.8714 (mtm180) cc_final: 0.8482 (mtm180)
REVERT: C   92 PHE cc_start: 0.8648 (t80) cc_final: 0.8309 (t80)
REVERT: C  148 ASN cc_start: 0.7014 (t0) cc_final: 0.6610 (p0)
REVERT: C  176 GLU cc_start: 0.8121 (mp0) cc_final: 0.7228 (mp0)
REVERT: C  181 GLU cc_start: 0.8045 (tt0) cc_final: 0.7606 (tt0)
REVERT: C  188 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7989 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6628 (tm-30)
REVERT: C  219 PHE cc_start: 0.8379 (t80) cc_final: 0.8078 (t80)
REVERT: C  271 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8233 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8482 (m100) cc_final: 0.8185 (m100)
  outliers start: 17
  outliers final: 9
  residues processed: 230
  average time/residue: 1.6662
  time to fit residues: 396.7698
Evaluate side-chains
  233 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 224
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 47 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0870
   chunk 23 optimal weight:    0.4980
   chunk 7 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
A 266 ASN
A 293 GLN
A 296 GLN
B  98 HIS
B 172 GLN
B 266 ASN
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN
B 296 GLN
C  98 HIS
C 124 GLN
C 266 ASN
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.139291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120471 restraints weight = 9560.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.34
r_work: 0.3460 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6798  Z= 0.272
  Angle     :  0.597   8.292   9222  Z= 0.295
  Chirality :  0.044   0.149   1050
  Planarity :  0.004   0.029   1158
  Dihedral  :  9.434  57.561   1125
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.43 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.29), residues: 804
  helix:  3.23 (0.28), residues: 258
  sheet:  0.88 (0.27), residues: 327
  loop : -0.96 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 230 
 HIS   0.009   0.002   HIS C  98 
 PHE   0.019   0.002   PHE B 204 
 TYR   0.011   0.001   TYR B 119 
 ARG   0.004   0.000   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8307 (mttt)
REVERT: A  147 MET cc_start: 0.7897 (mtm) cc_final: 0.7641 (mtp)
REVERT: A  175 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7470 (mtp85)
REVERT: A  176 GLU cc_start: 0.8127 (mp0) cc_final: 0.7101 (mp0)
REVERT: A  181 GLU cc_start: 0.8116 (tt0) cc_final: 0.7759 (tt0)
REVERT: A  194 GLU cc_start: 0.6593 (tm-30) cc_final: 0.6352 (tm-30)
REVERT: A  206 SER cc_start: 0.8650 (m) cc_final: 0.8441 (t)
REVERT: B  180 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7817 (mtp180)
REVERT: C   92 PHE cc_start: 0.8651 (t80) cc_final: 0.8426 (t80)
REVERT: C  148 ASN cc_start: 0.7119 (t0) cc_final: 0.6712 (p0)
REVERT: C  176 GLU cc_start: 0.8180 (mp0) cc_final: 0.7358 (mp0)
REVERT: C  181 GLU cc_start: 0.8080 (tt0) cc_final: 0.7736 (tt0)
REVERT: C  188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8106 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: C  212 GLN cc_start: 0.7304 (mp10) cc_final: 0.7033 (mp10)
REVERT: C  271 ARG cc_start: 0.8703 (mtm180) cc_final: 0.8277 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8498 (m100) cc_final: 0.8161 (m100)
REVERT: C  314 PHE cc_start: 0.8330 (m-10) cc_final: 0.8122 (m-10)
  outliers start: 20
  outliers final: 11
  residues processed: 227
  average time/residue: 1.5453
  time to fit residues: 364.0263
Evaluate side-chains
  225 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 214
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  197 SER
Chi-restraints excluded: chain C residue  257 GLU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 77 optimal weight:    0.1980
   chunk 12 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0070
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0980
   chunk 13 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.2798

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 208 GLN
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 186 GLN
B 293 GLN
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.140040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.121323 restraints weight = 9610.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.33
r_work: 0.3476 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6798  Z= 0.197
  Angle     :  0.554   7.204   9222  Z= 0.277
  Chirality :  0.044   0.171   1050
  Planarity :  0.003   0.027   1158
  Dihedral  :  7.895  59.947   1125
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.88 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.29), residues: 804
  helix:  3.25 (0.28), residues: 258
  sheet:  0.95 (0.27), residues: 327
  loop : -0.87 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 304 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.016   0.002   PHE C 204 
 TYR   0.007   0.001   TYR B 111 
 ARG   0.003   0.000   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8329 (mttt)
REVERT: A  147 MET cc_start: 0.7914 (mtm) cc_final: 0.7667 (mtp)
REVERT: A  194 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6376 (tm-30)
REVERT: A  206 SER cc_start: 0.8637 (m) cc_final: 0.8433 (t)
REVERT: B  180 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7806 (mtp180)
REVERT: C  148 ASN cc_start: 0.7145 (t0) cc_final: 0.6760 (p0)
REVERT: C  176 GLU cc_start: 0.8156 (mp0) cc_final: 0.7303 (mp0)
REVERT: C  181 GLU cc_start: 0.8058 (tt0) cc_final: 0.7699 (tt0)
REVERT: C  188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8085 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6656 (tm-30)
REVERT: C  211 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8168 (mt)
REVERT: C  212 GLN cc_start: 0.7294 (mp10) cc_final: 0.7061 (mp10)
REVERT: C  271 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8240 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8480 (m100) cc_final: 0.8130 (m100)
  outliers start: 23
  outliers final: 9
  residues processed: 224
  average time/residue: 1.6511
  time to fit residues: 382.9441
Evaluate side-chains
  219 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 209
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 186 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.138652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.119677 restraints weight = 9470.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.33
r_work: 0.3451 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6798  Z= 0.305
  Angle     :  0.583   7.589   9222  Z= 0.294
  Chirality :  0.044   0.188   1050
  Planarity :  0.004   0.041   1158
  Dihedral  :  6.531  45.948   1125
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.88 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.29), residues: 804
  helix:  3.17 (0.29), residues: 258
  sheet:  1.02 (0.27), residues: 324
  loop : -0.97 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 230 
 HIS   0.003   0.001   HIS C 130 
 PHE   0.020   0.002   PHE B 204 
 TYR   0.010   0.001   TYR B 119 
 ARG   0.009   0.001   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 MET cc_start: 0.7981 (mtm) cc_final: 0.7732 (mtp)
REVERT: A  176 GLU cc_start: 0.8069 (mp0) cc_final: 0.7333 (mp0)
REVERT: A  194 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6445 (tm-30)
REVERT: C   75 LEU cc_start: 0.7933 (mt) cc_final: 0.7711 (mt)
REVERT: C  148 ASN cc_start: 0.7206 (t0) cc_final: 0.6832 (p0)
REVERT: C  176 GLU cc_start: 0.8199 (mp0) cc_final: 0.7367 (mp0)
REVERT: C  180 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7657 (mtp180)
REVERT: C  181 GLU cc_start: 0.8118 (tt0) cc_final: 0.7737 (tt0)
REVERT: C  188 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.8090 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6694 (tm-30)
REVERT: C  271 ARG cc_start: 0.8678 (mtm180) cc_final: 0.8186 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8480 (m100) cc_final: 0.8152 (m100)
  outliers start: 22
  outliers final: 11
  residues processed: 216
  average time/residue: 1.5702
  time to fit residues: 351.7620
Evaluate side-chains
  218 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 207
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  257 GLU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 59 optimal weight:    0.0170
   chunk 28 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0770
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 293 GLN
B 293 GLN
C 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.139065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.120437 restraints weight = 9484.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.30
r_work: 0.3463 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6798  Z= 0.226
  Angle     :  0.553   7.419   9222  Z= 0.282
  Chirality :  0.044   0.185   1050
  Planarity :  0.004   0.030   1158
  Dihedral  :  5.696  32.242   1125
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.90 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.29), residues: 804
  helix:  3.25 (0.29), residues: 258
  sheet:  1.05 (0.26), residues: 324
  loop : -0.96 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 304 
 HIS   0.002   0.001   HIS C 130 
 PHE   0.030   0.002   PHE A 219 
 TYR   0.006   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 208
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  106 LYS cc_start: 0.8469 (tttp) cc_final: 0.8240 (ttpp)
REVERT: A  147 MET cc_start: 0.7963 (mtm) cc_final: 0.7722 (mtp)
REVERT: A  180 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7612 (mtp180)
REVERT: A  194 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6440 (tm-30)
REVERT: C  148 ASN cc_start: 0.7221 (t0) cc_final: 0.6839 (p0)
REVERT: C  176 GLU cc_start: 0.8161 (mp0) cc_final: 0.7322 (mp0)
REVERT: C  180 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7831 (mtp180)
REVERT: C  181 GLU cc_start: 0.8081 (tt0) cc_final: 0.7693 (tt0)
REVERT: C  188 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.8077 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: C  248 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7288 (mtpp)
REVERT: C  271 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8215 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8478 (m100) cc_final: 0.8158 (m100)
  outliers start: 18
  outliers final: 8
  residues processed: 209
  average time/residue: 1.6418
  time to fit residues: 355.5074
Evaluate side-chains
  216 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 208
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 35 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.138376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120015 restraints weight = 9504.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.28
r_work: 0.3448 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6798  Z= 0.295
  Angle     :  0.574   7.372   9222  Z= 0.294
  Chirality :  0.044   0.195   1050
  Planarity :  0.004   0.041   1158
  Dihedral  :  5.152  30.857   1125
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.33 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.30), residues: 804
  helix:  2.78 (0.29), residues: 279
  sheet:  0.95 (0.27), residues: 315
  loop : -1.43 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 230 
 HIS   0.003   0.001   HIS C 130 
 PHE   0.025   0.002   PHE A 219 
 TYR   0.009   0.001   TYR B 119 
 ARG   0.007   0.001   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8465 (tttp) cc_final: 0.8223 (ttpp)
REVERT: A  147 MET cc_start: 0.7944 (mtm) cc_final: 0.7700 (mtp)
REVERT: A  176 GLU cc_start: 0.8015 (mp0) cc_final: 0.7182 (mp0)
REVERT: A  180 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7596 (mtp180)
REVERT: A  194 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6409 (tm-30)
REVERT: A  197 SER cc_start: 0.8656 (p) cc_final: 0.8424 (m)
REVERT: A  248 LYS cc_start: 0.7598 (tppp) cc_final: 0.7387 (mtpt)
REVERT: C  148 ASN cc_start: 0.7187 (t0) cc_final: 0.6850 (p0)
REVERT: C  176 GLU cc_start: 0.8192 (mp0) cc_final: 0.7367 (mp0)
REVERT: C  181 GLU cc_start: 0.8114 (tt0) cc_final: 0.7747 (tt0)
REVERT: C  188 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.8094 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6708 (tm-30)
REVERT: C  248 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7397 (mtpp)
REVERT: C  271 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8192 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8479 (m100) cc_final: 0.8167 (m100)
REVERT: C  319 LYS cc_start: 0.8121 (tppt) cc_final: 0.7882 (ttmm)
  outliers start: 20
  outliers final: 12
  residues processed: 218
  average time/residue: 1.6156
  time to fit residues: 365.0744
Evaluate side-chains
  220 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 208
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 51 optimal weight:    0.3980
   chunk 65 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0870
   chunk 57 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.138383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.119925 restraints weight = 9536.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.30
r_work: 0.3454 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6798  Z= 0.253
  Angle     :  0.554   7.435   9222  Z= 0.286
  Chirality :  0.044   0.191   1050
  Planarity :  0.004   0.035   1158
  Dihedral  :  4.805  29.285   1125
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 23.77 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 804
  helix:  2.76 (0.29), residues: 279
  sheet:  0.95 (0.27), residues: 315
  loop : -1.41 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 230 
 HIS   0.002   0.001   HIS C 130 
 PHE   0.024   0.002   PHE A 219 
 TYR   0.008   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 214
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8458 (tttp) cc_final: 0.8215 (ttpp)
REVERT: A  147 MET cc_start: 0.7957 (mtm) cc_final: 0.7712 (mtp)
REVERT: A  180 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7628 (mtp180)
REVERT: A  194 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6447 (tm-30)
REVERT: A  197 SER cc_start: 0.8672 (p) cc_final: 0.8461 (m)
REVERT: A  268 ILE cc_start: 0.7964 (mm) cc_final: 0.7725 (mt)
REVERT: B  110 ARG cc_start: 0.7495 (ptm160) cc_final: 0.7132 (ptm160)
REVERT: B  197 SER cc_start: 0.8667 (p) cc_final: 0.8460 (m)
REVERT: C  148 ASN cc_start: 0.7196 (t0) cc_final: 0.6872 (p0)
REVERT: C  176 GLU cc_start: 0.8152 (mp0) cc_final: 0.7311 (mp0)
REVERT: C  181 GLU cc_start: 0.8077 (tt0) cc_final: 0.7711 (tt0)
REVERT: C  188 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8087 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6729 (tm-30)
REVERT: C  212 GLN cc_start: 0.7423 (mp10) cc_final: 0.7207 (mp10)
REVERT: C  304 TRP cc_start: 0.8465 (m100) cc_final: 0.8148 (m100)
REVERT: C  319 LYS cc_start: 0.8130 (tppt) cc_final: 0.7928 (ttmm)
  outliers start: 16
  outliers final: 13
  residues processed: 218
  average time/residue: 1.5763
  time to fit residues: 356.3958
Evaluate side-chains
  223 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 210
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 48 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.137617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.119103 restraints weight = 9585.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.30
r_work: 0.3442 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6798  Z= 0.324
  Angle     :  0.579   7.477   9222  Z= 0.299
  Chirality :  0.045   0.208   1050
  Planarity :  0.004   0.035   1158
  Dihedral  :  4.684  28.025   1125
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 24.35 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.30), residues: 804
  helix:  2.72 (0.29), residues: 279
  sheet:  0.97 (0.27), residues: 315
  loop : -1.42 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 230 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.022   0.002   PHE A 219 
 TYR   0.009   0.001   TYR B 119 
 ARG   0.008   0.001   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 206
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8471 (tttp) cc_final: 0.8201 (ttpp)
REVERT: A  143 GLN cc_start: 0.7971 (mm110) cc_final: 0.7633 (mm110)
REVERT: A  147 MET cc_start: 0.7962 (mtm) cc_final: 0.7723 (mtp)
REVERT: A  176 GLU cc_start: 0.7985 (mp0) cc_final: 0.7141 (mp0)
REVERT: A  180 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7639 (mtp180)
REVERT: A  181 GLU cc_start: 0.8116 (tt0) cc_final: 0.7494 (tt0)
REVERT: B  110 ARG cc_start: 0.7479 (ptm160) cc_final: 0.7198 (ptm160)
REVERT: C  148 ASN cc_start: 0.7187 (t0) cc_final: 0.6855 (p0)
REVERT: C  176 GLU cc_start: 0.8182 (mp0) cc_final: 0.7349 (mp0)
REVERT: C  181 GLU cc_start: 0.8125 (tt0) cc_final: 0.7745 (tt0)
REVERT: C  188 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.8094 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6749 (tm-30)
REVERT: C  271 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8290 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8496 (m100) cc_final: 0.8210 (m100)
  outliers start: 18
  outliers final: 12
  residues processed: 210
  average time/residue: 1.6286
  time to fit residues: 354.5431
Evaluate side-chains
  216 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 204
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  257 GLU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 41 optimal weight:    0.3980
   chunk 78 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 80 optimal weight:    0.1980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.138306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.120029 restraints weight = 9673.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.30
r_work: 0.3454 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6798  Z= 0.251
  Angle     :  0.559   7.263   9222  Z= 0.291
  Chirality :  0.044   0.207   1050
  Planarity :  0.004   0.035   1158
  Dihedral  :  4.543  26.771   1125
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 24.49 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.29), residues: 804
  helix:  2.74 (0.29), residues: 279
  sheet:  0.95 (0.27), residues: 315
  loop : -1.43 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 304 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.022   0.002   PHE A 236 
 TYR   0.007   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 175 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8461 (tttp) cc_final: 0.8203 (ttpp)
REVERT: A  143 GLN cc_start: 0.7969 (mm110) cc_final: 0.7627 (mm110)
REVERT: A  147 MET cc_start: 0.7944 (mtm) cc_final: 0.7723 (mtp)
REVERT: A  180 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7619 (mtp180)
REVERT: B  110 ARG cc_start: 0.7415 (ptm160) cc_final: 0.7152 (ptm160)
REVERT: B  268 ILE cc_start: 0.7832 (mm) cc_final: 0.7626 (mt)
REVERT: C  148 ASN cc_start: 0.7139 (t0) cc_final: 0.6838 (p0)
REVERT: C  176 GLU cc_start: 0.8140 (mp0) cc_final: 0.7251 (mp0)
REVERT: C  181 GLU cc_start: 0.8099 (tt0) cc_final: 0.7692 (tt0)
REVERT: C  188 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.8111 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6745 (tm-30)
REVERT: C  271 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8267 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8495 (m100) cc_final: 0.8206 (m100)
  outliers start: 17
  outliers final: 12
  residues processed: 204
  average time/residue: 1.6506
  time to fit residues: 348.5335
Evaluate side-chains
  213 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   97 LYS
Chi-restraints excluded: chain C residue  110 ARG
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0010
   chunk 61 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0970
   chunk 21 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN
C 186 GLN
C 279 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.138958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120638 restraints weight = 9683.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.30
r_work: 0.3462 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6798  Z= 0.212
  Angle     :  0.552   6.742   9222  Z= 0.288
  Chirality :  0.044   0.202   1050
  Planarity :  0.004   0.036   1158
  Dihedral  :  4.380  26.417   1125
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 24.93 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.30), residues: 804
  helix:  2.81 (0.30), residues: 279
  sheet:  0.85 (0.27), residues: 318
  loop : -1.35 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 304 
 HIS   0.005   0.001   HIS B  98 
 PHE   0.026   0.002   PHE A 236 
 TYR   0.007   0.001   TYR B 111 
 ARG   0.007   0.000   ARG A 175 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8098.36 seconds
wall clock time: 142 minutes 41.21 seconds (8561.21 seconds total)