Starting phenix.real_space_refine
on Thu Jul  2 07:55:46 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/07_2026/7eje_31160.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.008
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: 6
    Type Number    sf(0)   Gaussians
     P      27      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4677      2.51       5
     N    1341      2.21       5
     O    1515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "E"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Unusual residues: {' MG': 1, 'ANP': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.78, per 1000 atoms: 0.23
  Number of scatterers: 7602
  At special positions: 0
  Unit cell: (107.092, 75.748, 114.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      27     15.00
     Mg      3     11.99
     O    1515      8.00
     N    1341      7.00
     C    4677      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 322.6 milliseconds
  

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      52.2% alpha, 11.8% beta
      8 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 29
    Processing helix  chain 'A' and resid 34 through 42
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.776A  pdb=" N   ILE A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 97
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.561A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.855A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.535A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.962A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.923A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 34 through 42
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 48 through 54
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 3.776A  pdb=" N   ILE B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 97
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
      removed outlier: 3.562A  pdb=" N   LEU B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.854A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.535A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.961A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.922A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 29
    Processing helix  chain 'C' and resid 34 through 42
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 48 through 54
    Processing helix  chain 'C' and resid 56 through 63
      removed outlier: 3.775A  pdb=" N   ILE C  63 " --> pdb=" O   GLU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 89 through 97
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
      removed outlier: 3.563A  pdb=" N   LEU C 171 " --> pdb=" O   ARG C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.854A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.536A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.960A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU C 258 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.924A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA C 293 " --> pdb=" O   GLY C 289 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
      removed outlier: 8.366A  pdb=" N   VAL A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU A 219 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   THR A 266 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL A 221 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ALA A 157 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA A 192 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR A 159 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 304
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 126
      removed outlier: 8.367A  pdb=" N   VAL B 264 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU B 219 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   THR B 266 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL B 221 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA B 157 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA B 192 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TYR B 159 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 304
    Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126
      removed outlier: 8.367A  pdb=" N   VAL C 264 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU C 219 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   THR C 266 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   VAL C 221 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA C 157 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR C 159 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 299 through 304
    Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 330

    311 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2393
        1.33 -     1.45: 1187
        1.45 -     1.57: 4055
        1.57 -     1.69: 52
        1.69 -     1.81: 63
  Bond restraints: 7750
  Sorted by residual:
  bond pdb=" O3A ANP B 401 "
       pdb=" PB  ANP B 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.552  0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" O3A ANP C 403 "
       pdb=" PB  ANP C 403 "
    ideal  model  delta    sigma   weight residual
    1.700  1.552  0.148 2.00e-02 2.50e+03 5.49e+01
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.553  0.147 2.00e-02 2.50e+03 5.43e+01
  bond pdb=" C   MET B 158 "
       pdb=" N   TYR B 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.253  0.079 1.31e-02 5.83e+03 3.63e+01
  bond pdb=" C   MET C 158 "
       pdb=" N   TYR C 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.254  0.078 1.31e-02 5.83e+03 3.51e+01
  ... (remaining 7745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.16: 10255
        3.16 -     6.33: 258
        6.33 -     9.49: 30
        9.49 -    12.66: 6
       12.66 -    15.82: 3
  Bond angle restraints: 10552
  Sorted by residual:
  angle pdb=" C   LYS B 285 "
        pdb=" N   PRO B 286 "
        pdb=" CA  PRO B 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.62   -6.84 1.03e+00 9.43e-01 4.41e+01
  angle pdb=" C   LYS A 285 "
        pdb=" N   PRO A 286 "
        pdb=" CA  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.62   -6.84 1.03e+00 9.43e-01 4.41e+01
  angle pdb=" C   LYS C 285 "
        pdb=" N   PRO C 286 "
        pdb=" CA  PRO C 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.59   -6.81 1.03e+00 9.43e-01 4.37e+01
  angle pdb=" N   GLU C 124 "
        pdb=" CA  GLU C 124 "
        pdb=" C   GLU C 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.33   -9.85 1.80e+00 3.09e-01 2.99e+01
  angle pdb=" N   GLU B 124 "
        pdb=" CA  GLU B 124 "
        pdb=" C   GLU B 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.33   -9.85 1.80e+00 3.09e-01 2.99e+01
  ... (remaining 10547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.88: 4456
       32.88 -    65.76: 162
       65.76 -    98.64: 11
       98.64 -   131.51: 0
      131.51 -   164.39: 3
  Dihedral angle restraints: 4632
    sinusoidal: 1971
      harmonic: 2661
  Sorted by residual:
  dihedral pdb=" CA  ILE B 314 "
           pdb=" C   ILE B 314 "
           pdb=" N   TYR B 315 "
           pdb=" CA  TYR B 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.38   23.62     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ILE A 314 "
           pdb=" C   ILE A 314 "
           pdb=" N   TYR A 315 "
           pdb=" CA  TYR A 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.43   23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ILE C 314 "
           pdb=" C   ILE C 314 "
           pdb=" N   TYR C 315 "
           pdb=" CA  TYR C 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.45   23.55     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 4629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 999
       0.066 -    0.132: 194
       0.132 -    0.198: 4
       0.198 -    0.265: 3
       0.265 -    0.331: 3
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C3' ANP B 401 "
            pdb=" C2' ANP B 401 "
            pdb=" C4' ANP B 401 "
            pdb=" O3' ANP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C3' ANP C 403 "
            pdb=" C2' ANP C 403 "
            pdb=" C4' ANP C 403 "
            pdb=" O3' ANP C 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.69e+00
  ... (remaining 1200 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 158 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" C   MET B 158 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   MET B 158 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR B 159 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 158 "    0.015 2.00e-02 2.50e+03   3.00e-02 9.02e+00
        pdb=" C   MET A 158 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   MET A 158 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR A 159 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 158 "    0.014 2.00e-02 2.50e+03   2.96e-02 8.79e+00
        pdb=" C   MET C 158 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   MET C 158 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR C 159 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 69
        2.14 -     2.83: 2638
        2.83 -     3.52: 10853
        3.52 -     4.21: 17854
        4.21 -     4.90: 30158
  Nonbonded interactions: 61572
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 217 "
            pdb=" CG1 VAL B 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA C 217 "
            pdb=" CG1 VAL C 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA A 217 "
            pdb=" CG1 VAL A 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" CG2 VAL C 270 "
            pdb=" CG2 ILE C 287 "
     model   vdw
     1.579 3.880
  nonbonded pdb=" CG2 VAL A 270 "
            pdb=" CG2 ILE A 287 "
     model   vdw
     1.579 3.880
  ... (remaining 61567 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 22 through 336)
  selection = (chain 'B' and resid 22 through 336)
  selection = (chain 'C' and resid 22 through 336)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.180
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
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      :  0.009   0.148   7752  Z= 0.590
  Angle     :  1.301  15.821  10552  Z= 0.856
  Chirality :  0.053   0.331   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 15.343 164.392   2928
  Min Nonbonded Distance : 1.454

Molprobity Statistics.
  All-atom Clashscore : 42.12
  Ramachandran Plot:
    Outliers :  2.28 %
    Allowed  :  4.89 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  :  2.82 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.25), residues: 921
  helix: -2.32 (0.16), residues: 408
  sheet: -2.56 (0.47), residues: 114
  loop : -0.07 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 170 
 TYR   0.031   0.004   TYR A 315 
 PHE   0.020   0.002   PHE A 259 
 HIS   0.005   0.002   HIS A 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00901 /  0.57 ( 7750)
  covalent geometry    : angle       1.30142 /  0.86 (10552)
  hydrogen bonds       : bond        0.15732 / 10.70 (  327)
  hydrogen bonds       : angle       9.94827 /  7.21 (  887)
  Misc. bond           : bond        0.09494 /  6.46 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 294
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 ILE cc_start: 0.9122 (mt) cc_final: 0.8762 (mp)
REVERT: A  266 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8129 (m)
REVERT: A  290 ASN cc_start: 0.7529 (m110) cc_final: 0.7259 (m110)
REVERT: B  171 LEU cc_start: 0.8804 (mt) cc_final: 0.8332 (mt)
REVERT: B  220 ILE cc_start: 0.8979 (mt) cc_final: 0.8526 (mt)
REVERT: B  266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7993 (m)
REVERT: C  291 ILE cc_start: 0.9330 (mt) cc_final: 0.8870 (tt)
REVERT: C  301 TYR cc_start: 0.8033 (t80) cc_final: 0.7761 (t80)
  outliers start: 33
  outliers final: 8
  residues processed: 310
  average time/residue: 0.0954
  time to fit residues: 36.9989
Evaluate side-chains
  164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain C residue  235 ARG
Chi-restraints excluded: chain C residue  263 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  47 HIS
** A  62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 HIS
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
A 313 GLN
B  36 ASN
B  93 HIS
B 200 GLN
B 267 ASN
B 313 GLN
C  47 HIS
C  93 HIS
C 200 GLN
C 267 ASN
C 313 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.084589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.068720 restraints weight = 21807.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.071157 restraints weight = 11416.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.072809 restraints weight = 7373.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.073943 restraints weight = 5452.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.074607 restraints weight = 4420.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7752  Z= 0.211
  Angle     :  0.880   8.935  10552  Z= 0.464
  Chirality :  0.048   0.180   1203
  Planarity :  0.007   0.085   1296
  Dihedral  : 17.617 176.274   1261
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  1.19 %
    Allowed  :  3.91 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 12.10 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.26), residues: 921
  helix: -0.87 (0.22), residues: 405
  sheet: -0.90 (0.44), residues: 126
  loop : -0.67 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 130 
 TYR   0.028   0.003   TYR A 216 
 PHE   0.035   0.003   PHE B 126 
 HIS   0.010   0.002   HIS C 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.21 ( 7750)
  covalent geometry    : angle       0.88022 /  0.46 (10552)
  hydrogen bonds       : bond        0.04531 /  2.96 (  327)
  hydrogen bonds       : angle       6.52739 /  4.79 (  887)
  Misc. bond           : bond        0.00546 /  0.37 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9099 (pttp)
REVERT: A   59 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: A  124 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8340 (mm-30)
REVERT: A  158 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7881 (mtp)
REVERT: A  191 TYR cc_start: 0.9004 (t80) cc_final: 0.8791 (t80)
REVERT: A  218 LEU cc_start: 0.9490 (tp) cc_final: 0.9009 (tp)
REVERT: A  228 TYR cc_start: 0.8778 (m-80) cc_final: 0.8377 (m-80)
REVERT: A  301 TYR cc_start: 0.8664 (t80) cc_final: 0.8372 (t80)
REVERT: A  326 MET cc_start: 0.8292 (mmm) cc_final: 0.8084 (mmm)
REVERT: B   39 LYS cc_start: 0.9307 (ttpp) cc_final: 0.9107 (ptpp)
REVERT: B  124 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8473 (mm-30)
REVERT: B  158 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7865 (ptp)
REVERT: B  171 LEU cc_start: 0.9617 (mt) cc_final: 0.9398 (mt)
REVERT: B  191 TYR cc_start: 0.8815 (t80) cc_final: 0.8370 (t80)
REVERT: B  220 ILE cc_start: 0.9574 (mt) cc_final: 0.9213 (mm)
REVERT: B  235 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (pmt-80)
REVERT: B  301 TYR cc_start: 0.8686 (t80) cc_final: 0.8326 (t80)
REVERT: C  220 ILE cc_start: 0.9571 (mt) cc_final: 0.9301 (mm)
REVERT: C  235 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7296 (pmt170)
  outliers start: 31
  outliers final: 14
  residues processed: 192
  average time/residue: 0.0668
  time to fit residues: 17.5450
Evaluate side-chains
  162 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  330 ASN
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  235 ARG
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  330 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 87 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0010
   chunk 58 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.084938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.068815 restraints weight = 21253.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.071276 restraints weight = 11278.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.072934 restraints weight = 7332.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.074053 restraints weight = 5450.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.074756 restraints weight = 4443.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7752  Z= 0.158
  Angle     :  0.756   7.975  10552  Z= 0.397
  Chirality :  0.043   0.164   1203
  Planarity :  0.005   0.065   1296
  Dihedral  : 17.492 179.683   1253
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.67 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.26), residues: 921
  helix: -0.40 (0.23), residues: 423
  sheet: -0.14 (0.47), residues: 126
  loop : -0.75 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 130 
 TYR   0.021   0.002   TYR B  54 
 PHE   0.017   0.002   PHE C 126 
 HIS   0.008   0.002   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 7750)
  covalent geometry    : angle       0.75557 /  0.40 (10552)
  hydrogen bonds       : bond        0.03828 /  2.55 (  327)
  hydrogen bonds       : angle       5.75003 /  4.25 (  887)
  Misc. bond           : bond        0.00576 /  0.40 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8981 (pttm)
REVERT: A   59 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7705 (tm-30)
REVERT: A  137 CYS cc_start: 0.9182 (m) cc_final: 0.8680 (t)
REVERT: A  159 TYR cc_start: 0.9125 (t80) cc_final: 0.8185 (t80)
REVERT: A  191 TYR cc_start: 0.8924 (t80) cc_final: 0.8702 (t80)
REVERT: A  211 MET cc_start: 0.8288 (mmm) cc_final: 0.7818 (tpp)
REVERT: A  228 TYR cc_start: 0.8764 (m-80) cc_final: 0.8547 (m-80)
REVERT: A  301 TYR cc_start: 0.8672 (t80) cc_final: 0.8470 (t80)
REVERT: A  326 MET cc_start: 0.8262 (mmm) cc_final: 0.8054 (mmm)
REVERT: B   36 ASN cc_start: 0.9285 (t0) cc_final: 0.9064 (t0)
REVERT: B   39 LYS cc_start: 0.9396 (ttpp) cc_final: 0.9178 (ptpp)
REVERT: B   59 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: B  124 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8107 (tt0)
REVERT: B  171 LEU cc_start: 0.9562 (mt) cc_final: 0.9329 (mt)
REVERT: B  235 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7877 (ptt-90)
REVERT: B  301 TYR cc_start: 0.8672 (t80) cc_final: 0.8368 (t80)
REVERT: C  301 TYR cc_start: 0.8841 (t80) cc_final: 0.8526 (t80)
  outliers start: 27
  outliers final: 12
  residues processed: 172
  average time/residue: 0.0718
  time to fit residues: 16.8105
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  253 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 83 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 200 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.083404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.067375 restraints weight = 21833.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.069684 restraints weight = 11957.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.071251 restraints weight = 7960.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.072231 restraints weight = 6030.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.073031 restraints weight = 5018.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7752  Z= 0.164
  Angle     :  0.704   7.012  10552  Z= 0.370
  Chirality :  0.042   0.180   1203
  Planarity :  0.005   0.054   1296
  Dihedral  : 17.328 179.384   1243
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.40 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.27), residues: 921
  helix:  0.19 (0.25), residues: 423
  sheet: -0.12 (0.47), residues: 126
  loop : -0.82 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 130 
 TYR   0.035   0.002   TYR C  54 
 PHE   0.019   0.002   PHE C 259 
 HIS   0.005   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 7750)
  covalent geometry    : angle       0.70400 /  0.37 (10552)
  hydrogen bonds       : bond        0.03576 /  2.36 (  327)
  hydrogen bonds       : angle       5.23240 /  3.89 (  887)
  Misc. bond           : bond        0.00403 /  0.28 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9009 (pttm)
REVERT: A   59 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: A  124 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8328 (mm-30)
REVERT: A  137 CYS cc_start: 0.9212 (m) cc_final: 0.8831 (t)
REVERT: A  159 TYR cc_start: 0.9121 (t80) cc_final: 0.8378 (t80)
REVERT: A  228 TYR cc_start: 0.8885 (m-80) cc_final: 0.8636 (m-80)
REVERT: A  314 ILE cc_start: 0.9378 (mt) cc_final: 0.8981 (tt)
REVERT: B   36 ASN cc_start: 0.9267 (t0) cc_final: 0.9018 (t0)
REVERT: B   54 TYR cc_start: 0.8605 (m-80) cc_final: 0.8393 (m-80)
REVERT: B  124 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7979 (tt0)
REVERT: B  158 MET cc_start: 0.8235 (ptp) cc_final: 0.7956 (ptp)
REVERT: B  171 LEU cc_start: 0.9581 (mt) cc_final: 0.9342 (mt)
REVERT: B  210 MET cc_start: 0.7679 (mtp) cc_final: 0.7391 (ttm)
REVERT: C  124 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7899 (tt0)
REVERT: C  301 TYR cc_start: 0.8887 (t80) cc_final: 0.8585 (t80)
  outliers start: 33
  outliers final: 20
  residues processed: 165
  average time/residue: 0.0632
  time to fit residues: 14.4247
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0170
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.1822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.067516 restraints weight = 21543.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.069953 restraints weight = 11468.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071464 restraints weight = 7456.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.072671 restraints weight = 5603.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.073482 restraints weight = 4516.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.5780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7752  Z= 0.149
  Angle     :  0.710   7.289  10552  Z= 0.370
  Chirality :  0.042   0.157   1203
  Planarity :  0.005   0.051   1296
  Dihedral  : 17.199 179.450   1239
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 17.61 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.27), residues: 921
  helix:  0.51 (0.25), residues: 399
  sheet: -0.13 (0.50), residues: 114
  loop : -0.99 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  27 
 TYR   0.040   0.002   TYR C  54 
 PHE   0.011   0.002   PHE B 195 
 HIS   0.004   0.001   HIS B  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 ( 7750)
  covalent geometry    : angle       0.71035 /  0.37 (10552)
  hydrogen bonds       : bond        0.03533 /  2.35 (  327)
  hydrogen bonds       : angle       5.22245 /  3.87 (  887)
  Misc. bond           : bond        0.00369 /  0.26 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9020 (pttm)
REVERT: A   59 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: A  137 CYS cc_start: 0.9232 (m) cc_final: 0.8786 (t)
REVERT: A  159 TYR cc_start: 0.9089 (t80) cc_final: 0.8282 (t80)
REVERT: A  304 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7756 (ttmm)
REVERT: A  314 ILE cc_start: 0.9385 (mt) cc_final: 0.8970 (tt)
REVERT: B   54 TYR cc_start: 0.8456 (m-80) cc_final: 0.8218 (m-80)
REVERT: B  124 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8010 (tt0)
REVERT: B  171 LEU cc_start: 0.9597 (mt) cc_final: 0.9374 (mt)
REVERT: C  253 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9296 (mm)
REVERT: C  301 TYR cc_start: 0.8836 (t80) cc_final: 0.8632 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 160
  average time/residue: 0.0620
  time to fit residues: 14.0063
Evaluate side-chains
  154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.083387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.067151 restraints weight = 21503.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.069513 restraints weight = 11960.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.071061 restraints weight = 7978.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.072069 restraints weight = 6063.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.072876 restraints weight = 5027.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.6061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7752  Z= 0.136
  Angle     :  0.697   9.984  10552  Z= 0.357
  Chirality :  0.041   0.175   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 17.088 179.057   1239
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 18.55 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.27), residues: 921
  helix:  0.79 (0.26), residues: 399
  sheet: -0.24 (0.49), residues: 117
  loop : -0.92 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 130 
 TYR   0.026   0.001   TYR B 191 
 PHE   0.011   0.002   PHE B 195 
 HIS   0.003   0.001   HIS B  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 7750)
  covalent geometry    : angle       0.69709 /  0.36 (10552)
  hydrogen bonds       : bond        0.03151 /  2.06 (  327)
  hydrogen bonds       : angle       4.98808 /  3.71 (  887)
  Misc. bond           : bond        0.00387 /  0.27 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9039 (pttm)
REVERT: A   59 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7662 (tm-30)
REVERT: A  137 CYS cc_start: 0.9207 (m) cc_final: 0.8766 (t)
REVERT: A  159 TYR cc_start: 0.9087 (t80) cc_final: 0.8193 (t80)
REVERT: A  304 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7726 (ttmm)
REVERT: A  314 ILE cc_start: 0.9374 (mt) cc_final: 0.8950 (tt)
REVERT: B  124 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8182 (tt0)
REVERT: C  124 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7998 (tt0)
  outliers start: 33
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0599
  time to fit residues: 13.3593
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  178 TYR
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 75 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.067221 restraints weight = 21384.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.069679 restraints weight = 11539.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.071300 restraints weight = 7567.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.072242 restraints weight = 5658.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.073049 restraints weight = 4702.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.6209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7752  Z= 0.134
  Angle     :  0.680   8.238  10552  Z= 0.351
  Chirality :  0.041   0.150   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 17.027 179.169   1239
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.22 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.27), residues: 921
  helix:  0.84 (0.26), residues: 402
  sheet: -0.15 (0.49), residues: 117
  loop : -0.90 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 130 
 TYR   0.023   0.001   TYR A 191 
 PHE   0.013   0.002   PHE A 195 
 HIS   0.004   0.001   HIS B  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 7750)
  covalent geometry    : angle       0.67961 /  0.35 (10552)
  hydrogen bonds       : bond        0.03077 /  2.06 (  327)
  hydrogen bonds       : angle       4.89825 /  3.64 (  887)
  Misc. bond           : bond        0.00343 /  0.24 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9049 (pttm)
REVERT: A   59 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: A  124 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: A  137 CYS cc_start: 0.9267 (m) cc_final: 0.8806 (t)
REVERT: A  171 LEU cc_start: 0.9458 (mm) cc_final: 0.9208 (mm)
REVERT: A  314 ILE cc_start: 0.9389 (mt) cc_final: 0.8969 (tt)
REVERT: B  218 LEU cc_start: 0.9281 (tp) cc_final: 0.9055 (tp)
REVERT: C  124 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8075 (tt0)
  outliers start: 33
  outliers final: 22
  residues processed: 145
  average time/residue: 0.0606
  time to fit residues: 12.2525
Evaluate side-chains
  149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  178 TYR
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.2988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 HIS
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.080184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.063730 restraints weight = 21822.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.065979 restraints weight = 12169.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.067506 restraints weight = 8237.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.068477 restraints weight = 6242.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.069269 restraints weight = 5199.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.6437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7752  Z= 0.230
  Angle     :  0.750   8.390  10552  Z= 0.386
  Chirality :  0.043   0.198   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 16.980 179.388   1239
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.89 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 18.95 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.27), residues: 921
  helix:  0.99 (0.26), residues: 402
  sheet: -0.41 (0.48), residues: 117
  loop : -0.97 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 250 
 TYR   0.018   0.002   TYR B  54 
 PHE   0.015   0.002   PHE C 166 
 HIS   0.005   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00510 /  0.23 ( 7750)
  covalent geometry    : angle       0.75038 /  0.39 (10552)
  hydrogen bonds       : bond        0.03614 /  2.40 (  327)
  hydrogen bonds       : angle       5.02764 /  3.73 (  887)
  Misc. bond           : bond        0.00363 /  0.25 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 118
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9071 (pttm)
REVERT: A   59 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: A  124 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8696 (mm-30)
REVERT: A  137 CYS cc_start: 0.9261 (m) cc_final: 0.8808 (t)
REVERT: A  171 LEU cc_start: 0.9560 (mm) cc_final: 0.9294 (mm)
REVERT: A  326 MET cc_start: 0.8224 (mmm) cc_final: 0.7899 (mmm)
REVERT: B  218 LEU cc_start: 0.9341 (tp) cc_final: 0.9117 (tp)
REVERT: C  137 CYS cc_start: 0.9236 (m) cc_final: 0.8838 (t)
  outliers start: 37
  outliers final: 28
  residues processed: 140
  average time/residue: 0.0598
  time to fit residues: 11.7645
Evaluate side-chains
  145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  178 TYR
Chi-restraints excluded: chain C residue  263 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.065627 restraints weight = 21405.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.068054 restraints weight = 11566.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.069655 restraints weight = 7614.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.070663 restraints weight = 5687.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.071541 restraints weight = 4690.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.6557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7752  Z= 0.141
  Angle     :  0.720   9.373  10552  Z= 0.370
  Chirality :  0.042   0.175   1203
  Planarity :  0.004   0.047   1296
  Dihedral  : 16.930 177.820   1239
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.56 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.27), residues: 921
  helix:  0.97 (0.26), residues: 402
  sheet: -0.10 (0.49), residues: 117
  loop : -0.97 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 299 
 TYR   0.013   0.001   TYR B  54 
 PHE   0.015   0.002   PHE A 195 
 HIS   0.004   0.001   HIS B  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 7750)
  covalent geometry    : angle       0.72008 /  0.37 (10552)
  hydrogen bonds       : bond        0.03226 /  2.16 (  327)
  hydrogen bonds       : angle       4.81966 /  3.57 (  887)
  Misc. bond           : bond        0.00365 /  0.25 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9054 (pttm)
REVERT: A   59 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: A  137 CYS cc_start: 0.9340 (m) cc_final: 0.8779 (t)
REVERT: A  171 LEU cc_start: 0.9534 (mm) cc_final: 0.9235 (mm)
REVERT: A  326 MET cc_start: 0.8149 (mmm) cc_final: 0.7810 (mmm)
REVERT: B  218 LEU cc_start: 0.9333 (tp) cc_final: 0.9108 (tp)
REVERT: C  124 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7993 (tt0)
REVERT: C  229 ARG cc_start: 0.8430 (mtt180) cc_final: 0.7742 (tpt170)
  outliers start: 28
  outliers final: 24
  residues processed: 142
  average time/residue: 0.0822
  time to fit residues: 16.3317
Evaluate side-chains
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  178 TYR
Chi-restraints excluded: chain C residue  263 VAL
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 33 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    2.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.081259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.064698 restraints weight = 21782.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.067015 restraints weight = 12116.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.068443 restraints weight = 8113.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.069567 restraints weight = 6213.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.070366 restraints weight = 5110.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.6646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7752  Z= 0.173
  Angle     :  0.726   8.627  10552  Z= 0.374
  Chirality :  0.042   0.171   1203
  Planarity :  0.004   0.047   1296
  Dihedral  : 16.868 177.276   1239
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.45 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.10 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.27), residues: 921
  helix:  1.03 (0.26), residues: 402
  sheet:  0.04 (0.50), residues: 114
  loop : -0.98 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 299 
 TYR   0.020   0.001   TYR B  54 
 PHE   0.017   0.002   PHE A 195 
 HIS   0.004   0.001   HIS C 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.17 ( 7750)
  covalent geometry    : angle       0.72649 /  0.37 (10552)
  hydrogen bonds       : bond        0.03291 /  2.16 (  327)
  hydrogen bonds       : angle       4.81043 /  3.57 (  887)
  Misc. bond           : bond        0.00354 /  0.25 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9066 (pttm)
REVERT: A   59 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: A  137 CYS cc_start: 0.9310 (m) cc_final: 0.8804 (t)
REVERT: A  171 LEU cc_start: 0.9548 (mm) cc_final: 0.9267 (mm)
REVERT: A  326 MET cc_start: 0.8105 (mmm) cc_final: 0.7772 (mmm)
REVERT: B  218 LEU cc_start: 0.9331 (tp) cc_final: 0.9105 (tp)
REVERT: C  124 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7994 (tt0)
  outliers start: 26
  outliers final: 24
  residues processed: 139
  average time/residue: 0.0727
  time to fit residues: 13.9954
Evaluate side-chains
  145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  178 TYR
Chi-restraints excluded: chain C residue  263 VAL
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.081826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.065200 restraints weight = 21642.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.067530 restraints weight = 11832.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.069128 restraints weight = 7892.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.070111 restraints weight = 5932.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.070989 restraints weight = 4924.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.6754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7752  Z= 0.153
  Angle     :  0.724   9.512  10552  Z= 0.373
  Chirality :  0.041   0.166   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 16.861 176.840   1239
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.51 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.27), residues: 921
  helix:  0.99 (0.26), residues: 402
  sheet:  0.13 (0.51), residues: 114
  loop : -1.01 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  27 
 TYR   0.020   0.001   TYR B  54 
 PHE   0.016   0.002   PHE A 195 
 HIS   0.003   0.001   HIS C 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 7750)
  covalent geometry    : angle       0.72392 /  0.37 (10552)
  hydrogen bonds       : bond        0.03226 /  2.14 (  327)
  hydrogen bonds       : angle       4.75982 /  3.53 (  887)
  Misc. bond           : bond        0.00352 /  0.24 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1016.17 seconds
wall clock time: 18 minutes 19.46 seconds (1099.46 seconds total)