Starting phenix.real_space_refine
on Tue Mar  3 17:45:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eje_31160/03_2026/7eje_31160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/03_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_31160/03_2026/7eje_31160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_2026/7eje_31160.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_2026/7eje_31160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_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-5986/lib/python3.9/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: 1.79, per 1000 atoms: 0.24
  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: 0.74
  Conformation dependent library (CDL) restraints added in 263.8 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: 0.88
  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: 1.04

  Time building geometry restraints manager: 0.94 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: 10256
        3.16 -     6.33: 257
        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: 4528
       32.88 -    65.76: 174
       65.76 -    98.64: 11
       98.64 -   131.51: 0
      131.51 -   164.39: 3
  Dihedral angle restraints: 4716
    sinusoidal: 2055
      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 4713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1004
       0.066 -    0.132: 189
       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:             1.260
  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:                    0.020
  Process input model:                     8.510
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
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= 0.568
  Angle     :  1.298  15.821  10552  Z= 0.838
  Chirality :  0.052   0.331   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 15.521 164.392   3012
  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
  covalent geometry    : bond        0.00900 ( 7750)
  covalent geometry    : angle       1.29756 (10552)
  hydrogen bonds       : bond        0.15732 (  327)
  hydrogen bonds       : angle       9.94827 (  887)
  Misc. bond           : bond        0.09494 (    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  : 0.289 
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: 0.1173
  time to fit residues: 44.7417
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  : 0.187 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 HIS
A 138 HIS
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 200 GLN
C 267 ASN
C 313 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.083632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.067448 restraints weight = 21858.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.069903 restraints weight = 11500.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.071569 restraints weight = 7468.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.072601 restraints weight = 5553.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.073459 restraints weight = 4564.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   7752  Z= 0.187
  Angle     :  0.783   8.089  10552  Z= 0.414
  Chirality :  0.043   0.163   1203
  Planarity :  0.006   0.055   1296
  Dihedral  : 17.980 178.814   1345
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.47 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.17 %
    Favored  : 83.20 %
  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: -1.03 (0.25), residues: 921
  helix: -0.43 (0.23), residues: 423
  sheet: -0.91 (0.44), residues: 126
  loop : -0.69 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 130 
 TYR   0.019   0.002   TYR C 315 
 PHE   0.027   0.003   PHE A 126 
 HIS   0.006   0.002   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7750)
  covalent geometry    : angle       0.78318 (10552)
  hydrogen bonds       : bond        0.04268 (  327)
  hydrogen bonds       : angle       5.50723 (  887)
  Misc. bond           : bond        0.00741 (    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
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.276 
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: 0.9374 (OUTLIER) cc_final: 0.8969 (pttp)
REVERT: A   59 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: A  137 CYS cc_start: 0.9087 (m) cc_final: 0.8754 (t)
REVERT: A  158 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7683 (mtp)
REVERT: A  220 ILE cc_start: 0.9438 (mt) cc_final: 0.9124 (mm)
REVERT: A  243 MET cc_start: 0.8670 (tpp) cc_final: 0.8449 (mpp)
REVERT: B   39 LYS cc_start: 0.9304 (ttpp) cc_final: 0.9099 (ptpp)
REVERT: B   62 ASN cc_start: 0.9104 (p0) cc_final: 0.8903 (p0)
REVERT: B  124 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8249 (tt0)
REVERT: B  158 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7318 (mpp)
REVERT: B  171 LEU cc_start: 0.9603 (mt) cc_final: 0.9394 (mt)
REVERT: B  191 TYR cc_start: 0.8967 (t80) cc_final: 0.8766 (t80)
REVERT: B  218 LEU cc_start: 0.9309 (tp) cc_final: 0.9085 (tp)
REVERT: B  237 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: C   59 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7850 (tm-30)
  outliers start: 27
  outliers final: 11
  residues processed: 190
  average time/residue: 0.0762
  time to fit residues: 19.6218
Evaluate side-chains
  157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  104 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  195 PHE
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  104 THR
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  253 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 HIS
A 200 GLN
B  34 ASN
B  36 ASN
B 200 GLN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.080496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.064512 restraints weight = 21748.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.066819 restraints weight = 11874.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.068343 restraints weight = 7854.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.069319 restraints weight = 5909.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.070109 restraints weight = 4886.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.6006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7752  Z= 0.208
  Angle     :  0.720   7.016  10552  Z= 0.376
  Chirality :  0.041   0.156   1203
  Planarity :  0.005   0.054   1296
  Dihedral  : 17.462 179.070   1329
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 15.86 %
    Favored  : 79.30 %
  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: -0.43 (0.26), residues: 921
  helix:  0.42 (0.25), residues: 426
  sheet: -0.95 (0.47), residues: 114
  loop : -0.75 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 130 
 TYR   0.019   0.002   TYR A 191 
 PHE   0.016   0.002   PHE C 126 
 HIS   0.009   0.002   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 7750)
  covalent geometry    : angle       0.72007 (10552)
  hydrogen bonds       : bond        0.03597 (  327)
  hydrogen bonds       : angle       5.00921 (  887)
  Misc. bond           : bond        0.00452 (    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
  180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.254 
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: 0.9295 (OUTLIER) cc_final: 0.9016 (pttp)
REVERT: A  124 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: A  171 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9362 (mt)
REVERT: A  304 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8248 (ttmm)
REVERT: B   39 LYS cc_start: 0.9369 (ttpp) cc_final: 0.9121 (ptpp)
REVERT: B   59 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8047 (tm-30)
REVERT: B  124 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8131 (tt0)
REVERT: B  137 CYS cc_start: 0.9172 (m) cc_final: 0.8661 (m)
REVERT: B  158 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7350 (mpp)
REVERT: B  210 MET cc_start: 0.8161 (mtp) cc_final: 0.7917 (ttm)
REVERT: C  137 CYS cc_start: 0.9222 (m) cc_final: 0.8998 (t)
REVERT: C  253 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9271 (mm)
REVERT: C  301 TYR cc_start: 0.8895 (t80) cc_final: 0.8689 (t80)
  outliers start: 36
  outliers final: 20
  residues processed: 165
  average time/residue: 0.0813
  time to fit residues: 18.0339
Evaluate side-chains
  155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  171 LEU
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   36 ASN
Chi-restraints excluded: chain B residue   59 GLU
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  124 GLU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  158 MET
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   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** 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  36 ASN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.082043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.066264 restraints weight = 21858.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.068627 restraints weight = 11686.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.070200 restraints weight = 7614.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.071222 restraints weight = 5660.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.072009 restraints weight = 4628.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.6422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7752  Z= 0.134
  Angle     :  0.653   7.196  10552  Z= 0.341
  Chirality :  0.040   0.149   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.881 172.817   1326
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  2.93 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.61 %
    Favored  : 77.69 %
  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: -0.29 (0.26), residues: 921
  helix:  0.57 (0.25), residues: 426
  sheet: -0.88 (0.47), residues: 117
  loop : -0.73 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 229 
 TYR   0.025   0.002   TYR B  54 
 PHE   0.014   0.002   PHE B 259 
 HIS   0.005   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7750)
  covalent geometry    : angle       0.65329 (10552)
  hydrogen bonds       : bond        0.03066 (  327)
  hydrogen bonds       : angle       4.71508 (  887)
  Misc. bond           : bond        0.00383 (    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
  180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.209 
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: 0.9321 (OUTLIER) cc_final: 0.9055 (pttm)
REVERT: A  124 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8552 (mm-30)
REVERT: A  137 CYS cc_start: 0.9263 (m) cc_final: 0.8895 (t)
REVERT: A  159 TYR cc_start: 0.9108 (t80) cc_final: 0.8369 (t80)
REVERT: A  304 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8261 (ttmm)
REVERT: B   39 LYS cc_start: 0.9364 (ttpp) cc_final: 0.9146 (ptpp)
REVERT: B  124 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8123 (tt0)
REVERT: B  137 CYS cc_start: 0.9138 (m) cc_final: 0.8656 (m)
REVERT: B  210 MET cc_start: 0.8288 (mtp) cc_final: 0.8033 (ttm)
  outliers start: 35
  outliers final: 22
  residues processed: 163
  average time/residue: 0.0808
  time to fit residues: 17.8199
Evaluate side-chains
  161 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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 A residue  304 LYS
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  131 THR
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  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  235 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7944

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

Flipped N/Q/H residues before XYZ refinement:
** 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  36 ASN
** 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 = 0.3338 r_free = 0.3338 target = 0.083114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.066894 restraints weight = 21708.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.069296 restraints weight = 11715.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070943 restraints weight = 7703.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.071964 restraints weight = 5740.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072861 restraints weight = 4727.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.6782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7752  Z= 0.128
  Angle     :  0.652   7.248  10552  Z= 0.336
  Chirality :  0.040   0.150   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.534 170.375   1323
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.28 %
    Favored  : 77.42 %
  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: -0.14 (0.27), residues: 921
  helix:  0.81 (0.26), residues: 405
  sheet: -0.35 (0.49), residues: 111
  loop : -0.90 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.025   0.002   TYR B  54 
 PHE   0.011   0.002   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7750)
  covalent geometry    : angle       0.65219 (10552)
  hydrogen bonds       : bond        0.02927 (  327)
  hydrogen bonds       : angle       4.62065 (  887)
  Misc. bond           : bond        0.00332 (    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
  177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9062 (pttm)
REVERT: A  124 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8368 (mm-30)
REVERT: A  125 MET cc_start: 0.8782 (mmt) cc_final: 0.8579 (mmp)
REVERT: A  137 CYS cc_start: 0.9190 (m) cc_final: 0.8708 (t)
REVERT: A  159 TYR cc_start: 0.9077 (t80) cc_final: 0.8222 (t80)
REVERT: A  304 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (ttmm)
REVERT: B   39 LYS cc_start: 0.9334 (ttpp) cc_final: 0.9024 (pptt)
REVERT: B  124 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8095 (tt0)
REVERT: B  137 CYS cc_start: 0.9122 (m) cc_final: 0.8602 (m)
REVERT: B  158 MET cc_start: 0.8326 (mtp) cc_final: 0.7378 (mtp)
REVERT: B  314 ILE cc_start: 0.9395 (mt) cc_final: 0.9047 (tt)
REVERT: C  124 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8013 (tt0)
REVERT: C  258 GLU cc_start: 0.7103 (pt0) cc_final: 0.6780 (pt0)
  outliers start: 32
  outliers final: 20
  residues processed: 161
  average time/residue: 0.0800
  time to fit residues: 17.5618
Evaluate side-chains
  158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
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  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  102 ILE
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  257 ASP
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** 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  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.079935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.063529 restraints weight = 21918.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.065840 restraints weight = 11982.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.067406 restraints weight = 7974.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.068280 restraints weight = 6022.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.069079 restraints weight = 5064.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.6984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7752  Z= 0.189
  Angle     :  0.677   7.210  10552  Z= 0.349
  Chirality :  0.040   0.151   1203
  Planarity :  0.004   0.055   1296
  Dihedral  : 16.629 169.974   1323
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.67 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.22 %
    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: -0.13 (0.26), residues: 921
  helix:  0.79 (0.25), residues: 423
  sheet: -0.44 (0.49), residues: 114
  loop : -0.88 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.034   0.002   TYR C 228 
 PHE   0.012   0.002   PHE A 195 
 HIS   0.004   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7750)
  covalent geometry    : angle       0.67732 (10552)
  hydrogen bonds       : bond        0.03223 (  327)
  hydrogen bonds       : angle       4.70170 (  887)
  Misc. bond           : bond        0.00388 (    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
  168 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9078 (pttm)
REVERT: A  137 CYS cc_start: 0.9192 (m) cc_final: 0.8796 (t)
REVERT: A  304 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8180 (ttmm)
REVERT: B   39 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9063 (pptt)
REVERT: B  124 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8018 (tt0)
REVERT: B  137 CYS cc_start: 0.9083 (m) cc_final: 0.8558 (m)
REVERT: B  158 MET cc_start: 0.8467 (mtp) cc_final: 0.7495 (mtp)
  outliers start: 35
  outliers final: 28
  residues processed: 152
  average time/residue: 0.0763
  time to fit residues: 16.0802
Evaluate side-chains
  158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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   72 ASP
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  210 MET
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  315 TYR
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  124 GLU
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  315 TYR
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  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
C 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.080936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.064744 restraints weight = 21714.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.067099 restraints weight = 11897.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.068659 restraints weight = 7860.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.069665 restraints weight = 5911.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.070135 restraints weight = 4893.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.7235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7752  Z= 0.144
  Angle     :  0.665  10.596  10552  Z= 0.341
  Chirality :  0.039   0.148   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.518 168.384   1323
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.49 %
    Favored  : 75.81 %
  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: -0.11 (0.26), residues: 921
  helix:  0.76 (0.25), residues: 423
  sheet: -0.28 (0.49), residues: 114
  loop : -0.88 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.027   0.002   TYR B  54 
 PHE   0.014   0.001   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7750)
  covalent geometry    : angle       0.66487 (10552)
  hydrogen bonds       : bond        0.02924 (  327)
  hydrogen bonds       : angle       4.52639 (  887)
  Misc. bond           : bond        0.00362 (    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
  168 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.378 
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: 0.9332 (OUTLIER) cc_final: 0.9086 (pttm)
REVERT: A  124 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8536 (mm-30)
REVERT: A  137 CYS cc_start: 0.9197 (m) cc_final: 0.8780 (t)
REVERT: A  291 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9240 (tt)
REVERT: B   39 LYS cc_start: 0.9364 (ttpp) cc_final: 0.9129 (pptt)
REVERT: B  124 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7824 (mm-30)
REVERT: B  137 CYS cc_start: 0.9074 (m) cc_final: 0.8573 (m)
REVERT: B  158 MET cc_start: 0.8372 (mtp) cc_final: 0.7451 (mtp)
  outliers start: 35
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0726
  time to fit residues: 15.2557
Evaluate side-chains
  156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  314 ILE
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  102 ILE
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  238 LEU
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  263 VAL
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 25 optimal weight:    0.3980
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** B  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 = 0.3322 r_free = 0.3322 target = 0.082154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.065882 restraints weight = 21914.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.068237 restraints weight = 12072.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.069739 restraints weight = 8029.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070873 restraints weight = 6109.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.071460 restraints weight = 5004.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.7413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7752  Z= 0.136
  Angle     :  0.671   9.434  10552  Z= 0.343
  Chirality :  0.039   0.142   1203
  Planarity :  0.004   0.057   1296
  Dihedral  : 16.513 169.788   1323
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 21.24 %
    Favored  : 74.73 %
  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:  1.15 (0.26), residues: 399
  sheet: -1.11 (0.44), residues: 138
  loop : -0.56 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 130 
 TYR   0.029   0.002   TYR B  54 
 PHE   0.017   0.002   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7750)
  covalent geometry    : angle       0.67067 (10552)
  hydrogen bonds       : bond        0.02857 (  327)
  hydrogen bonds       : angle       4.44525 (  887)
  Misc. bond           : bond        0.00329 (    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
  165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.281 
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: 0.9338 (OUTLIER) cc_final: 0.9089 (pttm)
REVERT: A  137 CYS cc_start: 0.9211 (m) cc_final: 0.8774 (t)
REVERT: A  159 TYR cc_start: 0.9003 (t80) cc_final: 0.7981 (t80)
REVERT: B   39 LYS cc_start: 0.9367 (ttpp) cc_final: 0.9145 (pptt)
REVERT: B  124 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7814 (mm-30)
REVERT: B  137 CYS cc_start: 0.9073 (m) cc_final: 0.8607 (m)
REVERT: B  158 MET cc_start: 0.8338 (mtp) cc_final: 0.7423 (mtp)
  outliers start: 30
  outliers final: 21
  residues processed: 150
  average time/residue: 0.0788
  time to fit residues: 16.2411
Evaluate side-chains
  149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  220 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  314 ILE
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  102 ILE
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0020
   chunk 73 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.083405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.067386 restraints weight = 21706.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.069783 restraints weight = 11714.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.071395 restraints weight = 7690.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.072476 restraints weight = 5745.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.073161 restraints weight = 4695.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.7597

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= 0.129
  Angle     :  0.683   9.005  10552  Z= 0.347
  Chirality :  0.039   0.144   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.122 170.477   1323
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.77 %
    Favored  : 74.87 %
  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:  0.27 (0.27), residues: 921
  helix:  1.17 (0.26), residues: 402
  sheet: -0.56 (0.39), residues: 162
  loop : -0.48 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 130 
 TYR   0.028   0.002   TYR B  54 
 PHE   0.010   0.001   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7750)
  covalent geometry    : angle       0.68309 (10552)
  hydrogen bonds       : bond        0.02688 (  327)
  hydrogen bonds       : angle       4.37668 (  887)
  Misc. bond           : bond        0.00262 (    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
  159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.9157 (p0) cc_final: 0.8952 (p0)
REVERT: A  137 CYS cc_start: 0.9183 (m) cc_final: 0.8754 (t)
REVERT: A  159 TYR cc_start: 0.8979 (t80) cc_final: 0.8089 (t80)
REVERT: B   39 LYS cc_start: 0.9360 (ttpp) cc_final: 0.9150 (pptt)
REVERT: B  124 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7741 (mm-30)
REVERT: B  137 CYS cc_start: 0.9114 (m) cc_final: 0.8655 (m)
REVERT: B  158 MET cc_start: 0.8324 (mtp) cc_final: 0.7394 (mtp)
REVERT: C  124 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8055 (tt0)
  outliers start: 25
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0798
  time to fit residues: 16.2245
Evaluate side-chains
  148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
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  220 ILE
Chi-restraints excluded: chain A residue  314 ILE
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  102 ILE
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  315 TYR
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  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 = 0.3306 r_free = 0.3306 target = 0.081575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.065420 restraints weight = 21905.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.067788 restraints weight = 11880.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.069351 restraints weight = 7838.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.070367 restraints weight = 5879.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.070945 restraints weight = 4845.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.7633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7752  Z= 0.158
  Angle     :  0.690   8.001  10552  Z= 0.352
  Chirality :  0.039   0.153   1203
  Planarity :  0.004   0.055   1296
  Dihedral  : 15.868 167.203   1323
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.56 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.31 %
    Favored  : 74.19 %
  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:  0.26 (0.27), residues: 921
  helix:  1.04 (0.25), residues: 423
  sheet: -0.57 (0.39), residues: 165
  loop : -0.40 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 250 
 TYR   0.027   0.002   TYR B  54 
 PHE   0.017   0.002   PHE A 259 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7750)
  covalent geometry    : angle       0.69007 (10552)
  hydrogen bonds       : bond        0.02891 (  327)
  hydrogen bonds       : angle       4.35247 (  887)
  Misc. bond           : bond        0.00291 (    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
  156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 PHE cc_start: 0.9020 (p90) cc_final: 0.8600 (p90)
REVERT: A  137 CYS cc_start: 0.9180 (m) cc_final: 0.8793 (t)
REVERT: A  159 TYR cc_start: 0.9015 (t80) cc_final: 0.8155 (t80)
REVERT: B   39 LYS cc_start: 0.9405 (ttpp) cc_final: 0.9199 (pptt)
REVERT: B  124 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7950 (mm-30)
REVERT: B  137 CYS cc_start: 0.9036 (m) cc_final: 0.8583 (m)
REVERT: B  158 MET cc_start: 0.8328 (mtp) cc_final: 0.7439 (mtp)
REVERT: B  238 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8474 (tp)
REVERT: C  191 TYR cc_start: 0.8116 (t80) cc_final: 0.7694 (t80)
  outliers start: 26
  outliers final: 21
  residues processed: 141
  average time/residue: 0.0749
  time to fit residues: 14.6303
Evaluate side-chains
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
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  220 ILE
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  315 TYR
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  124 GLU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  315 TYR
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0770
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    3.0146

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 HIS
B 267 ASN
B 290 ASN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.078858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.062453 restraints weight = 22019.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.064600 restraints weight = 12470.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.066065 restraints weight = 8482.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.067069 restraints weight = 6534.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.067707 restraints weight = 5436.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.7704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   7752  Z= 0.216
  Angle     :  0.748  12.187  10552  Z= 0.381
  Chirality :  0.041   0.158   1203
  Planarity :  0.005   0.052   1296
  Dihedral  : 16.024 167.914   1323
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.78 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.04 %
    Favored  : 74.19 %
  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:  0.30 (0.27), residues: 921
  helix:  1.18 (0.25), residues: 414
  sheet: -0.51 (0.39), residues: 165
  loop : -0.53 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 250 
 TYR   0.032   0.002   TYR C 228 
 PHE   0.022   0.002   PHE A 259 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 7750)
  covalent geometry    : angle       0.74826 (10552)
  hydrogen bonds       : bond        0.03283 (  327)
  hydrogen bonds       : angle       4.55065 (  887)
  Misc. bond           : bond        0.00374 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1134.10 seconds
wall clock time: 20 minutes 21.48 seconds (1221.48 seconds total)