Starting phenix.real_space_refine
on Wed Mar 12 09:50:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eje_31160/03_2025/7eje_31160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/03_2025/7eje_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_2025/7eje_31160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_2025/7eje_31160.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_2025/7eje_31160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/03_2025/7eje_31160.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "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}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 4.91, per 1000 atoms: 0.65
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 2.88
  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: 2.15

  Time building geometry restraints manager: 2.56 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:             0.740
  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:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.710
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.100
-------------------------------------------------------------------------------
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   7750  Z= 0.556
  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 : 41.99
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.005   0.002   HIS A 138 
 PHE   0.020   0.002   PHE A 259 
 TYR   0.031   0.004   TYR A 315 
 ARG   0.007   0.001   ARG A 170 

*********************** 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  : 0.871 
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: A  220 ILE cc_start: 0.9123 (mt) cc_final: 0.8756 (mp)
REVERT: A  266 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8126 (m)
REVERT: A  290 ASN cc_start: 0.7529 (m110) cc_final: 0.7262 (m110)
REVERT: B  171 LEU cc_start: 0.8804 (mt) cc_final: 0.8331 (mt)
REVERT: B  220 ILE cc_start: 0.8980 (mt) cc_final: 0.8519 (mt)
REVERT: B  266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7995 (m)
REVERT: C  291 ILE cc_start: 0.9330 (mt) cc_final: 0.8868 (tt)
REVERT: C  301 TYR cc_start: 0.8033 (t80) cc_final: 0.7759 (t80)
  outliers start: 33
  outliers final: 8
  residues processed: 310
  average time/residue: 0.2842
  time to fit residues: 108.0293
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  : 0.798 
-------------------------------------------------------------------------------
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 78 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   overall best weight:    2.5584

-------------------------------------------------------------------------------
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 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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.082421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.066213 restraints weight = 21706.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.068610 restraints weight = 11559.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.070192 restraints weight = 7587.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7750  Z= 0.304
  Angle     :  0.785   7.783  10552  Z= 0.417
  Chirality :  0.043   0.153   1203
  Planarity :  0.006   0.055   1296
  Dihedral  : 17.966 179.491   1345
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.37 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 13.84 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.25), residues: 921
  helix: -0.52 (0.22), residues: 426
  sheet: -0.94 (0.44), residues: 126
  loop : -0.57 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 294 
 PHE   0.025   0.003   PHE A 126 
 TYR   0.021   0.002   TYR C 315 
 ARG   0.008   0.001   ARG A 130 

*********************** 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
  196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.851 
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: A   39 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8952 (pttp)
REVERT: A   59 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: A  129 PHE cc_start: 0.8952 (p90) cc_final: 0.8520 (p90)
REVERT: A  158 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7768 (mtp)
REVERT: A  218 LEU cc_start: 0.9421 (tp) cc_final: 0.9096 (tp)
REVERT: B   54 TYR cc_start: 0.8697 (m-10) cc_final: 0.8486 (m-80)
REVERT: B  124 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8218 (mm-30)
REVERT: B  137 CYS cc_start: 0.9059 (m) cc_final: 0.8433 (m)
REVERT: B  158 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7816 (mtp)
REVERT: B  189 VAL cc_start: 0.9368 (t) cc_final: 0.9145 (t)
REVERT: B  218 LEU cc_start: 0.9339 (tp) cc_final: 0.9084 (tp)
REVERT: B  237 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: B  265 ILE cc_start: 0.9475 (mm) cc_final: 0.9273 (mm)
  outliers start: 26
  outliers final: 12
  residues processed: 185
  average time/residue: 0.2027
  time to fit residues: 50.2740
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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  287 ILE
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 31 optimal weight:   10.0000
   chunk 57 optimal weight:    0.1980
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
A 199 HIS
A 200 GLN
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 199 HIS
B 200 GLN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.079803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.063555 restraints weight = 21780.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.065878 restraints weight = 11943.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.067436 restraints weight = 7917.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.5998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7750  Z= 0.322
  Angle     :  0.728   7.078  10552  Z= 0.380
  Chirality :  0.042   0.156   1203
  Planarity :  0.005   0.054   1296
  Dihedral  : 17.434 178.570   1329
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.45 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 15.19 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.26), residues: 921
  helix:  0.36 (0.24), residues: 426
  sheet: -1.01 (0.47), residues: 114
  loop : -0.84 (0.28), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS C  47 
 PHE   0.017   0.002   PHE C 126 
 TYR   0.019   0.002   TYR A 191 
 ARG   0.005   0.001   ARG A 130 

*********************** 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
  185 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 142
  time to evaluate  : 0.946 
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: 0.9297 (OUTLIER) cc_final: 0.9047 (pttp)
REVERT: A  137 CYS cc_start: 0.9141 (m) cc_final: 0.8858 (t)
REVERT: A  158 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (mtp)
REVERT: A  159 TYR cc_start: 0.9165 (t80) cc_final: 0.8629 (t80)
REVERT: A  171 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9374 (mt)
REVERT: A  304 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8215 (ttmm)
REVERT: B   59 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7926 (tm-30)
REVERT: B  124 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8198 (tt0)
REVERT: B  137 CYS cc_start: 0.9088 (m) cc_final: 0.8672 (m)
REVERT: B  158 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7485 (mpp)
REVERT: B  210 MET cc_start: 0.8221 (mtp) cc_final: 0.7957 (ttm)
REVERT: C   57 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8547 (tptp)
REVERT: C  124 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8262 (tt0)
REVERT: C  137 CYS cc_start: 0.9196 (m) cc_final: 0.8978 (t)
REVERT: C  253 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9304 (mm)
  outliers start: 43
  outliers final: 23
  residues processed: 165
  average time/residue: 0.2521
  time to fit residues: 56.6735
Evaluate side-chains
  155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
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  158 MET
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  104 THR
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   41 LEU
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  122 ILE
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  263 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  291 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0980
   chunk 4 optimal weight:   10.0000
   chunk 57 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0030
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.083633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.067293 restraints weight = 21370.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.069604 restraints weight = 11705.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.071230 restraints weight = 7806.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.6488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7750  Z= 0.178
  Angle     :  0.646   7.387  10552  Z= 0.335
  Chirality :  0.039   0.149   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.782 171.667   1329
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.37 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.55 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.27), residues: 921
  helix:  0.91 (0.26), residues: 402
  sheet: -0.68 (0.49), residues: 114
  loop : -0.78 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  47 
 PHE   0.011   0.002   PHE A 129 
 TYR   0.017   0.002   TYR B  54 
 ARG   0.005   0.001   ARG A 130 

*********************** 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
  177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.899 
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  137 CYS cc_start: 0.9147 (m) cc_final: 0.8774 (t)
REVERT: A  159 TYR cc_start: 0.9149 (t80) cc_final: 0.8657 (t80)
REVERT: A  304 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8250 (ttmm)
REVERT: B   59 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7650 (tm-30)
REVERT: B  137 CYS cc_start: 0.9049 (m) cc_final: 0.8649 (m)
REVERT: B  210 MET cc_start: 0.8271 (mtp) cc_final: 0.8016 (ttm)
REVERT: C   57 LYS cc_start: 0.8614 (tmtt) cc_final: 0.8342 (tptp)
REVERT: C  124 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8257 (tt0)
REVERT: C  137 CYS cc_start: 0.9178 (m) cc_final: 0.8959 (t)
REVERT: C  171 LEU cc_start: 0.9369 (mp) cc_final: 0.8872 (mt)
  outliers start: 29
  outliers final: 13
  residues processed: 165
  average time/residue: 0.2736
  time to fit residues: 60.5050
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
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  315 TYR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 39 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    2.6046

-------------------------------------------------------------------------------
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**
B 267 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 = 0.3275 r_free = 0.3275 target = 0.079631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.063177 restraints weight = 21699.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.065482 restraints weight = 11996.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.067021 restraints weight = 8018.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.6836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7750  Z= 0.281
  Angle     :  0.688   7.862  10552  Z= 0.354
  Chirality :  0.040   0.162   1203
  Planarity :  0.005   0.055   1296
  Dihedral  : 16.679 170.523   1323
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.56 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.22 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.27), residues: 921
  helix:  0.79 (0.26), residues: 426
  sheet: -0.71 (0.49), residues: 117
  loop : -0.84 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  47 
 PHE   0.010   0.002   PHE A 195 
 TYR   0.036   0.002   TYR B  54 
 ARG   0.006   0.001   ARG A 229 

*********************** 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
  167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 CYS cc_start: 0.9168 (m) cc_final: 0.8716 (t)
REVERT: A  304 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8181 (ttmm)
REVERT: B   59 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7974 (tm-30)
REVERT: B  137 CYS cc_start: 0.9079 (m) cc_final: 0.8594 (m)
REVERT: B  204 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9341 (mm)
REVERT: C   57 LYS cc_start: 0.8664 (tmtt) cc_final: 0.8397 (tptp)
  outliers start: 31
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1870
  time to fit residues: 39.0054
Evaluate side-chains
  146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  140 LEU
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  315 TYR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  122 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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**
** 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 = 0.3308 r_free = 0.3308 target = 0.081314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065289 restraints weight = 21527.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.067578 restraints weight = 11877.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.069125 restraints weight = 7900.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.7116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7750  Z= 0.198
  Angle     :  0.661   8.180  10552  Z= 0.340
  Chirality :  0.040   0.152   1203
  Planarity :  0.004   0.057   1296
  Dihedral  : 16.470 169.351   1323
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.91 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.76 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 921
  helix:  0.81 (0.25), residues: 417
  sheet: -0.38 (0.50), residues: 114
  loop : -0.89 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.031   0.002   PHE C 259 
 TYR   0.035   0.002   TYR B  54 
 ARG   0.005   0.000   ARG A 130 

*********************** 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
  164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8590 (mm-30)
REVERT: A  137 CYS cc_start: 0.9115 (m) cc_final: 0.8732 (t)
REVERT: A  304 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (ttmm)
REVERT: B   59 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8056 (tm-30)
REVERT: B  137 CYS cc_start: 0.9012 (m) cc_final: 0.8587 (m)
REVERT: C   57 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8384 (tptp)
REVERT: C  124 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8118 (tt0)
  outliers start: 29
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1755
  time to fit residues: 37.3888
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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  195 PHE
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   59 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  251 MET
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   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
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 37 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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**
** 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 = 0.3281 r_free = 0.3281 target = 0.080096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.063731 restraints weight = 21560.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.066004 restraints weight = 11900.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.067563 restraints weight = 7957.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.7305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7750  Z= 0.243
  Angle     :  0.680  10.328  10552  Z= 0.347
  Chirality :  0.040   0.159   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.540 170.526   1323
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.99 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 20.43 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.27), residues: 921
  helix:  0.83 (0.25), residues: 420
  sheet: -0.91 (0.41), residues: 153
  loop : -0.46 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.017   0.002   PHE A 195 
 TYR   0.030   0.002   TYR B  54 
 ARG   0.004   0.000   ARG A 130 

*********************** 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
  154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.933 
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  137 CYS cc_start: 0.9215 (m) cc_final: 0.8906 (t)
REVERT: B   59 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8214 (tm-30)
REVERT: B  137 CYS cc_start: 0.9073 (m) cc_final: 0.8607 (m)
REVERT: B  158 MET cc_start: 0.8551 (mtt) cc_final: 0.8011 (mtp)
REVERT: C   57 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8451 (tptp)
  outliers start: 29
  outliers final: 26
  residues processed: 139
  average time/residue: 0.2117
  time to fit residues: 41.5096
Evaluate side-chains
  149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
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  171 LEU
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   59 GLU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  251 MET
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   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  314 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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**
** 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 = 0.3313 r_free = 0.3313 target = 0.081522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.065540 restraints weight = 21719.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.067809 restraints weight = 11978.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.069364 restraints weight = 7985.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.7467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7750  Z= 0.200
  Angle     :  0.656   8.540  10552  Z= 0.339
  Chirality :  0.040   0.164   1203
  Planarity :  0.004   0.058   1296
  Dihedral  : 16.418 170.119   1323
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.91 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.70 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.27), residues: 921
  helix:  0.90 (0.25), residues: 420
  sheet: -0.66 (0.42), residues: 150
  loop : -0.47 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.016   0.001   PHE A 195 
 TYR   0.028   0.002   TYR B  54 
 ARG   0.004   0.000   ARG A 130 

*********************** 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
  159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 CYS cc_start: 0.9169 (m) cc_final: 0.8876 (t)
REVERT: B   59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8208 (tm-30)
REVERT: B  137 CYS cc_start: 0.9008 (m) cc_final: 0.8544 (m)
REVERT: B  158 MET cc_start: 0.8509 (mtt) cc_final: 0.7999 (mtp)
REVERT: C   57 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8439 (tptp)
  outliers start: 28
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1861
  time to fit residues: 37.8014
Evaluate side-chains
  143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
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  210 MET
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   59 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  314 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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**
** 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 = 0.080776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.064469 restraints weight = 21870.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.066783 restraints weight = 11927.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.068344 restraints weight = 7927.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.7594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7750  Z= 0.223
  Angle     :  0.694  10.367  10552  Z= 0.351
  Chirality :  0.040   0.154   1203
  Planarity :  0.004   0.057   1296
  Dihedral  : 15.964 168.476   1323
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.45 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.37 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 921
  helix:  1.01 (0.25), residues: 420
  sheet: -0.51 (0.40), residues: 162
  loop : -0.42 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.017   0.001   PHE A 195 
 TYR   0.026   0.001   TYR B  54 
 ARG   0.006   0.000   ARG A 130 

*********************** 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
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.9213 (p0) cc_final: 0.8994 (p0)
REVERT: A  137 CYS cc_start: 0.9217 (m) cc_final: 0.8879 (t)
REVERT: B   59 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8235 (tm-30)
REVERT: B  137 CYS cc_start: 0.9041 (m) cc_final: 0.8577 (m)
REVERT: B  158 MET cc_start: 0.8548 (mtt) cc_final: 0.8049 (mtp)
REVERT: C  124 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8286 (mm-30)
  outliers start: 24
  outliers final: 21
  residues processed: 138
  average time/residue: 0.2262
  time to fit residues: 44.5656
Evaluate side-chains
  146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  210 MET
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   59 GLU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
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   64 LYS
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  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 75 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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**
** 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 = 0.3258 r_free = 0.3258 target = 0.078875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.062820 restraints weight = 22005.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.065014 restraints weight = 12263.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.066500 restraints weight = 8262.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.7650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7750  Z= 0.288
  Angle     :  0.714   8.694  10552  Z= 0.367
  Chirality :  0.041   0.167   1203
  Planarity :  0.004   0.054   1296
  Dihedral  : 16.006 171.006   1323
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.67 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.37 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 921
  helix:  1.04 (0.25), residues: 420
  sheet: -0.49 (0.40), residues: 165
  loop : -0.42 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.011   0.002   PHE C 259 
 TYR   0.028   0.002   TYR B  54 
 ARG   0.005   0.000   ARG A 130 

********************** 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
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.827 
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   62 ASN cc_start: 0.9167 (p0) cc_final: 0.8938 (p0)
REVERT: A  137 CYS cc_start: 0.9126 (m) cc_final: 0.8820 (t)
REVERT: B   59 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8198 (tm-30)
REVERT: C  124 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8348 (mm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 140
  average time/residue: 0.2323
  time to fit residues: 44.7731
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  : 1.775 
-------------------------------------------------------------------------------
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  171 LEU
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  210 MET
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   59 GLU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  195 PHE
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   64 LYS
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 64 optimal weight:    0.2980
   chunk 56 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 242 GLN
A 267 ASN
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.081027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.065133 restraints weight = 21630.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.067380 restraints weight = 11958.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.068869 restraints weight = 8017.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.7815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7750  Z= 0.207
  Angle     :  0.689   9.488  10552  Z= 0.350
  Chirality :  0.040   0.145   1203
  Planarity :  0.004   0.055   1296
  Dihedral  : 15.900 171.891   1323
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.91 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.24 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 921
  helix:  1.05 (0.25), residues: 417
  sheet: -0.22 (0.40), residues: 162
  loop : -0.49 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  47 
 PHE   0.011   0.001   PHE C 259 
 TYR   0.023   0.002   TYR B  54 
 ARG   0.006   0.000   ARG A 130 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2613.44 seconds
wall clock time: 49 minutes 7.46 seconds (2947.46 seconds total)