Starting phenix.real_space_refine
on Mon Nov 17 18:44:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eje_31160/11_2025/7eje_31160.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eje_31160/11_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eje_31160/11_2025/7eje_31160.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eje_31160/11_2025/7eje_31160.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eje_31160/11_2025/7eje_31160.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eje_31160/11_2025/7eje_31160.map"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      27      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4677      2.51       5
     N    1341      2.21       5
     O    1515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 1.97, per 1000 atoms: 0.26
  Number of scatterers: 7602
  At special positions: 0
  Unit cell: (107.092, 75.748, 114.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      27     15.00
     Mg      3     11.99
     O    1515      8.00
     N    1341      7.00
     C    4677      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 426.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      52.2% alpha, 11.8% beta
      8 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 29
    Processing helix  chain 'A' and resid 34 through 42
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.776A  pdb=" N   ILE A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 97
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.561A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.855A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.535A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.962A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.923A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 34 through 42
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 48 through 54
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 3.776A  pdb=" N   ILE B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 97
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
      removed outlier: 3.562A  pdb=" N   LEU B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.854A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.535A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.961A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.922A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 29
    Processing helix  chain 'C' and resid 34 through 42
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 48 through 54
    Processing helix  chain 'C' and resid 56 through 63
      removed outlier: 3.775A  pdb=" N   ILE C  63 " --> pdb=" O   GLU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 89 through 97
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
      removed outlier: 3.563A  pdb=" N   LEU C 171 " --> pdb=" O   ARG C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.854A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 212
      removed outlier: 3.573A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.536A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.960A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU C 258 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.924A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA C 293 " --> pdb=" O   GLY C 289 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
      removed outlier: 8.366A  pdb=" N   VAL A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU A 219 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   THR A 266 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL A 221 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ALA A 157 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA A 192 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR A 159 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 304
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 126
      removed outlier: 8.367A  pdb=" N   VAL B 264 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU B 219 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   THR B 266 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   VAL B 221 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA B 157 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA B 192 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TYR B 159 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 304
    Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126
      removed outlier: 8.367A  pdb=" N   VAL C 264 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU C 219 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   THR C 266 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   VAL C 221 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA C 157 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR C 159 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 299 through 304
    Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 330

    311 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.96 seconds

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

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

  Histogram of bond angle deviations from ideal:
        0.00 -     3.16: 10256
        3.16 -     6.33: 257
        6.33 -     9.49: 30
        9.49 -    12.66: 6
       12.66 -    15.82: 3
  Bond angle restraints: 10552
  Sorted by residual:
  angle pdb=" C   LYS B 285 "
        pdb=" N   PRO B 286 "
        pdb=" CA  PRO B 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.62   -6.84 1.03e+00 9.43e-01 4.41e+01
  angle pdb=" C   LYS A 285 "
        pdb=" N   PRO A 286 "
        pdb=" CA  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.62   -6.84 1.03e+00 9.43e-01 4.41e+01
  angle pdb=" C   LYS C 285 "
        pdb=" N   PRO C 286 "
        pdb=" CA  PRO C 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.59   -6.81 1.03e+00 9.43e-01 4.37e+01
  angle pdb=" N   GLU C 124 "
        pdb=" CA  GLU C 124 "
        pdb=" C   GLU C 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.33   -9.85 1.80e+00 3.09e-01 2.99e+01
  angle pdb=" N   GLU B 124 "
        pdb=" CA  GLU B 124 "
        pdb=" C   GLU B 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.33   -9.85 1.80e+00 3.09e-01 2.99e+01
  ... (remaining 10547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.88: 4528
       32.88 -    65.76: 174
       65.76 -    98.64: 11
       98.64 -   131.51: 0
      131.51 -   164.39: 3
  Dihedral angle restraints: 4716
    sinusoidal: 2055
      harmonic: 2661
  Sorted by residual:
  dihedral pdb=" CA  ILE B 314 "
           pdb=" C   ILE B 314 "
           pdb=" N   TYR B 315 "
           pdb=" CA  TYR B 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.38   23.62     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ILE A 314 "
           pdb=" C   ILE A 314 "
           pdb=" N   TYR A 315 "
           pdb=" CA  TYR A 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.43   23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ILE C 314 "
           pdb=" C   ILE C 314 "
           pdb=" N   TYR C 315 "
           pdb=" CA  TYR C 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.45   23.55     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 4713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1004
       0.066 -    0.132: 189
       0.132 -    0.198: 4
       0.198 -    0.265: 3
       0.265 -    0.331: 3
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" C3' ANP B 401 "
            pdb=" C2' ANP B 401 "
            pdb=" C4' ANP B 401 "
            pdb=" O3' ANP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C3' ANP C 403 "
            pdb=" C2' ANP C 403 "
            pdb=" C4' ANP C 403 "
            pdb=" O3' ANP C 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.69    0.33 2.00e-01 2.50e+01 2.69e+00
  ... (remaining 1200 not shown)

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

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 69
        2.14 -     2.83: 2638
        2.83 -     3.52: 10853
        3.52 -     4.21: 17854
        4.21 -     4.90: 30158
  Nonbonded interactions: 61572
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 217 "
            pdb=" CG1 VAL B 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA C 217 "
            pdb=" CG1 VAL C 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA A 217 "
            pdb=" CG1 VAL A 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" CG2 VAL C 270 "
            pdb=" CG2 ILE C 287 "
     model   vdw
     1.579 3.880
  nonbonded pdb=" CG2 VAL A 270 "
            pdb=" CG2 ILE A 287 "
     model   vdw
     1.579 3.880
  ... (remaining 61567 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 22 through 336)
  selection = (chain 'B' and resid 22 through 336)
  selection = (chain 'C' and resid 22 through 336)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.580
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.148   7752  Z= 0.568
  Angle     :  1.298  15.821  10552  Z= 0.838
  Chirality :  0.052   0.331   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 15.521 164.392   3012
  Min Nonbonded Distance : 1.454

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

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

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00900 ( 7750)
  covalent geometry    : angle       1.29756 (10552)
  hydrogen bonds       : bond        0.15732 (  327)
  hydrogen bonds       : angle       9.94827 (  887)
  Misc. bond           : bond        0.09494 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 294
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 ILE cc_start: 0.9123 (mt) cc_final: 0.8762 (mp)
REVERT: A  266 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8128 (m)
REVERT: A  290 ASN cc_start: 0.7529 (m110) cc_final: 0.7259 (m110)
REVERT: B  171 LEU cc_start: 0.8804 (mt) cc_final: 0.8332 (mt)
REVERT: B  220 ILE cc_start: 0.8980 (mt) cc_final: 0.8527 (mt)
REVERT: B  266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7993 (m)
REVERT: C  291 ILE cc_start: 0.9330 (mt) cc_final: 0.8870 (tt)
REVERT: C  301 TYR cc_start: 0.8033 (t80) cc_final: 0.7761 (t80)
  outliers start: 33
  outliers final: 8
  residues processed: 310
  average time/residue: 0.1304
  time to fit residues: 49.9248
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  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  235 ARG
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain C residue  235 ARG
Chi-restraints excluded: chain C residue  263 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 HIS
A 138 HIS
A 200 GLN
A 313 GLN
B  36 ASN
B  93 HIS
B 200 GLN
B 267 ASN
B 313 GLN
C  47 HIS
C 200 GLN
C 267 ASN
C 313 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.083632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.067429 restraints weight = 21858.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.069879 restraints weight = 11532.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.071531 restraints weight = 7495.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.072686 restraints weight = 5582.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.073419 restraints weight = 4534.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.5086

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

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.47 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.17 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.25), residues: 921
  helix: -0.43 (0.23), residues: 423
  sheet: -0.91 (0.44), residues: 126
  loop : -0.69 (0.31), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7750)
  covalent geometry    : angle       0.78318 (10552)
  hydrogen bonds       : bond        0.04268 (  327)
  hydrogen bonds       : angle       5.50723 (  887)
  Misc. bond           : bond        0.00741 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8971 (pttp)
REVERT: A   59 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: A  137 CYS cc_start: 0.9091 (m) cc_final: 0.8756 (t)
REVERT: A  158 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (mtp)
REVERT: A  220 ILE cc_start: 0.9437 (mt) cc_final: 0.9124 (mm)
REVERT: A  243 MET cc_start: 0.8671 (tpp) cc_final: 0.8451 (mpp)
REVERT: B   39 LYS cc_start: 0.9306 (ttpp) cc_final: 0.9099 (ptpp)
REVERT: B   62 ASN cc_start: 0.9106 (p0) cc_final: 0.8905 (p0)
REVERT: B  124 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8247 (tt0)
REVERT: B  158 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7315 (mpp)
REVERT: B  171 LEU cc_start: 0.9603 (mt) cc_final: 0.9395 (mt)
REVERT: B  191 TYR cc_start: 0.8969 (t80) cc_final: 0.8765 (t80)
REVERT: B  218 LEU cc_start: 0.9312 (tp) cc_final: 0.9087 (tp)
REVERT: B  237 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: C   59 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7854 (tm-30)
  outliers start: 27
  outliers final: 11
  residues processed: 190
  average time/residue: 0.0869
  time to fit residues: 22.4114
Evaluate side-chains
  157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  253 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   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  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 HIS
A 200 GLN
B  34 ASN
B  36 ASN
B 200 GLN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.080820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.064730 restraints weight = 21676.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.067054 restraints weight = 11873.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.068502 restraints weight = 7850.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.069669 restraints weight = 5960.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.070421 restraints weight = 4854.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7752  Z= 0.197
  Angle     :  0.710   7.064  10552  Z= 0.371
  Chirality :  0.041   0.152   1203
  Planarity :  0.005   0.052   1296
  Dihedral  : 17.467 179.346   1329
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 16.13 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 921
  helix:  0.39 (0.25), residues: 426
  sheet: -0.91 (0.47), residues: 114
  loop : -0.74 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 130 
 TYR   0.019   0.002   TYR A 191 
 PHE   0.016   0.002   PHE C 126 
 HIS   0.008   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 7750)
  covalent geometry    : angle       0.71012 (10552)
  hydrogen bonds       : bond        0.03524 (  327)
  hydrogen bonds       : angle       4.98414 (  887)
  Misc. bond           : bond        0.00455 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.299 
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: 0.9299 (OUTLIER) cc_final: 0.9021 (pttp)
REVERT: A  124 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8447 (mm-30)
REVERT: A  171 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9359 (mt)
REVERT: A  304 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (ttmm)
REVERT: B   39 LYS cc_start: 0.9348 (ttpp) cc_final: 0.9092 (ptpp)
REVERT: B   59 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8037 (tm-30)
REVERT: B  124 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8121 (tt0)
REVERT: B  137 CYS cc_start: 0.9193 (m) cc_final: 0.8671 (m)
REVERT: B  210 MET cc_start: 0.8219 (mtp) cc_final: 0.7978 (ttm)
REVERT: C   59 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: C  137 CYS cc_start: 0.9205 (m) cc_final: 0.8945 (t)
REVERT: C  253 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9273 (mm)
REVERT: C  301 TYR cc_start: 0.8894 (t80) cc_final: 0.8639 (t80)
  outliers start: 34
  outliers final: 19
  residues processed: 166
  average time/residue: 0.0929
  time to fit residues: 20.7031
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  124 GLU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  270 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.082818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.067167 restraints weight = 21811.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.069550 restraints weight = 11613.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.071162 restraints weight = 7544.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.072256 restraints weight = 5571.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072773 restraints weight = 4513.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.6446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7752  Z= 0.128
  Angle     :  0.650   7.905  10552  Z= 0.339
  Chirality :  0.039   0.147   1203
  Planarity :  0.004   0.055   1296
  Dihedral  : 16.800 172.862   1323
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.04 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.88 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 921
  helix:  0.69 (0.26), residues: 408
  sheet: -0.71 (0.48), residues: 114
  loop : -0.79 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 229 
 TYR   0.024   0.002   TYR B  54 
 PHE   0.012   0.002   PHE A 259 
 HIS   0.005   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7750)
  covalent geometry    : angle       0.64999 (10552)
  hydrogen bonds       : bond        0.02981 (  327)
  hydrogen bonds       : angle       4.71350 (  887)
  Misc. bond           : bond        0.00359 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 0.278 
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: 0.9324 (OUTLIER) cc_final: 0.9049 (pttm)
REVERT: A  124 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8487 (mm-30)
REVERT: A  137 CYS cc_start: 0.9267 (m) cc_final: 0.8797 (t)
REVERT: A  159 TYR cc_start: 0.9070 (t80) cc_final: 0.8538 (t80)
REVERT: A  220 ILE cc_start: 0.9436 (mm) cc_final: 0.8692 (mm)
REVERT: A  304 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8238 (ttmm)
REVERT: B   59 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7888 (tm-30)
REVERT: B  137 CYS cc_start: 0.9136 (m) cc_final: 0.8653 (m)
REVERT: B  158 MET cc_start: 0.7860 (mtp) cc_final: 0.7645 (mtp)
REVERT: C   59 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: C  124 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8133 (tt0)
REVERT: C  137 CYS cc_start: 0.9258 (m) cc_final: 0.9057 (t)
  outliers start: 31
  outliers final: 17
  residues processed: 168
  average time/residue: 0.0909
  time to fit residues: 20.4862
Evaluate side-chains
  155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
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 53 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 290 ASN
** 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**
C  93 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.081928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.066161 restraints weight = 21924.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.068487 restraints weight = 11806.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.070042 restraints weight = 7736.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.071146 restraints weight = 5765.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.071839 restraints weight = 4676.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.6769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7752  Z= 0.144
  Angle     :  0.659   7.440  10552  Z= 0.341
  Chirality :  0.040   0.156   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.617 171.529   1323
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 18.68 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.27), residues: 921
  helix:  0.75 (0.26), residues: 408
  sheet: -0.45 (0.49), residues: 114
  loop : -0.87 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  27 
 TYR   0.027   0.002   TYR B  54 
 PHE   0.011   0.002   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7750)
  covalent geometry    : angle       0.65856 (10552)
  hydrogen bonds       : bond        0.03072 (  327)
  hydrogen bonds       : angle       4.68490 (  887)
  Misc. bond           : bond        0.00343 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9067 (pttm)
REVERT: A  124 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: A  137 CYS cc_start: 0.9153 (m) cc_final: 0.8767 (t)
REVERT: A  159 TYR cc_start: 0.9110 (t80) cc_final: 0.8315 (t80)
REVERT: A  304 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8074 (ttmm)
REVERT: B   39 LYS cc_start: 0.9358 (ttpp) cc_final: 0.9085 (pptt)
REVERT: B   59 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8070 (tm-30)
REVERT: B  137 CYS cc_start: 0.9122 (m) cc_final: 0.8611 (m)
REVERT: B  158 MET cc_start: 0.7940 (mtp) cc_final: 0.7675 (mtp)
REVERT: B  285 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8511 (mmmt)
REVERT: C  124 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8057 (tt0)
REVERT: C  258 GLU cc_start: 0.7079 (pt0) cc_final: 0.6721 (pt0)
  outliers start: 30
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0820
  time to fit residues: 17.7819
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  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  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  251 MET
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   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    2.7386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.080109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.063777 restraints weight = 22049.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066036 restraints weight = 12356.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.067543 restraints weight = 8342.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.068497 restraints weight = 6344.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.069321 restraints weight = 5287.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.7009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7752  Z= 0.196
  Angle     :  0.686   7.401  10552  Z= 0.356
  Chirality :  0.041   0.152   1203
  Planarity :  0.005   0.056   1296
  Dihedral  : 16.618 169.098   1323
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.56 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.22 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.26), residues: 921
  helix:  0.90 (0.25), residues: 417
  sheet: -0.42 (0.50), residues: 114
  loop : -0.90 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  27 
 TYR   0.034   0.002   TYR C 228 
 PHE   0.013   0.002   PHE A 195 
 HIS   0.004   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 7750)
  covalent geometry    : angle       0.68608 (10552)
  hydrogen bonds       : bond        0.03309 (  327)
  hydrogen bonds       : angle       4.69440 (  887)
  Misc. bond           : bond        0.00393 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9084 (pttm)
REVERT: A  137 CYS cc_start: 0.9129 (m) cc_final: 0.8791 (t)
REVERT: A  159 TYR cc_start: 0.9082 (t80) cc_final: 0.8266 (t80)
REVERT: A  211 MET cc_start: 0.7964 (tmm) cc_final: 0.7219 (tmm)
REVERT: A  304 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8223 (ttmm)
REVERT: B   59 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8132 (tm-30)
REVERT: B  137 CYS cc_start: 0.9061 (m) cc_final: 0.8566 (m)
REVERT: B  158 MET cc_start: 0.8074 (mtp) cc_final: 0.7676 (mtp)
  outliers start: 33
  outliers final: 26
  residues processed: 147
  average time/residue: 0.0786
  time to fit residues: 15.9903
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  220 ILE
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  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  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  315 TYR
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.081235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.065096 restraints weight = 21776.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.067421 restraints weight = 11944.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.069021 restraints weight = 7906.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.070018 restraints weight = 5912.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070810 restraints weight = 4869.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.7242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7752  Z= 0.148
  Angle     :  0.666   7.546  10552  Z= 0.344
  Chirality :  0.040   0.152   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.532 167.866   1323
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.02 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 19.62 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.26), residues: 921
  helix:  0.91 (0.25), residues: 417
  sheet: -0.11 (0.51), residues: 111
  loop : -0.89 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 130 
 TYR   0.030   0.002   TYR B  54 
 PHE   0.016   0.002   PHE B 259 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7750)
  covalent geometry    : angle       0.66564 (10552)
  hydrogen bonds       : bond        0.03052 (  327)
  hydrogen bonds       : angle       4.55576 (  887)
  Misc. bond           : bond        0.00363 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9085 (pttm)
REVERT: A  137 CYS cc_start: 0.9158 (m) cc_final: 0.8768 (t)
REVERT: A  211 MET cc_start: 0.8161 (tmm) cc_final: 0.7811 (tmm)
REVERT: A  304 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8170 (ttmm)
REVERT: B   39 LYS cc_start: 0.9374 (ttpp) cc_final: 0.9162 (pptt)
REVERT: B   59 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8127 (tm-30)
REVERT: B  137 CYS cc_start: 0.9062 (m) cc_final: 0.8587 (m)
REVERT: B  158 MET cc_start: 0.8015 (mtp) cc_final: 0.7642 (mtp)
  outliers start: 34
  outliers final: 24
  residues processed: 145
  average time/residue: 0.0864
  time to fit residues: 17.3290
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  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  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  251 MET
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  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  315 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 3 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0030
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0594

-------------------------------------------------------------------------------
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 199 HIS
** 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 = 0.3340 r_free = 0.3340 target = 0.083234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.066825 restraints weight = 21924.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.069214 restraints weight = 12104.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.070836 restraints weight = 8029.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.071731 restraints weight = 6022.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.072550 restraints weight = 5035.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.7403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7752  Z= 0.131
  Angle     :  0.649   7.982  10552  Z= 0.334
  Chirality :  0.039   0.151   1203
  Planarity :  0.004   0.058   1296
  Dihedral  : 16.505 169.214   1323
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.83 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 921
  helix:  0.99 (0.25), residues: 420
  sheet: -0.16 (0.50), residues: 114
  loop : -0.76 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 130 
 TYR   0.026   0.002   TYR B  54 
 PHE   0.015   0.001   PHE A 195 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7750)
  covalent geometry    : angle       0.64867 (10552)
  hydrogen bonds       : bond        0.02874 (  327)
  hydrogen bonds       : angle       4.42606 (  887)
  Misc. bond           : bond        0.00328 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9098 (pttm)
REVERT: A  137 CYS cc_start: 0.9160 (m) cc_final: 0.8835 (t)
REVERT: A  211 MET cc_start: 0.8121 (tmm) cc_final: 0.7578 (tmm)
REVERT: A  220 ILE cc_start: 0.9571 (mm) cc_final: 0.9220 (mm)
REVERT: A  291 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9195 (tt)
REVERT: B   59 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8181 (tm-30)
REVERT: B  137 CYS cc_start: 0.9068 (m) cc_final: 0.8537 (m)
REVERT: B  158 MET cc_start: 0.7980 (mtp) cc_final: 0.7611 (mtp)
  outliers start: 28
  outliers final: 19
  residues processed: 146
  average time/residue: 0.0864
  time to fit residues: 17.3796
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  291 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   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  144 CYS
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  257 ASP
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    2.3786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.080089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.063750 restraints weight = 21929.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.066036 restraints weight = 12159.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.067567 restraints weight = 8169.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.068652 restraints weight = 6190.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.069220 restraints weight = 5093.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.7525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7752  Z= 0.183
  Angle     :  0.708   8.603  10552  Z= 0.362
  Chirality :  0.040   0.153   1203
  Planarity :  0.004   0.054   1296
  Dihedral  : 16.180 167.540   1323
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.99 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.18 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.27), residues: 921
  helix:  1.12 (0.25), residues: 417
  sheet: -0.58 (0.41), residues: 159
  loop : -0.51 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 130 
 TYR   0.027   0.002   TYR B  54 
 PHE   0.009   0.002   PHE B 126 
 HIS   0.003   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7750)
  covalent geometry    : angle       0.70849 (10552)
  hydrogen bonds       : bond        0.03301 (  327)
  hydrogen bonds       : angle       4.60336 (  887)
  Misc. bond           : bond        0.00343 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.9202 (p0) cc_final: 0.8992 (p0)
REVERT: A  137 CYS cc_start: 0.9176 (m) cc_final: 0.8786 (t)
REVERT: A  211 MET cc_start: 0.8055 (tmm) cc_final: 0.7748 (tmm)
REVERT: B   46 PHE cc_start: 0.9237 (m-80) cc_final: 0.8910 (m-80)
REVERT: B   59 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (tm-30)
REVERT: B  158 MET cc_start: 0.8017 (mtp) cc_final: 0.7599 (mtp)
REVERT: B  220 ILE cc_start: 0.9603 (mm) cc_final: 0.8503 (mm)
  outliers start: 26
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0787
  time to fit residues: 15.1849
Evaluate side-chains
  143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  270 VAL
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   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
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  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0670
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 77 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.7522

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3293 r_free = 0.3293 target = 0.080842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.064709 restraints weight = 22057.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.066997 restraints weight = 12351.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.068489 restraints weight = 8292.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.069551 restraints weight = 6300.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.070215 restraints weight = 5181.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.7618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7752  Z= 0.159
  Angle     :  0.708  11.810  10552  Z= 0.361
  Chirality :  0.040   0.152   1203
  Planarity :  0.004   0.054   1296
  Dihedral  : 15.906 164.441   1323
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 22.45 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.27), residues: 921
  helix:  0.99 (0.25), residues: 420
  sheet: -0.50 (0.42), residues: 147
  loop : -0.50 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 130 
 TYR   0.026   0.002   TYR B  54 
 PHE   0.008   0.001   PHE B 259 
 HIS   0.005   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7750)
  covalent geometry    : angle       0.70770 (10552)
  hydrogen bonds       : bond        0.03085 (  327)
  hydrogen bonds       : angle       4.50564 (  887)
  Misc. bond           : bond        0.00312 (    2)

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.293 
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: 0.9189 (m) cc_final: 0.8785 (t)
REVERT: A  211 MET cc_start: 0.8002 (tmm) cc_final: 0.7520 (tmm)
REVERT: B   46 PHE cc_start: 0.9247 (m-80) cc_final: 0.8912 (m-80)
REVERT: B   59 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8126 (tm-30)
REVERT: B  158 MET cc_start: 0.8012 (mtp) cc_final: 0.7682 (mtp)
REVERT: B  220 ILE cc_start: 0.9395 (mm) cc_final: 0.9183 (mm)
  outliers start: 22
  outliers final: 20
  residues processed: 141
  average time/residue: 0.0893
  time to fit residues: 17.2215
Evaluate side-chains
  145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ASN
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  270 VAL
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   61 ILE
Chi-restraints excluded: chain B residue  102 ILE
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   63 ILE
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  137 CYS
Chi-restraints excluded: chain C residue  220 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 290 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 = 0.3245 r_free = 0.3245 target = 0.078613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.061968 restraints weight = 22291.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.064181 restraints weight = 12551.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.065698 restraints weight = 8523.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.066682 restraints weight = 6512.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.067331 restraints weight = 5419.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.7665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7752  Z= 0.225
  Angle     :  0.749   8.747  10552  Z= 0.385
  Chirality :  0.041   0.208   1203
  Planarity :  0.005   0.051   1296
  Dihedral  : 16.126 168.597   1323
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  5.54 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.18 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.27), residues: 921
  helix:  1.03 (0.25), residues: 420
  sheet: -0.55 (0.40), residues: 162
  loop : -0.48 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.030   0.002   TYR C 228 
 PHE   0.012   0.002   PHE C 259 
 HIS   0.004   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 7750)
  covalent geometry    : angle       0.74931 (10552)
  hydrogen bonds       : bond        0.03507 (  327)
  hydrogen bonds       : angle       4.68294 (  887)
  Misc. bond           : bond        0.00374 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1202.29 seconds
wall clock time: 21 minutes 35.42 seconds (1295.42 seconds total)