Starting phenix.real_space_refine
on Fri Aug 22 22:05:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w89_37349/08_2025/8w89_37349.cif"
  }
  resolution = 3.0
  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=  -0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5229      2.51       5
     N    1419      2.21       5
     O    1521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8230
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1934
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2283
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 10
          Unusual residues: {'PEA': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.22
  Number of scatterers: 8230
  At special positions: 0
  Unit cell: (81.536, 100.672, 132.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1521      8.00
     N    1419      7.00
     C    5229      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 282.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.5% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 35
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.724A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.735A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.188A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.650A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.617A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 52
      removed outlier: 4.354A  pdb=" N   LYS R  52 " --> pdb=" O   ILE R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 76
      removed outlier: 3.607A  pdb=" N   LEU R  61 " --> pdb=" O   PRO R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 85
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 231
    Processing helix  chain 'R' and resid 247 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 275 through 279
      removed outlier: 4.137A  pdb=" N   HIS R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR R 279 " --> pdb=" O   PHE R 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 275 through 279'
    Processing helix  chain 'R' and resid 282 through 306
      removed outlier: 3.612A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP R 291 " --> pdb=" O   ASP R 287 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 316
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 3.632A  pdb=" N   PHE A  70 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.784A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.699A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.886A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.651A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.881A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.507A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.518A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.503A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.548A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1806
        1.33 -     1.46: 2217
        1.46 -     1.58: 4297
        1.58 -     1.71: 0
        1.71 -     1.84: 88
  Bond restraints: 8408
  Sorted by residual:
  bond pdb=" CA  TYR R 122 "
       pdb=" C   TYR R 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.053 1.27e-02 6.20e+03 1.75e+01
  bond pdb=" CA  ARG N  98 "
       pdb=" C   ARG N  98 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.37e-02 5.33e+03 1.43e+01
  bond pdb=" CA  THR A 216 "
       pdb=" C   THR A 216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.042 1.21e-02 6.83e+03 1.18e+01
  bond pdb=" CA  TRP B 297 "
       pdb=" C   TRP B 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.039 1.18e-02 7.18e+03 1.07e+01
  bond pdb=" CA  ASN R 296 "
       pdb=" C   ASN R 296 "
    ideal  model  delta    sigma   weight residual
    1.524  1.482  0.041 1.29e-02 6.01e+03 1.02e+01
  ... (remaining 8403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 11015
        2.10 -     4.20: 297
        4.20 -     6.29: 64
        6.29 -     8.39: 7
        8.39 -    10.49: 5
  Bond angle restraints: 11388
  Sorted by residual:
  angle pdb=" N   GLN R  53 "
        pdb=" CA  GLN R  53 "
        pdb=" C   GLN R  53 "
      ideal   model   delta    sigma   weight residual
     113.38  104.99    8.39 1.23e+00 6.61e-01 4.65e+01
  angle pdb=" N   HIS R  50 "
        pdb=" CA  HIS R  50 "
        pdb=" C   HIS R  50 "
      ideal   model   delta    sigma   weight residual
     111.36  118.67   -7.31 1.09e+00 8.42e-01 4.50e+01
  angle pdb=" N   ARG R  23 "
        pdb=" CA  ARG R  23 "
        pdb=" C   ARG R  23 "
      ideal   model   delta    sigma   weight residual
     111.28  104.39    6.89 1.09e+00 8.42e-01 3.99e+01
  angle pdb=" N   GLN B 259 "
        pdb=" CA  GLN B 259 "
        pdb=" C   GLN B 259 "
      ideal   model   delta    sigma   weight residual
     109.14  117.78   -8.64 1.49e+00 4.50e-01 3.36e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     110.24  117.28   -7.04 1.47e+00 4.63e-01 2.29e+01
  ... (remaining 11383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 4545
       17.55 -    35.10: 367
       35.10 -    52.65: 68
       52.65 -    70.20: 12
       70.20 -    87.75: 5
  Dihedral angle restraints: 4997
    sinusoidal: 1957
      harmonic: 3040
  Sorted by residual:
  dihedral pdb=" N   ASP B 258 "
           pdb=" C   ASP B 258 "
           pdb=" CA  ASP B 258 "
           pdb=" CB  ASP B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.20   -9.40     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.27   30.73     1      1.00e+01 1.00e-02 1.35e+01
  dihedral pdb=" C   VAL R 288 "
           pdb=" N   VAL R 288 "
           pdb=" CA  VAL R 288 "
           pdb=" CB  VAL R 288 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.56    8.56     0      2.50e+00 1.60e-01 1.17e+01
  ... (remaining 4994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1083
       0.076 -    0.152: 146
       0.152 -    0.229: 29
       0.229 -    0.305: 11
       0.305 -    0.381: 3
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  ASP B 258 "
            pdb=" N   ASP B 258 "
            pdb=" C   ASP B 258 "
            pdb=" CB  ASP B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  PHE R 268 "
            pdb=" N   PHE R 268 "
            pdb=" C   PHE R 268 "
            pdb=" CB  PHE R 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  TRP A  96 "
            pdb=" N   TRP A  96 "
            pdb=" C   TRP A  96 "
            pdb=" CB  TRP A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 1269 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  94 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   VAL R  94 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   VAL R  94 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PHE R  95 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R  48 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   ILE R  48 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ILE R  48 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER R  49 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 265 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO R 266 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO R 266 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 266 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2856
        2.85 -     3.36: 7727
        3.36 -     3.87: 13913
        3.87 -     4.39: 16285
        4.39 -     4.90: 28042
  Nonbonded interactions: 68823
  Sorted by model distance:
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG1 THR R  37 "
            pdb=" OG1 THR R 298 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   SER R 115 "
            pdb=" OG  SER R 118 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" ND1 HIS B 311 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.430 3.120
  ... (remaining 68818 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.670
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.400
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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      :  0.006   0.053   8411  Z= 0.412
  Angle     :  0.826  10.489  11394  Z= 0.525
  Chirality :  0.063   0.381   1272
  Planarity :  0.005   0.067   1452
  Dihedral  : 13.331  87.748   3024
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  2.24 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1031
  helix:  2.05 (0.26), residues: 392
  sheet:  0.11 (0.36), residues: 216
  loop : -0.58 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  19 
 TYR   0.021   0.001   TYR A 210 
 PHE   0.023   0.002   PHE B 235 
 TRP   0.027   0.002   TRP A  96 
 HIS   0.002   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 8408)
  covalent geometry    : angle       0.82577 (11388)
  SS BOND              : bond        0.00271 (    3)
  SS BOND              : angle       0.51538 (    6)
  hydrogen bonds       : bond        0.16982 (  422)
  hydrogen bonds       : angle       6.60317 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B   34 THR cc_start: 0.8595 (p) cc_final: 0.8055 (p)
REVERT: B  175 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7335 (mp10)
REVERT: G   21 MET cc_start: 0.7482 (mtm) cc_final: 0.7245 (mmt)
REVERT: R  182 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4802 (p)
  outliers start: 8
  outliers final: 0
  residues processed: 163
  average time/residue: 0.5069
  time to fit residues: 87.5285
Evaluate side-chains
  131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 223 ASN
B 220 GLN
B 259 GLN
R  53 GLN
R 175 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.161163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.127315 restraints weight = 10383.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.41
r_work: 0.3396 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8411  Z= 0.125
  Angle     :  0.540   6.531  11394  Z= 0.289
  Chirality :  0.043   0.356   1272
  Planarity :  0.004   0.047   1452
  Dihedral  :  4.507  58.209   1142
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.35 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.08 (0.26), residues: 1031
  helix:  2.33 (0.26), residues: 396
  sheet:  0.20 (0.36), residues: 194
  loop : -0.52 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  19 
 TYR   0.016   0.001   TYR A 210 
 PHE   0.018   0.001   PHE A  70 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8408)
  covalent geometry    : angle       0.53937 (11388)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.40974 (    6)
  hydrogen bonds       : bond        0.04408 (  422)
  hydrogen bonds       : angle       4.84363 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 THR cc_start: 0.8868 (p) cc_final: 0.8579 (p)
REVERT: B  101 MET cc_start: 0.8708 (mtp) cc_final: 0.8400 (mtp)
REVERT: B  153 ASP cc_start: 0.6793 (p0) cc_final: 0.6356 (m-30)
REVERT: B  175 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7426 (mp10)
REVERT: B  293 ASN cc_start: 0.7912 (m-40) cc_final: 0.7145 (p0)
REVERT: N   12 VAL cc_start: 0.8596 (p) cc_final: 0.8238 (m)
REVERT: R  143 MET cc_start: 0.7842 (mtt) cc_final: 0.7447 (mtm)
REVERT: R  166 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7508 (mptp)
REVERT: R  182 CYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5473 (p)
REVERT: R  273 MET cc_start: 0.7580 (mmm) cc_final: 0.7305 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 153
  average time/residue: 0.4263
  time to fit residues: 69.8501
Evaluate side-chains
  137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0770
   chunk 55 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0670
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 130 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.161923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128494 restraints weight = 10410.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.41
r_work: 0.3415 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8411  Z= 0.106
  Angle     :  0.503   6.290  11394  Z= 0.269
  Chirality :  0.041   0.297   1272
  Planarity :  0.004   0.041   1452
  Dihedral  :  4.368  56.374   1142
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.92 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1031
  helix:  2.28 (0.25), residues: 397
  sheet:  0.21 (0.35), residues: 197
  loop : -0.38 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.023   0.001   TYR R 172 
 PHE   0.040   0.001   PHE A  70 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8408)
  covalent geometry    : angle       0.50285 (11388)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       0.99270 (    6)
  hydrogen bonds       : bond        0.03903 (  422)
  hydrogen bonds       : angle       4.59411 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 ASN cc_start: 0.8732 (t0) cc_final: 0.8166 (m110)
REVERT: B  101 MET cc_start: 0.8675 (mtp) cc_final: 0.8397 (mtp)
REVERT: B  153 ASP cc_start: 0.6688 (p0) cc_final: 0.6278 (m-30)
REVERT: B  228 ASP cc_start: 0.8218 (m-30) cc_final: 0.8009 (m-30)
REVERT: B  269 ILE cc_start: 0.8472 (mm) cc_final: 0.8067 (mm)
REVERT: B  293 ASN cc_start: 0.7919 (m-40) cc_final: 0.7296 (p0)
REVERT: N   12 VAL cc_start: 0.8554 (p) cc_final: 0.8186 (m)
REVERT: R  143 MET cc_start: 0.7884 (mtt) cc_final: 0.7582 (mtm)
REVERT: R  158 MET cc_start: 0.7193 (ttm) cc_final: 0.6689 (ttm)
REVERT: R  166 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7263 (mptp)
REVERT: R  207 LEU cc_start: 0.8604 (tp) cc_final: 0.8377 (tp)
  outliers start: 19
  outliers final: 7
  residues processed: 154
  average time/residue: 0.4442
  time to fit residues: 73.2359
Evaluate side-chains
  142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 TYR
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 119 GLN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121970 restraints weight = 10696.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.48
r_work: 0.3329 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   8411  Z= 0.201
  Angle     :  0.578   6.582  11394  Z= 0.308
  Chirality :  0.043   0.133   1272
  Planarity :  0.004   0.035   1452
  Dihedral  :  4.737  56.997   1142
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.82 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1031
  helix:  2.17 (0.25), residues: 399
  sheet:  0.01 (0.35), residues: 190
  loop : -0.45 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  19 
 TYR   0.028   0.002   TYR A 210 
 PHE   0.044   0.002   PHE A  70 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 8408)
  covalent geometry    : angle       0.57769 (11388)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       1.02534 (    6)
  hydrogen bonds       : bond        0.04542 (  422)
  hydrogen bonds       : angle       4.83519 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7635 (mtpt)
REVERT: B  269 ILE cc_start: 0.8455 (mm) cc_final: 0.8072 (mm)
REVERT: G   17 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7201 (pp20)
REVERT: G   42 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6884 (mp0)
REVERT: N   12 VAL cc_start: 0.8604 (p) cc_final: 0.8201 (m)
REVERT: N   76 LYS cc_start: 0.8627 (mptt) cc_final: 0.8254 (mptt)
REVERT: N   77 ASN cc_start: 0.7043 (m-40) cc_final: 0.6631 (p0)
REVERT: N   83 MET cc_start: 0.8267 (mtp) cc_final: 0.7857 (mtp)
REVERT: R  166 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7151 (mptp)
  outliers start: 23
  outliers final: 7
  residues processed: 144
  average time/residue: 0.4769
  time to fit residues: 73.2850
Evaluate side-chains
  135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0370
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    2.1464

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 146 GLN
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.154638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120106 restraints weight = 10548.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.44
r_work: 0.3301 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086   8411  Z= 0.230
  Angle     :  0.608   8.032  11394  Z= 0.322
  Chirality :  0.046   0.373   1272
  Planarity :  0.004   0.041   1452
  Dihedral  :  4.900  55.866   1142
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.72 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.67 (0.25), residues: 1031
  helix:  1.92 (0.25), residues: 398
  sheet: -0.27 (0.35), residues: 190
  loop : -0.56 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  19 
 TYR   0.020   0.002   TYR R 172 
 PHE   0.037   0.002   PHE A  70 
 TRP   0.016   0.002   TRP N  47 
 HIS   0.006   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 8408)
  covalent geometry    : angle       0.60773 (11388)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       1.00335 (    6)
  hydrogen bonds       : bond        0.04783 (  422)
  hydrogen bonds       : angle       4.98628 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7682 (mtpt)
REVERT: B  153 ASP cc_start: 0.6794 (p0) cc_final: 0.6519 (m-30)
REVERT: G   42 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6946 (mp0)
REVERT: N   12 VAL cc_start: 0.8595 (p) cc_final: 0.8172 (m)
REVERT: N   77 ASN cc_start: 0.7128 (m-40) cc_final: 0.6618 (p0)
REVERT: N   80 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6420 (m-80)
REVERT: N   83 MET cc_start: 0.8312 (mtp) cc_final: 0.8003 (mtp)
REVERT: R  166 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7259 (mptp)
  outliers start: 21
  outliers final: 9
  residues processed: 138
  average time/residue: 0.4609
  time to fit residues: 67.6331
Evaluate side-chains
  129 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Chi-restraints excluded: chain R residue  269 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.156152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.121932 restraints weight = 10485.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.44
r_work: 0.3329 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8411  Z= 0.160
  Angle     :  0.580   9.782  11394  Z= 0.305
  Chirality :  0.044   0.404   1272
  Planarity :  0.004   0.042   1452
  Dihedral  :  4.765  56.978   1142
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.73 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.71 (0.26), residues: 1031
  helix:  1.92 (0.25), residues: 399
  sheet: -0.30 (0.35), residues: 193
  loop : -0.47 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.019   0.001   TYR R 172 
 PHE   0.034   0.002   PHE A  70 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8408)
  covalent geometry    : angle       0.57999 (11388)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       0.67696 (    6)
  hydrogen bonds       : bond        0.04369 (  422)
  hydrogen bonds       : angle       4.88512 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  157 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7679 (mtpt)
REVERT: B  153 ASP cc_start: 0.6841 (p0) cc_final: 0.6398 (m-30)
REVERT: B  234 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8943 (m-80)
REVERT: B  269 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8090 (mm)
REVERT: G   42 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6954 (mp0)
REVERT: N   12 VAL cc_start: 0.8559 (p) cc_final: 0.8146 (m)
REVERT: N   83 MET cc_start: 0.8281 (mtp) cc_final: 0.7972 (mtp)
REVERT: R   52 LYS cc_start: 0.7657 (mtmp) cc_final: 0.7299 (mtmm)
REVERT: R  166 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7140 (mptp)
  outliers start: 23
  outliers final: 10
  residues processed: 140
  average time/residue: 0.5018
  time to fit residues: 74.8297
Evaluate side-chains
  136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.157848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123688 restraints weight = 10563.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.44
r_work: 0.3352 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8411  Z= 0.128
  Angle     :  0.562  11.939  11394  Z= 0.294
  Chirality :  0.043   0.406   1272
  Planarity :  0.004   0.043   1452
  Dihedral  :  4.599  56.501   1142
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.52 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1031
  helix:  2.00 (0.25), residues: 399
  sheet: -0.14 (0.35), residues: 184
  loop : -0.50 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.019   0.001   TYR R 172 
 PHE   0.032   0.001   PHE A  70 
 TRP   0.021   0.002   TRP R 310 
 HIS   0.003   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8408)
  covalent geometry    : angle       0.56150 (11388)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.62903 (    6)
  hydrogen bonds       : bond        0.04068 (  422)
  hydrogen bonds       : angle       4.78342 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.8800 (mtp) cc_final: 0.8518 (mtp)
REVERT: B  153 ASP cc_start: 0.6809 (p0) cc_final: 0.6381 (m-30)
REVERT: B  234 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8947 (m-80)
REVERT: G   42 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7022 (mp0)
REVERT: N    3 GLN cc_start: 0.7805 (pt0) cc_final: 0.7279 (tt0)
REVERT: N   12 VAL cc_start: 0.8552 (p) cc_final: 0.8149 (m)
REVERT: N   13 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7102 (tp-100)
REVERT: N   77 ASN cc_start: 0.7876 (t0) cc_final: 0.7516 (t0)
REVERT: N   83 MET cc_start: 0.8248 (mtp) cc_final: 0.7978 (mtp)
  outliers start: 19
  outliers final: 12
  residues processed: 141
  average time/residue: 0.4664
  time to fit residues: 70.0675
Evaluate side-chains
  141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.155481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121101 restraints weight = 10660.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.45
r_work: 0.3317 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   8411  Z= 0.195
  Angle     :  0.606  11.275  11394  Z= 0.320
  Chirality :  0.045   0.407   1272
  Planarity :  0.004   0.045   1452
  Dihedral  :  4.731  54.351   1142
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.30 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1031
  helix:  1.87 (0.25), residues: 399
  sheet: -0.25 (0.35), residues: 185
  loop : -0.54 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.016   0.002   TYR R 172 
 PHE   0.032   0.002   PHE A  70 
 TRP   0.030   0.002   TRP R 310 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 8408)
  covalent geometry    : angle       0.60641 (11388)
  SS BOND              : bond        0.00285 (    3)
  SS BOND              : angle       0.68824 (    6)
  hydrogen bonds       : bond        0.04501 (  422)
  hydrogen bonds       : angle       4.94644 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7630 (mtpt)
REVERT: B  153 ASP cc_start: 0.6824 (p0) cc_final: 0.6351 (m-30)
REVERT: B  176 GLN cc_start: 0.8997 (mt0) cc_final: 0.8759 (tt0)
REVERT: B  234 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8954 (m-80)
REVERT: B  269 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8096 (mm)
REVERT: G   42 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7119 (mp0)
REVERT: N   12 VAL cc_start: 0.8545 (p) cc_final: 0.8111 (m)
REVERT: N   83 MET cc_start: 0.8277 (mtp) cc_final: 0.7970 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 138
  average time/residue: 0.4487
  time to fit residues: 66.0881
Evaluate side-chains
  133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 76 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0970
   chunk 5 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 146 GLN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.160331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.126036 restraints weight = 10487.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.47
r_work: 0.3386 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8411  Z= 0.118
  Angle     :  0.574  13.044  11394  Z= 0.299
  Chirality :  0.043   0.413   1272
  Planarity :  0.004   0.045   1452
  Dihedral  :  4.510  54.273   1142
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.43 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.75 (0.26), residues: 1031
  helix:  1.99 (0.26), residues: 399
  sheet: -0.11 (0.35), residues: 173
  loop : -0.57 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  27 
 TYR   0.016   0.001   TYR R 172 
 PHE   0.030   0.001   PHE A  70 
 TRP   0.034   0.002   TRP R 310 
 HIS   0.004   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8408)
  covalent geometry    : angle       0.57445 (11388)
  SS BOND              : bond        0.00166 (    3)
  SS BOND              : angle       0.61742 (    6)
  hydrogen bonds       : bond        0.03918 (  422)
  hydrogen bonds       : angle       4.76351 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7587 (mtpt)
REVERT: B  101 MET cc_start: 0.8687 (mtp) cc_final: 0.8395 (mtp)
REVERT: B  153 ASP cc_start: 0.6846 (p0) cc_final: 0.6347 (m-30)
REVERT: B  234 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8799 (m-80)
REVERT: G   42 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7186 (mp0)
REVERT: N    3 GLN cc_start: 0.7765 (pt0) cc_final: 0.7118 (tt0)
REVERT: N   12 VAL cc_start: 0.8468 (p) cc_final: 0.8052 (m)
REVERT: N   77 ASN cc_start: 0.7763 (t0) cc_final: 0.7534 (t0)
REVERT: N   83 MET cc_start: 0.8197 (mtp) cc_final: 0.7885 (mtp)
REVERT: R  166 LYS cc_start: 0.6664 (mptp) cc_final: 0.6427 (mptp)
  outliers start: 14
  outliers final: 9
  residues processed: 134
  average time/residue: 0.4591
  time to fit residues: 65.6599
Evaluate side-chains
  132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 146 GLN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.156797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121967 restraints weight = 10557.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.52
r_work: 0.3332 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   8411  Z= 0.188
  Angle     :  0.616  11.967  11394  Z= 0.322
  Chirality :  0.045   0.419   1272
  Planarity :  0.004   0.046   1452
  Dihedral  :  4.677  51.648   1142
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.64 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1031
  helix:  1.88 (0.25), residues: 398
  sheet: -0.28 (0.35), residues: 185
  loop : -0.52 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.017   0.002   TYR R 172 
 PHE   0.030   0.002   PHE A  70 
 TRP   0.047   0.002   TRP R 310 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 8408)
  covalent geometry    : angle       0.61564 (11388)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.64327 (    6)
  hydrogen bonds       : bond        0.04438 (  422)
  hydrogen bonds       : angle       4.93232 ( 1233)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7560 (mtpt)
REVERT: B  234 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8869 (m-80)
REVERT: B  269 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7970 (pp)
REVERT: G   42 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7190 (mp0)
REVERT: N    3 GLN cc_start: 0.7717 (pt0) cc_final: 0.6928 (tt0)
REVERT: N   12 VAL cc_start: 0.8470 (p) cc_final: 0.8035 (m)
REVERT: N   83 MET cc_start: 0.8191 (mtp) cc_final: 0.7847 (mtp)
REVERT: R  166 LYS cc_start: 0.6676 (mptp) cc_final: 0.6414 (mptp)
  outliers start: 20
  outliers final: 11
  residues processed: 132
  average time/residue: 0.4331
  time to fit residues: 60.8474
Evaluate side-chains
  133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain R residue  265 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.0050
   chunk 57 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
B  75 GLN
N  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.158492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123919 restraints weight = 10491.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.48
r_work: 0.3356 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097   8411  Z= 0.160
  Angle     :  0.672  21.348  11394  Z= 0.369
  Chirality :  0.047   0.578   1272
  Planarity :  0.005   0.116   1452
  Dihedral  :  4.716  52.142   1142
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 20.54 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.70 (0.26), residues: 1031
  helix:  1.93 (0.26), residues: 398
  sheet: -0.31 (0.35), residues: 185
  loop : -0.49 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.017   0.001   TYR R 172 
 PHE   0.031   0.002   PHE A  70 
 TRP   0.053   0.002   TRP R 310 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8408)
  covalent geometry    : angle       0.67213 (11388)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       0.61872 (    6)
  hydrogen bonds       : bond        0.04235 (  422)
  hydrogen bonds       : angle       4.88585 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2226.47 seconds
wall clock time: 38 minutes 45.62 seconds (2325.62 seconds total)